Guro Kristine Kleivi Sahlberg

• Torland, Anne Vold; Geisler, Jürgen; Azimzade, Youness; Frafjord, Astri; Nilsen, Hogne Røed & Buer, Linn [Show all 15 contributors for this article] (2026). Multi-platform analysis of the tumor immune microenvironment associated with breast cancer subtypes. Oncoimmunology. ISSN 2162-4011. 15(1). doi: 10.1080/2162402X.2025.2610535. Full text in Research Archive Show summary

  Breast cancer is genetically and histologically heterogenous, and is influenced by a variety of factors, including the tumor microenvironment (TME). The PAM50 subtypes; Luminal A, Luminal B, Normal-like, Basal-like and Her2-enriched, are associated with different tumor phenotypes and overall survival. The quantity and quality of immune cell infiltration in breast tumors play a key role in cancer development and progression and are associated with survival and treatment response. We used multiplex immunohistochemistry, single-cell RNA sequencing, and two deconvolution algorithms to explore the immune landscape across PAM50 subtypes. Immunostaining of CD3+ T cells, tryptase+ mast cells, CD20+ B cells, CD68+ CD163+ macrophages, and CD66b+ granulocytes revealed marked differences in tumor immune infiltrates according to breast cancer subtypes. Luminal tumors were relatively deprived of T cells and B cells, while exhibiting sparse to moderate amounts of macrophage infiltration. In contrast, Her2-enriched tumors exhibited a moderate immune presence, with sparse to moderate T cell infiltration and moderate infiltration of B cells and macrophages. At the other end of the spectrum, Basal-like tumors stood out for their strikingly rich immune environment and are heavily infiltrated by T cells, B cells, and macrophages. The results from the single-cell and deconvolution analyses confirmed subtype-specific immune microenvironments, which also allowed us to observe increased levels of natural killer (NK) and CD8+ T cells in Her2-enriched and Basal-like subtypes. In conclusion, our findings demonstrate significant differences in the immune tumor microenvironmentbetween the established breast cancer molecular subtypes.

• Hovda, Tone; Sober, Siim; Padrik, Peeter; Kruuv-Kao, Krista; Grindedal, Eli Marie & Vamre, Tone Bøe Aaman [Show all 9 contributors for this article] (2026). A clinical pilot study for personalized risk-based breast cancer screening utilizing a polygenic risk score. PLOS ONE. 21(7). doi: 10.1371/journal.pone.0345431. Full text in Research Archive Show summary

  Background Population-based mammographic screening is primarily age-based. However, breast cancer risk is multifactorial, and women may benefit from personalized risk-based screening. This pilot study aimed to explore the use of polygenic risk score (PRS) as a tool for risk stratification in personalized screening. Methods We included 80 women aged 40–49 years referred for clinical mammography. Exclusion criteria were prior breast cancer or premalignant breast disease, and previous genetic testing. After DNA collection, PRS was calculated from 2805 Single Nucleotide Polymorphisms (SNPs). Screening recommendations were based on each participant’s relative 10-year breast cancer risk estimated from PRS and compared with the 10-year risk of an average woman of the same age. Women with a self-reported family history of cancer meeting standard criteria were referred for gene panel testing for pathogenic variants in high-risk genes. A follow up questionnaire regarding participants’ experiences was distributed 6–9 months after PRS testing. Results Mean age was 45.2 years (SD 2.8). Mean relative 10-year breast cancer risk was 1.18 (SD 0.57). Based on PRS, 40 participants were recommended standard biennial screening 50–69 years, while 40 were advised to begin biennial screening before age 50. Among these, 7 were recommended annual mammography from when their 10-year risk reached twice that of an average 50-year-old. Twenty-one women underwent gene panel testing; no pathogenic variants in breast cancer genes were identified. Five women were advised annual mammography from 40–60 years due to family history of breast cancer, regardless of PRS. Most respondents viewed breast cancer risk assessment positively and did not report increased anxiety after testing. Conclusions In this pilot cohort, PRS-based risk stratification led to earlier or more intensive screening recommendations in half of the participants, while family history also influenced management.

• Spillum, Maren-Kathrine Guriby; Sahlberg, Guro Kristine Kleivi; Skjerven, Helle Kristine & Mjøsund, Nina Helen (2026). Nurses' and Physicians' Experiences With Digital Remote Patient Monitoring—Transforming the Boundaries of Breast Cancer Care. Journal of Clinical Nursing (JCN). ISSN 0962-1067. doi: 10.1111/jocn.70394. Full text in Research Archive
• Billaud, Amandine; Figlioli, Gisella; Mooser, Clémence; Casamassima, Irene; Azzoni, Violette & Srivatsa, Jahnavi [Show all 50 contributors for this article] (2025). Large-scale meta-analysis and precision functional assays identify FANCM regions in which PTVs confer different risks for ER-negative and triple-negative breast cancer. Breast. ISSN 0960-9776. 85, p. 1–13. doi: 10.1016/j.breast.2025.104619. Full text in Research Archive Show summary

  The breast cancer risk conferred by germline protein truncating variants (PTVs) in known and putative breast cancer genes has been extensively investigated. However, the effect of FANCM PTVs on breast cancer risk remains unclear. Our previous clinical, genetic and functional results on the N-terminal p.Arg658∗ and the two C-terminal p.Gln1701∗ and p.Gly1906Alafs∗12 variants suggested that FANCM PTVs may confer different risks for ER-negative (ER-neg) and triple-negative (TN) breast cancer subtypes. Here, we performed meta-analyses of seven studies totaling 144 681 breast cancer cases and 123 632 controls. FANCM PTVs were tested for association with breast cancer risk overall and the disease clinical subtypes by single variant and burden analyses. Two CRISPR-Cas9-based functional assays were also conducted to test the fitness of cells after knock-in of the p.Arg658∗, p.Gln1701∗ and p.Gly1906Alafs∗12 PTVs and the sensitivity of different FANCM regions to genome editing. Our results suggest that the N-terminal FANCM region upstream of p.Tyr725 harbors essential functions, whereas downstream regions appear dispensable. This is supported by our genetic data which indicate that all FANCM PTVs, excluding the two C-terminal p.Gln1701∗ and p.Gly1906Alafs∗12, are associated with an increased risk of ER-neg (OR = 1.41, P = 0.023) and TN (OR = 1.64, P = 0.0023). Notably, PTVs upstream of AA position 670 are associated with a moderate risk of developing TN breast cancer, and that even when the p.Arg658∗ carriers were excluded from the analysis. Importantly, our results confirm previous data indicating that p.Arg658∗ carriers are at moderate risk of developing ER-neg (OR = 2.08, P = 0.030) and TN (OR = 3.26; P = 0.0034), whereas carriers of p.Gln1701∗ and p.Gly1906Alafs∗12 should not be considered at increased risk. Our data are useful for counseling carriers of FANCM PTVs, but further analyses are warranted to obtain more precise risk estimates.

• Fjørtoft, Marit Otterlei; Garred, Øystein; Lingjærde, Ole Christian; Johannesen, Karin Teien; Ottestad, Lars & Bergheim, Inger Riise [Show all 29 contributors for this article] (2025). Single-cell analysis reveals tumour size as a key driver of immune cell profile alterations in primary breast tumours and corresponding lymph nodes. BJC Reports. 3(1). doi: 10.1038/s44276-025-00152-3. Full text in Research Archive Show summary

  At diagnosis, 30–40% of women with breast cancer have metastases in sentinel (SN) or axillary lymph nodes (ALN). Nodal status is a strong prognostic factor and guides treatment decisions. Immune checkpoint inhibition has shown some efficacy, which can increase in the neoadjuvant setting. A better understanding of how tumour cells in primary tumours and metastatic lymph nodes shape the local immune microenvironment may provide clues for more individualized therapeutic interventions. Methods We conducted deep immunophenotypic analysis of 29 primary breast tumours and 36 lymph nodes from 38 patients with primary operable breast cancer. Results The immune profile of the primary tumour was not predictive of the lymph node immune profile or metastatic status. Primary tumours showed prominent CD8 T cell exhaustion and activated regulatory T cells, and the frequencies of these subsets were associated with tumour size. The immune cell profile in lymph nodes were different from the profile in primary tumours, except for the ALN+ nodes, which displayed a T-cell profile more similar to primary tumours. The frequencies of the T cell subsets in lymph nodeswere associated with metastatic size. Tumour cells from smaller metastases exhibited a distinct phenotype compared to those from larger tumour deposits, and the size of the tumour cell deposit impacted the local immune cell composition. Conclusion The tumour size of primary tumours and metastatic size in lymph nodes are the main drivers of changes in immune cell composition

• Zanti, Maria; O'Mahony, Denise; Parsons, Michael T.; Dorling, Leila; Dennis, Joe & Boddicker, Nicholas J. [Show all 50 contributors for this article] (2025). Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification. Nature Communications. 16(1). doi: 10.1038/s41467-025-59979-6. Full text in Research Archive Show summary

  Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyze germline sequencing data of BRCA1 and BRCA2 from 96,691 female breast cancer cases and 302,116 controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observe 11,207 BRCA1 and BRCA2 variants, with 6909 being coding, covering 23.4% of BRCA1 and BRCA2 VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control likelihood ratio (ccLR) evidence is highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.3% specificity for BRCA1 and 93.3% sensitivity and 86.6% specificity for BRCA2. This approach provides case-control evidence for 787 unclassified variants; these include 579 with strong or moderate benign evidence and 10 with strong pathogenic evidence for which ccLR evidence is sufficient to alter clinical classification.

• Padrik, Peeter; Tõnisson, Neeme; Hovda, Tone; Sahlberg, Guro Kristine Kleivi; Hovig, Eivind & Costa, Luís [Show all 21 contributors for this article] (2025). Guidance for the Clinical Use of the Breast Cancer Polygenic Risk Scores. Cancers. 17(7). doi: 10.3390/cancers17071056. Full text in Research Archive
• Hoppe, Reiner; Winter, Stefan; Lo, Wing-Yee; Michailidou, Kyriaki; Bolla, Manjeet K. & Keeman, Renske [Show all 50 contributors for this article] (2025). Lessons learned from a candidate gene study investigating aromatase inhibitor treatment outcome in breast cancer. NPJ breast cancer. 11(1), p. 1–15. doi: 10.1038/s41523-025-00733-y. Full text in Research Archive Show summary

  The role of germline genetics in adjuvant aromatase inhibitor (AI) treatment efficacy in ER-positive breast cancer is poorly understood. We employed a two-stage candidate gene approach to examine associations between survival endpoints and common germline variants in 753 endocrine resistance-related genes. For a discovery cohort, we screened the Breast Cancer Association Consortium database (n ≥ 90,000 cases) and retrieved 2789 AI-treated patients. Cox model-based analysis revealed 125 variants associated with overall, distant relapse-free, and relapse-free survival (p-value ≤ 1E-04). In validation analysis using five independent cohorts (n = 8857), none of the six selected candidates representing major linkage blocks at CELA2B/CASP9, NR1I2/GSK3B, LRP1B, and MIR143HG (CARMN) were validated. We discuss potential reasons for the failed validation and replication of published findings, including study/treatment heterogeneity and other limitations inherent to genomic treatment outcome studies. For the future, we envision prospective longitudinal studies with sufficiently long follow-up and endpoints that reflect the dynamic nature of endocrine resistance.

• Davidson, Aimee L.; Michailidou, Kyriaki; Parsons, Michael T.; Fortuno, Cristina; Bolla, Manjeet K. & Wang, Qin [Show all 50 contributors for this article] (2024). Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset. American Journal of Human Genetics. ISSN 0002-9297. 111(9), p. 2059–2069. doi: 10.1016/j.ajhg.2024.07.004. Full text in Research Archive Show summary

  Co-observation of a gene variant with a pathogenic variant in another gene that explains the disease presentation has been designated as evidence against pathogenicity for commonly used variant classification guidelines. Multiple variant curation expert panels have specified, from consensus opinion, that this evidence type is not applicable for the classification of breast cancer predisposition gene variants. Statistical analysis of sequence data for 55,815 individuals diagnosed with breast cancer from the BRIDGES sequencing project was undertaken to formally assess the utility of co-observation data for germline variant classification. Our analysis included expected loss-of-function variants in 11 breast cancer predisposition genes and pathogenic missense variants in BRCA1, BRCA2, and TP53. We assessed whether co-observation of pathogenic variants in two different genes occurred more or less often than expected under the assumption of independence. Co-observation of pathogenic variants in each of BRCA1, BRCA2, and PALB2 with the remaining genes was less frequent than expected. This evidence for depletion remained after adjustment for age at diagnosis, study design (familial versus population-based), and country. Co-observation of a variant of uncertain significance in BRCA1, BRCA2, or PALB2 with a pathogenic variant in another breast cancer gene equated to supporting evidence against pathogenicity following criterion strength assignment based on the likelihood ratio and showed utility in reclassification of missense BRCA1 and BRCA2 variants identified in BRIDGES. Our approach has applicability for assessing the value of co-observation as a predictor of variant pathogenicity in other clinical contexts, including for gene-specific guidelines developed by ClinGen Variant Curation Expert Panels.

• Sharma, Abhibhav; Debik, Julia; Naume, Bjørn; Ohnstad, Hege Oma; Sahlberg, Guro Kristine Kleivi & Borgen, Elin [Show all 25 contributors for this article] (2024). Comprehensive multi-omics analysis of breast cancer reveals distinct long-term prognostic subtypes. Oncogenesis. 13(1), p. 1–13. doi: 10.1038/s41389-024-00521-6. Full text in Research Archive Show summary

  Breast cancer (BC) is a leading cause of cancer-related death worldwide. The diverse nature and heterogeneous biology of BC pose challenges for survival prediction, as patients with similar diagnoses often respond differently to treatment. Clinically relevant BC intrinsic subtypes have been established through gene expression profiling and are implemented in the clinic. While these intrinsic subtypes show a significant association with clinical outcomes, their long-term survival prediction beyond 5 years often deviates from expected clinical outcomes. This study aimed to identify naturally occurring long-term prognostic subgroups of BC based on an integrated multi-omics analysis. This study incorporates a clinical cohort of 335 untreated BC patients from the Oslo2 study with long-term follow-up (>12 years). Multi-Omics Factor Analysis (MOFA+) was employed to integrate transcriptomic, proteomic, and metabolomic data obtained from the tumor tissues. Our analysis revealed three prominent multi-omics clusters of BC patients with significantly different long-term prognoses (p = 0.005). The multi-omics clusters were validated in two independent large cohorts, METABRIC and TCGA. Importantly, a lack of prognostic association to long-term follow-up above 12 years in the previously established intrinsic subtypes was shown for these cohorts. Through a systems-biology approach, we identified varying enrichment levels of cell-cycle and immune-related pathways among the prognostic clusters. Integrated multi-omics analysis of BC revealed three distinct clusters with unique clinical and biological characteristics. Notably, these multi-omics clusters displayed robust associations with long-term survival, outperforming the established intrinsic subtypes.

• Kildal, Wanja; Cyll, Karolina Urszula; Kalsnes, Joakim; Islam, Rakibul; Julbø, Frida Marie Ihle & Pradhan, Manohar [Show all 35 contributors for this article] (2024). Deep learning for automated scoring of immunohistochemically stained tumour tissue sections – Validation across tumour types based on patient outcomes. Heliyon. 10(13), p. 1–19. doi: 10.1016/j.heliyon.2024.e32529. Full text in Research Archive Show summary

  We aimed to develop deep learning (DL) models to detect protein expression in immunohistochemically (IHC) stained tissue-sections, and to compare their accuracy and performance with manually scored clinically relevant proteins in common cancer types. Five cancer patient cohorts (colon, two prostate, breast, and endometrial) were included. We developed separate DL models for scoring IHC-stained tissue-sections with nuclear, cytoplasmic, and membranous staining patterns. For training, we used images with annotations of cells with positive and negative staining from the colon cohort stained for Ki-67 and PMS2 (nuclear model), the prostate cohort 1 stained for PTEN (cytoplasmic model) and β-catenin (membranous model). The nuclear DL model was validated for MSH6 in the colon, MSH6 and PMS2 in the endometrium, Ki-67 and CyclinB1 in prostate, and oestrogen and progesterone receptors in the breast cancer cohorts. The cytoplasmic DL model was validated for PTEN and Mapre2, and the membranous DL model for CD44 and Flotillin1, all in prostate cohorts. When comparing the results of manual and DL scores in the validation sets, using manual scores as the ground truth, we observed an average correct classification rate of 91.5 % (76.9–98.5 %) for the nuclear model, 85.6 % (73.3–96.6 %) for the cytoplasmic model, and 78.4 % (75.5–84.3 %) for the membranous model. In survival analyses, manual and DL scores showed similar prognostic impact, with similar hazard ratios and p-values for all DL models. Our findings demonstrate that DL models offer a promising alternative to manual IHC scoring, providing efficiency and reproducibility across various data sources and markers.

• Yiangou, Kristia; Mavaddat, Nasim; Dennis, Joe; Zanti, Maria; Wang, Qin & Bolla, Manjeet K. [Show all 50 contributors for this article] (2024). Polygenic score distribution differences across European ancestry populations: implications for breast cancer risk prediction. Breast Cancer Research. ISSN 1465-5411. 26:189(1), p. 1–14. doi: 10.1186/s13058-024-01947-x. Full text in Research Archive Show summary

  Background The 313-variant polygenic risk score (PRS313) provides a promising tool for clinical breast cancer risk prediction. However, evaluation of the PRS313 across different European populations which could influence risk estimation has not been performed. Methods We explored the distribution of PRS313 across European populations using genotype data from 94,072 females without breast cancer diagnosis, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 223,316 females without breast cancer diagnosis from the UK Biobank. The mean PRS was calculated by country in the BCAC dataset and by country of birth in the UK Biobank. We explored different approaches to reduce the observed heterogeneity in the mean PRS across the countries, and investigated the implications of the distribution variability in risk prediction. Results The mean PRS313 differed markedly across European countries, being highest in individuals from Greece and Italy and lowest in individuals from Ireland. Using the overall European PRS313 distribution to define risk categories, leads to overestimation and underestimation of risk in some individuals from these countries. Adjustment for principal components explained most of the observed heterogeneity in the mean PRS. The mean estimates derived when using an empirical Bayes approach were similar to the predicted means after principal component adjustment. Conclusions Our results demonstrate that PRS distribution differs even within European ancestry populations leading to underestimation or overestimation of risk in specific European countries, which could potentially influence clinical management of some individuals if is not appropriately accounted for. Population-specific PRS distributions may be used in breast cancer risk estimation to ensure predicted risks are correctly calibrated across risk categories.

• Torland, Lilly Anne; Lai, Xiaoran; Kumar, Surendra; Riis, Margit; Geisler, Jürgen & Lüders, Torben [Show all 10 contributors for this article] (2024). Benign breast tumors may arise on different immunological backgrounds. Molecular Oncology. ISSN 1574-7891. 18(10), p. 2495–2509. doi: 10.1002/1878-0261.13655. Full text in Research Archive Show summary

  Benign breast tumors are a nonthreatening condition defined as abnormal cell growth within the breast without the ability to invade nearby tissue. However, benign lesions hold valuable biological information that can lead us toward better understanding of tumor biology. In this study, we have used two pathway analysis algorithms, Pathifier and gene set variation analysis (GSVA), to identify biological differences between normal breast tissue, benign tumors and malignant tumors in our clinical dataset. Our results revealed that one-third of all pathways that were significantly different between benign and malignant tumors were immune-related pathways, and 227 of them were validated by both methods and in the METABRIC dataset. Furthermore, five of these pathways (all including genes involved in cytokine and interferon signaling) were related to overall survival in cancer patients in both datasets. The cellular moieties that contribute to immune differences in malignant and benign tumors were analyzed using the deconvolution tool, CIBERSORT. The results showed that levels of some immune cells were specifically higher in benign than in malignant tumors, and this was especially the case for resting dendritic cells and follicular T-helper cells. Understanding the distinct immune profiles of benign and malignant breast tumors may aid in developing noninvasive diagnostic methods to differentiate between them in the future.

• Figlioli, Gisella; Billaud, Amandine; Ahearn, Thomas U.; Antonenkova, Natalia N.; Becher, Heiko & Beckmann, Matthias W. [Show all 114 contributors for this article] (2023). FANCM missense variants and breast cancer risk: a case-control association study of 75,156 European women. European Journal of Human Genetics. ISSN 1018-4813. 31(5), p. 578–587. doi: 10.1038/s41431-022-01257-w. Full text in Research Archive Show summary

  Evidence from literature, including the BRIDGES study, indicates that germline protein truncating variants (PTVs) in FANCM confer moderately increased risk of ER-negative and triple-negative breast cancer (TNBC), especially for women with a family history of the disease. Association between FANCM missense variants (MVs) and breast cancer risk has been postulated. In this study, we further used the BRIDGES study to test 689 FANCM MVs for association with breast cancer risk, overall and in ER-negative and TNBC subtypes, in 39,885 cases (7566 selected for family history) and 35,271 controls of European ancestry. Sixteen common MVs were tested individually; the remaining rare 673 MVs were tested by burden analyses considering their position and pathogenicity score. We also conducted a meta-analysis of our results and those from published studies. We did not find evidence for association for any of the 16 variants individually tested. The rare MVs were significantly associated with increased risk of ER-negative breast cancer by burden analysis comparing familial cases to controls (OR = 1.48; 95% CI 1.07–2.04; P = 0.017). Higher ORs were found for the subgroup of MVs located in functional domains or predicted to be pathogenic. The meta-analysis indicated that FANCM MVs overall are associated with breast cancer risk (OR = 1.22; 95% CI 1.08–1.38; P = 0.002). Our results support the definition from previous analyses of FANCM as a moderate-risk breast cancer gene and provide evidence that FANCM MVs could be low/moderate risk factors for ER-negative and TNBC subtypes. Further genetic and functional analyses are necessary to clarify better the increased risks due to FANCM MVs

• Morra, Anna; Schreurs, Maartje A. C.; Andrulis, Irene L.; Anton-Culver, Hoda; Augustinsson, Annelie & Beckmann, Matthias W. [Show all 125 contributors for this article] (2023). Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer-specific survival. Cancer Medicine. 12(15), p. 16142–16162. doi: 10.1002/cam4.6272. Full text in Research Archive Show summary

  Background - Breast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC-specific survival (BCSS) compared to non-carriers.<p> <p>Aim - To assessed the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS.<p> <p>Methods - Analyses were based on 82,701 women diagnosed with a first primary invasive BC including 963 CHEK2 c.1100delC carriers; median follow-up was 9.1 years. Differential associations with treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi-state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death.<p> <p>Results - There was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status. The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR (95% CI): 0.66 (0.55–0.78)]. No association was observed with radiotherapy. Results from the multi-state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non-carriers also after accounting for CBC occurrence [HR (95% CI): 1.30 (1.09–1.56)].<p> <p>Conclusion - Systemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk.

• Figlioli, Gisella; Billaud, Amandine; Wang, Qin; Bolla, Manjeet K.; Dennis, Joe & Lush, Michael [Show all 96 contributors for this article] (2023). Spectrum and Frequency of Germline FANCM Protein-Truncating Variants in 44,803 European Female Breast Cancer Cases. Cancers. 15(13). doi: 10.3390/cancers15133313. Full text in Research Archive Show summary

  FANCM germline protein truncating variants (PTVs) are moderate-risk factors for ER-negative breast cancer. We previously described the spectrum of FANCM PTVs in 114 European breast cancer cases. In the present, larger cohort, we report the spectrum and frequency of four common and 62 rare FANCM PTVs found in 274 carriers detected among 44,803 breast cancer cases. We confirmed that p.Gln1701* was the most common PTV in Northern Europe with lower frequencies in Southern Europe. In contrast, p.Gly1906Alafs*12 was the most common PTV in Southern Europe with decreasing frequencies in Central and Northern Europe. We verified that p.Arg658* was prevalent in Central Europe and had highest frequencies in Eastern Europe. We also confirmed that the fourth most common PTV, p.Gln498Thrfs*7, might be a founder variant from Lithuania. Based on the frequency distribution of the carriers of rare PTVs, we showed that the FANCM PTVs spectra in Southwestern and Central Europe were much more heterogeneous than those from Northeastern Europe. These findings will inform the development of more efficient FANCM genetic testing strategies for breast cancer cases from specific European populations.

• Levi, Hagai; Carmi, Shai; Rosset, Saharon; Yerushalmi, Rinat; Zick, Aviad & Yablonski-Peretz, Tamar [Show all 155 contributors for this article] (2023). Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel. Journal of Medical Genetics. ISSN 0022-2593. 60(12), p. 1186–1197. doi: 10.1136/jmg-2023-109185. Full text in Research Archive Show summary

  Background Polygenic risk score (PRS), calculated based on genome-wide association studies (GWASs), can improve breast cancer (BC) risk assessment. To date, most BC GWASs have been performed in individuals of European (EUR) ancestry, and the generalisation of EUR-based PRS to other populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women. Methods We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel. Results In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28). Conclusions Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.

• Morra, Anna; Mavaddat, Nasim; Muranen, Taru A.; Ahearn, Thomas U.; Allen, Jamie & Andrulis, Irene L. [Show all 84 contributors for this article] (2023). The impact of coding germline variants on contralateral breast cancer risk and survival. American Journal of Human Genetics. ISSN 0002-9297. 110(3), p. 475–486. doi: 10.1016/j.ajhg.2023.02.003. Full text in Research Archive Show summary

  Evidence linking coding germline variants in breast cancer (BC)-susceptibility genes other than BRCA1, BRCA2, and CHEK2 with contralateral breast cancer (CBC) risk and breast cancer-specific survival (BCSS) is scarce. The aim of this study was to assess the association of protein-truncating variants (PTVs) and rare missense variants (MSVs) in nine known (ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53) and 25 suspected BC-susceptibility genes with CBC risk and BCSS. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated with Cox regression models. Analyses included 34,401 women of European ancestry diagnosed with BC, including 676 CBCs and 3,449 BC deaths; the median follow-up was 10.9 years. Subtype analyses were based on estrogen receptor (ER) status of the first BC. Combined PTVs and pathogenic/likely pathogenic MSVs in BRCA1, BRCA2, and TP53 and PTVs in CHEK2 and PALB2 were associated with increased CBC risk [HRs (95% CIs): 2.88 (1.70–4.87), 2.31 (1.39–3.85), 8.29 (2.53–27.21), 2.25 (1.55–3.27), and 2.67 (1.33–5.35), respectively]. The strongest evidence of association with BCSS was for PTVs and pathogenic/likely pathogenic MSVs in BRCA2 (ER-positive BC) and TP53 and PTVs in CHEK2 [HRs (95% CIs): 1.53 (1.13–2.07), 2.08 (0.95–4.57), and 1.39 (1.13–1.72), respectively, after adjusting for tumor characteristics and treatment]. HRs were essentially unchanged when censoring for CBC, suggesting that these associations are not completely explained by increased CBC risk, tumor characteristics, or treatment. There was limited evidence of associations of PTVs and/or rare MSVs with CBC risk or BCSS for the 25 suspected BC genes. The CBC findings are relevant to treatment decisions, follow-up, and screening after BC diagnosis.

• Hovda, Tone; Larsen, Marthe; Romundstad, Linda; Sahlberg, Guro Kristine Kleivi & Hofvind, Solveig Sand-Hanssen (2023). Breast cancer missed at screening; hindsight or mistakes? European Journal of Radiology. ISSN 0720-048X. 165. doi: 10.1016/j.ejrad.2023.110913. Full text in Research Archive Show summary

  Purpose - To investigate radiologists’ interpretation scores of screening mammograms prior to diagnosis of screen-detected and interval breast cancers retrospectively classified as missed or true negative.<p> <p>Methods - We included data on radiologists’ interpretation scores at screening prior to diagnosis for 1223 screen-detected and 1007 interval cancer cases classified as missed or true negative in an informed consensus-based review. All prior screening examinations were independently scored 1–5 by two radiologists; score 1 by both was considered concordant negative, score ≥ 2 by one radiologist discordant, and score ≥ 2 by both concordant positive. We analyzed associations between interpretation, review categories, mammographic features and histopathological findings using descriptive statistics and logistic regression.<p> <p>Results - Among screen-detected cancers, 31% of missed and 10% of true negative cancers had discordant or concordant positive interpretation at prior screening. The corresponding percentages for interval cancer were 21% and 8%. Age-adjusted odds ratio (OR) and 95% confidence interval (CI) for missed screen-detected cancer was 3.8 (95% CI: 2.6–5.4) after discordant and 5.5 (95% CI: 3.2–9.5) after concordant positive interpretation, using concordant negative as reference. Corresponding ORs for missed interval cancer were 3.0 (95% CI: 2.0–4.5) for discordant and 6.3 (95% CI: 2.3–17.5) for concordant positive interpretation. Asymmetry was the dominating mammographic feature at prior screening for all, except concordant positive screen-detected cancers where a mass dominated. Histopathological characteristics did not vary statistically with interpretation.<p> <p>Conclusions - Most cancers were interpreted negatively at screening prior to diagnosis. Increased risk for missed screen-detected or interval cancer was observed after positive interpretation at prior screening.

• Mueller, Stefanie H.; Lai, Alvina G.; Valkovskaya, Maria; Michailidou, Kyriaki; Bolla, Manjeet K. & Wang, Qin [Show all 207 contributors for this article] (2023). Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry. Genome Medicine. 15(7). doi: 10.1186/s13073-022-01152-5. Full text in Research Archive Show summary

  Background Low‐frequency variants play an important role in breast cancer (BC) susceptibility. Gene‐based meth‐ ods can increase power by combining multiple variants in the same gene and help identify target genes. Methods We evaluated the potential of gene‐based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low‐frequency variants were aggregated for individual genes’ coding and regulatory regions. Association results in European ancestry samples were compared to single‐marker association results in the same cohort. Gene‐based associations were also combined in meta‐analysis across individu‐ als with European, Asian, African, and Latin American and Hispanic ancestry. Results In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10−6) and AC058822.1 (P = 1.47 × 10−4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta‐analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C. Conclusions Using extended gene‐based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single‐marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10−5), demonstrating the importance of diversifying study cohorts.

• Svartdal, Lisa Gregusson; Haugen, Mads; Hongisto, Vesa; Aure, Miriam Ragle; Leivonen, Suvi-Katri & Kristensen, Vessela N. [Show all 10 contributors for this article] (2023). High-throughput screen in vitro identifies dasatinib as a candidate for combinatorial treatment with HER2-targeting drugs in breast cancer. PLOS ONE. 18(1). doi: 10.1371/journal.pone.0280507. Full text in Research Archive Show summary

  Human epidermal growth factor receptor 2-positive (HER2+) breast cancer is an aggressive subtype of this disease. Targeted treatment has improved outcome, but there is still a need for new therapeutic strategies as some patients respond poorly to treatment. Our aim was to identify compounds that substantially affect viability in HER2+ breast cancer cells in response to combinatorial treatment. We performed a high-throughput drug screen of 278 compounds in combination with trastuzumab and lapatinib using two HER2+ breast cancer cell lines (KPL4 and SUM190PT). The most promising drugs were validated in vitro and in vivo, and downstream molecular changes of the treatments were analyzed. The screen revealed multiple drugs that could be used in combination with lapatinib and/or trastuzumab. The Src-inhibitor dasatinib showed the largest combinatorial effect together with lapatinib in the KPL4 cell line compared to treatment with dasatinib alone (p < 0.01). In vivo, only lapatinib significantly reduced tumor growth (p < 0.05), whereas dasatinib alone, or in combination with lapatinib, did not show significant effects. Protein analyses of the treated xenografts showed significant alterations in protein levels compared to untreated controls, suggesting that all drugs reached the tumor and exerted a measurable effect. In silico analyses suggested activation of apoptosis and reduced activity of survival pathways by all treatments, but the opposite pattern was observed for the combinatorial treatment compared to lapatinib alone.

• Skjerven, Helle; Myklebust, Even Moa; Korvald, Christian; Stubberud, Kjetil; Hovda, Tone & Porojnicu, Alina Carmen [Show all 10 contributors for this article] (2023). Long-term follow-up of complex oncoplastic breast-conserving surgery, standard breast conservation and skin-sparing mastectomy in DCIS - a register-based study. European Journal of Surgical Oncology. ISSN 0748-7983. 50(2). doi: 10.1016/j.ejso.2023.107938. Full text in Research Archive
• Skjerven, Helle; Myklebust, Even Moa; Korvald, Christian; Porojnicu, Alina Carmen; Kåresen, Rolf & Hofvind, Solveig Sand-Hanssen [Show all 8 contributors for this article] (2022). Oncological outcomes after simple and skin-sparing mastectomy of ductal carcinoma in situ: A register-based cohort study of 576 Norwegian women. European Journal of Surgical Oncology. ISSN 0748-7983. doi: 10.1016/j.ejso.2022.11.594. Full text in Research Archive
• Dorling, Leila; Carvalho, Sara; Allen, Jamie; Parsons, Michael T.; Fortuno, Cristina & Kristensen, Vessela N. [Show all 50 contributors for this article] (2022). Breast cancer risks associated with missense variants in breast cancer susceptibility genes. Genome Medicine. 14(1), p. 1–17. doi: 10.1186/s13073-022-01052-8. Full text in Research Archive Show summary

  Background: Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain. Methods: We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to ana‑ lyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to fve in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated. Results: The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47–2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best ftting models were well calibrated in the validation set. Conclusions: These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility

• Bjørklund, Sunniva; Aure, Miriam Ragle; Häkkinen, Jari; Vallon-Christersson, Johan; Kumar, Surendra & Evensen, Katrine Bull [Show all 34 contributors for this article] (2022). Subtype and cell type specific expression of lncRNAs provide insight into breast cancer. Communications Biology. 5(1), p. 1–14. doi: 10.1038/s42003-022-03559-7. Full text in Research Archive Show summary

  Abstract Long non-coding RNAs (lncRNAs) are involved in breast cancer pathogenesis through chromatin remodeling, transcriptional and post-transcriptional gene regulation. We report robust associations between lncRNA expression and breast cancer clinicopathological features in two population-based cohorts: SCAN-B and TCGA. Using co-expression analysis of lncRNAs with protein coding genes, we discovered three distinct clusters of lncRNAs. In silico cell type deconvolution coupled with single-cell RNA-seq analyses revealed that these three clusters were driven by cell type specific expression of lncRNAs. In one cluster lncRNAs were expressed by cancer cells and were mostly associated with the estrogen signaling pathways. In the two other clusters, lncRNAs were expressed either by immune cells or fibroblasts of the tumor microenvironment. To further investigate the cis-regulatory regions driving lncRNA expression in breast cancer, we identified subtype-specific transcription factor (TF) occupancy at lncRNA promoters. We also integrated lncRNA expression with DNA methylation data to identify long-range regulatory regions for lncRNA which were validated using ChiA-Pet-Pol2 loops. lncRNAs play an important role in shaping the gene regulatory landscape in breast cancer. We provide a detailed subtype and cell type-specific expression of lncRNA, which improves the understanding of underlying transcriptional regulation in breast cancer.

• Dixon-Suen, Suzanne C.; Lewis, Sarah; Martin, Richard M.; English, Dallas R.; Boyle, Terry & Giles, Graham G. [Show all 174 contributors for this article] (2022). Physical activity, sedentary time and breast cancer risk: a Mendelian randomisation study. British Journal of Sports Medicine. ISSN 0306-3674. 56(20), p. 1157–1170. doi: 10.1136/bjsports-2021-105132. Full text in Research Archive Show summary

  Objectives Physical inactivity and sedentary behaviour are associated with higher breast cancer risk in observational studies, but ascribing causality is difficult. Mendelian randomisation (MR) assesses causality by simulating randomised trial groups using genotype. We assessed whether lifelong physical activity or sedentary time, assessed using genotype, may be causally associated with breast cancer risk overall, pre/post-menopause, and by case-groups defined by tumour characteristics. Methods We performed two-sample inverse-variance-weighted MR using individual-level Breast Cancer Association Consortium case-control data from 130 957 European-ancestry women (69 838 invasive cases), and published UK Biobank data (n=91 105–377 234). Genetic instruments were single nucleotide polymorphisms (SNPs) associated in UK Biobank with wrist-worn accelerometer-measured overall physical activity (nsnps=5) or sedentary time (nsnps=6), or accelerometer-measured (nsnps=1) or self-reported (nsnps=5) vigorous physical activity. Results Greater genetically-predicted overall activity was associated with lower breast cancer overall risk (OR=0.59; 95% confidence interval (CI) 0.42 to 0.83 per-standard deviation (SD;~8 milligravities acceleration)) and for most case-groups. Genetically-predicted vigorous activity was associated with lower risk of pre/perimenopausal breast cancer (OR=0.62; 95% CI 0.45 to 0.87,≥3 vs. 0 self-reported days/week), with consistent estimates for most case-groups. Greater genetically-predicted sedentary time was associated with higher hormone-receptor-negative tumour risk (OR=1.77; 95% CI 1.07 to 2.92 per-SD (~7% time spent sedentary)), with elevated estimates for most case-groups. Results were robust to sensitivity analyses examining pleiotropy (including weighted-median-MR, MR-Egger). Conclusion Our study provides strong evidence that greater overall physical activity, greater vigorous activity, and lower sedentary time are likely to reduce breast cancer risk. More widespread adoption of active lifestyles may reduce the burden from the most common cancer in women.

• Dennis, Joe; Tyrer, Jonathan P.; Walker, Logan C.; Michailidou, Kyriaki; Dorling, Leila & Kristensen, Vessela N. [Show all 50 contributors for this article] (2022). Rare germline copy number variants (CNVs) and breast cancer risk. Communications Biology. 5, p. 1–15. doi: 10.1038/s42003-021-02990-6. Full text in Research Archive Show summary

  Germline copy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. Gene burden tests detected the strongest association for deletions in BRCA1 (P = 3.7E−18). Nine other genes were associated with a p-value < 0.01 including known susceptibility genes CHEK2 (P = 0.0008), ATM (P = 0.002) and BRCA2 (P = 0.008). Outside the known genes we detected associations with p-values < 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci. To the best of our knowledge, this is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance.

• Ahearn, Thomas U.; Zhang, Haoyu; Michailidou, Kyriaki; Milne, Roger L.; Bolla, Manjeet K. & Dennis, Joe [Show all 205 contributors for this article] (2022). Common variants in breast cancer risk loci predispose to distinct tumor subtypes. Breast Cancer Research. ISSN 1465-5411. 24(1), p. 1–13. doi: 10.1186/s13058-021-01484-x. Full text in Research Archive Show summary

  Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.

• Normann, Lisa Svartdal; Haugen, Mads Haugland; Aure, Miriam Ragle; Kristensen, Vessela N.; Mælandsmo, Gunhild Mari & Sahlberg, Kristine Kleivi (2022). miR-101-5p Acts as a Tumor Suppressor in HER2-Positive Breast Cancer Cells and Improves Targeted Therapy. Breast Cancer: Targets and Therapy. 14, p. 25–39. doi: 10.2147/BCTT.S338404. Full text in Research Archive Show summary

  Purpose: Human epidermal growth factor receptor 2 positive (HER2+) breast cancers responding poorly to targeted therapy need improved treatment options. miR-101-5p has shown tumor-suppressive properties in multiple cancer forms, and we assessed the effect and mechanism of action of this miRNA in HER2+ breast cancer. Methods: Expression levels of miR-101-5p in two clinical datasets, TCGA and METABRIC, were compared between tumor and normal adjacent samples, and across molecular subtypes and HER2 status. The ability of miR-101-5p to sensitize for treatment with lapatinib, tucatinib and trastuzumab was explored in HER2+ breast cancer cells responding poorly to such targeted drugs. Proliferation and apoptosis assays and downstream protein analysis were performed. Results: Expression levels of miR-101-5p were significantly lower in tumor compared to normal adjacent tissue (p < 0.001), and particularly low in HER2+ tumors, both the HER2-enriched subtype (p ≤ 0.037) and clinical HER2-status (p < 0.001). In a HER2+ cell line (KPL4) responding poorly to targeted drugs, miR-101-5p overexpression inhibited proliferation (p < 0.001), and combinatorial treatment with lapatinib and trastuzumab significantly further decreased this inhibition (p = 0.004). Proteomic data and in silico analyses revealed PI3K/Akt- and HER2-pathways among the predicted regulated pathways. miR-101-5p alone (p = 0.018) and in combination with lapatinib and trastuzumab (p < 0.001) induced apoptosis, while the targeted drugs alone did not exert any significant effect neither on proliferation nor apoptosis. Conclusion: miR-101-5p acts as a tumor suppressor by inducing apoptosis in HER2+ breast cancer and sensitizes cells with initially poor response to lapatinib and trastuzumab.

• Wolowczyk, Camilla; Neckmann, Ulrike; Aure, Miriam Ragle; Hall, Martina; Johannessen, Bjarne & Zhao, Sen [Show all 14 contributors for this article] (2022). NRF2 drives an oxidative stress response predictive of breast cancer. Free Radical Biology & Medicine. ISSN 0891-5849. 184, p. 170–184. doi: 10.1016/j.freeradbiomed.2022.03.029. Full text in Research Archive Show summary

  Many breast cancer patients are diagnosed with small, well-differentiated, hormone receptor-positive tumors. Risk of relapse is not easily identified in these patients, resulting in overtreatment. To identify metastasis-related gene expression patterns, we compared the transcriptomes of the non-metastatic 67NR and metastatic 66cl4 cell lines from the murine 4T1 mammary tumor model. The transcription factor nuclear factor, erythroid 2-like 2 (NRF2, encoded by NFE2L2) was constitutively activated in the metastatic cells and tumors, and correspondingly a subset of established NRF2-regulated genes was also upregulated. Depletion of NRF2 increased basal levels of reactive oxygen species (ROS) and severely reduced ability to form primary tumors and lung metastases. Consistently, a set of NRF2-controlled genes was elevated in breast cancer biopsies. Sixteen of these were combined into a gene expression signature that significantly improves the PAM50 ROR score, and is an independent, strong predictor of prognosis, even in hormone receptor-positive tumors.

• Skjerven, Helle; Danielsen, Anders Skyrud; Schlichting, Ellen; Sahlberg, Kristine Kleivi & Hofvind, Solveig Sand-Hanssen (2022). Treatment of Ductal Carcinoma in situ: A Register-Based Study of Norwegian Women Diagnosed between 1995 and 2018. Breast Care. ISSN 1661-3791. 17(5), p. 486–494. doi: 10.1159/000524564. Full text in Research Archive Show summary

  The incidence of ductal carcinoma in situ (DCIS) has increased after implementation of mammographic screening. The lesion represents management challenges due to its undetermined growth pattern. We aimed to explore treatment of women aged 48–71 years diagnosed with DCIS between 1995 and 2018, by detection mode and histopathological characteristics. Material and Methods: Data on surgical treatment and radiation therapy (RT) of 4,995 women diagnosed with DCIS were retrieved from the Cancer Registry of Norway. We described the percentage and frequency of breast-conserving treatment (BCT) for participants in BreastScreen Norway (screen-detected) and nonparticipants. We estimated the relative risk (RR) of BCT, using log-binomial regression models. Results: Use of BCT increased from about 40% in 1995 to 85% in 2018. Use of BCT was more common among older than younger women and more commonly used for screen-detected versus tumors detected outside the screening program. Nine out of ten women with tumors ≤10 mm were treated with BCT and two out of ten with tumors >50 mm. RT was given to 89.3% of the women with tumors ≤10 mm, 34.1% of those with tumors classified as van Nuys’ grade 1 and <10 mm and 96.0% of the tumors >50 mm. Use of BCT was less common for tumors >50 mm compared to <10 mm (RR adjusted for age, detection mode, van Nuys’ grade, and localization: 0.26, 95% CI: 0.19–0.36). Conclusion: BCT was increasingly used among women diagnosed with DCIS in Norway during the period from 1995 to 2018, particularly for screen-detected, small lesions with low van Nuys’ grade.

• Morra, Anna; Escala-Garcia, Maria; Beesley, Jonathan; Keeman, Renske; Canisius, Sander & Ahearn, Thomas U. [Show all 50 contributors for this article] (2021). Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment. Breast Cancer Research. ISSN 1465-5411. 23:86(1), p. 1–18. doi: 10.1186/s13058-021-01450-7. Full text in Research Archive Show summary

  Background Given the high heterogeneity among breast tumors, associations between common germline genetic variants and survival that may exist within specific subgroups could go undetected in an unstratified set of breast cancer patients. Methods We performed genome-wide association analyses within 15 subgroups of breast cancer patients based on prognostic factors, including hormone receptors, tumor grade, age, and type of systemic treatment. Analyses were based on 91,686 female patients of European ancestry from the Breast Cancer Association Consortium, including 7531 breast cancer-specific deaths over a median follow-up of 8.1 years. Cox regression was used to assess associations of common germline variants with 15-year and 5-year breast cancer-specific survival. We assessed the probability of these associations being true positives via the Bayesian false discovery probability (BFDP < 0.15). Results Evidence of associations with breast cancer-specific survival was observed in three patient subgroups, with variant rs5934618 in patients with grade 3 tumors (15-year-hazard ratio (HR) [95% confidence interval (CI)] 1.32 [1.20, 1.45], P = 1.4E−08, BFDP = 0.01, per G allele); variant rs4679741 in patients with ER-positive tumors treated with endocrine therapy (15-year-HR [95% CI] 1.18 [1.11, 1.26], P = 1.6E−07, BFDP = 0.09, per G allele); variants rs1106333 (15-year-HR [95% CI] 1.68 [1.39,2.03], P = 5.6E−08, BFDP = 0.12, per A allele) and rs78754389 (5-year-HR [95% CI] 1.79 [1.46,2.20], P = 1.7E−08, BFDP = 0.07, per A allele), in patients with ER-negative tumors treated with chemotherapy. Conclusions We found evidence of four loci associated with breast cancer-specific survival within three patient subgroups. There was limited evidence for the existence of associations in other patient subgroups. However, the power for many subgroups is limited due to the low number of events. Even so, our results suggest that the impact of common germline genetic variants on breast cancer-specific survival might be limited.

• Park, Hanla A.; Neumeyer, Sonja; Michailidou, Kyriaki; Bolla, Manjeet K.; Wang, Qin & Kristensen, Vessela N. [Show all 50 contributors for this article] (2021). Mendelian randomisation study of smoking exposure in relation to breast cancer risk. British Journal of Cancer. ISSN 0007-0920. 125(8), p. 1135–1145. doi: 10.1038/s41416-021-01432-8. Full text in Research Archive Show summary

  Abstract Background Despite a modest association between tobacco smoking and breast cancer risk reported by recent epidemiological studies, it is still equivocal whether smoking is causally related to breast cancer risk. Methods We applied Mendelian randomisation (MR) to evaluate a potential causal effect of cigarette smoking on breast cancer risk. Both individual-level data as well as summary statistics for 164 single-nucleotide polymorphisms (SNPs) reported in genome-wide association studies of lifetime smoking index (LSI) or cigarette per day (CPD) were used to obtain MR effect estimates. Data from 108,420 invasive breast cancer cases and 87,681 controls were used for the LSI analysis and for the CPD analysis conducted among ever-smokers from 26,147 cancer cases and 26,072 controls. Sensitivity analyses were conducted to address pleiotropy. Results Genetically predicted LSI was associated with increased breast cancer risk (OR 1.18 per SD, 95% CI: 1.07–1.30, P  = 0.11 × 10 –2 ), but there was no evidence of association for genetically predicted CPD (OR 1.02, 95% CI: 0.78–1.19, P  = 0.85). The sensitivity analyses yielded similar results and showed no strong evidence of pleiotropic effect. Conclusion Our MR study provides supportive evidence for a potential causal association with breast cancer risk for lifetime smoking exposure but not cigarettes per day among smokers.

• Aure, Miriam Ragle; Fleischer, Thomas; Bjørklund, Sunniva; Ankill, Jørgen; Mondragón, Jaime Abraham Castro & Børresen-Dale, Anne-Lise [Show all 11 contributors for this article] (2021). Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer. Genome Medicine. 13:72, p. 1–21. doi: 10.1186/s13073-021-00880-4. Full text in Research Archive Show summary

  Background Abnormal DNA methylation is observed as an early event in breast carcinogenesis. However, how such alterations arise is still poorly understood. microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and play key roles in various biological processes. Here, we integrate miRNA expression and DNA methylation at CpGs to study how miRNAs may affect the breast cancer methylome and how DNA methylation may regulate miRNA expression. Methods miRNA expression and DNA methylation data from two breast cancer cohorts, Oslo2 (n = 297) and The Cancer Genome Atlas (n = 439), were integrated through a correlation approach that we term miRNA-methylation Quantitative Trait Loci (mimQTL) analysis. Hierarchical clustering was used to identify clusters of miRNAs and CpGs that were further characterized through analysis of mRNA/protein expression, clinicopathological features, in silico deconvolution, chromatin state and accessibility, transcription factor binding, and long-range interaction data. Results Clustering of the significant mimQTLs identified distinct groups of miRNAs and CpGs that reflect important biological processes associated with breast cancer pathogenesis. Notably, two major miRNA clusters were related to immune or fibroblast infiltration, hence identifying miRNAs associated with cells of the tumor microenvironment, while another large cluster was related to estrogen receptor (ER) signaling. Studying the chromatin landscape surrounding CpGs associated with the estrogen signaling cluster, we found that miRNAs from this cluster are likely to be regulated through DNA methylation of enhancers bound by FOXA1, GATA2, and ER-alpha. Further, at the hub of the estrogen cluster, we identified hsa-miR-29c-5p as negatively correlated with the mRNA and protein expression of DNA methyltransferase DNMT3A, a key enzyme regulating DNA methylation. We found deregulation of hsa-miR-29c-5p already present in pre-invasive breast lesions and postulate that hsa-miR-29c-5p may trigger early event abnormal DNA methylation in ER-positive breast cancer. Conclusions We describe how miRNA expression and DNA methylation interact and associate with distinct breast cancer phenotypes.

• Ben-Elazar, Shay; Aure, Miriam Ragle; Jonsdottir, Kristin; Leivonen, Suvi-Katri; Kristensen, Vessela N. & Janssen, Emiel [Show all 9 contributors for this article] (2021). miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer. PLoS Computational Biology. ISSN 1553-734X. 17(2). doi: 10.1371/JOURNAL.PCBI.1008608. Full text in Research Archive Show summary

  Different miRNA profiling protocols and technologies introduce differences in the resulting quantitative expression profiles. These include differences in the presence (and measurability) of certain miRNAs. We present and examine a method based on quantile normalization, Adjusted Quantile Normalization (AQuN), to combine miRNA expression data from multiple studies in breast cancer into a single joint dataset for integrative analysis. By pooling multiple datasets, we obtain increased statistical power, surfacing patterns that do not emerge as statistically significant when separately analyzing these datasets. To merge several datasets, as we do here, one needs to overcome both technical and batch differences between these datasets. We compare several approaches for merging and jointly analyzing miRNA datasets. We investigate the statistical confidence for known results and highlight potential new findings that resulted from the joint analysis using AQuN. In particular, we detect several miRNAs to be differentially expressed in estrogen receptor (ER) positive versus ER negative samples. In addition, we identify new potential biomarkers and therapeutic targets for both clinical groups. As a specific example, using the AQuN-derived dataset we detect hsa-miR-193b-5p to have a statistically significant over-expression in the ER positive group, a phenomenon that was not previously reported. Furthermore, as demonstrated by functional assays in breast cancer cell lines, overexpression of hsa-miR-193b-5p in breast cancer cell lines resulted in decreased cell viability in addition to inducing apoptosis. Together, these observations suggest a novel functional role for this miRNA in breast cancer. Packages implementing AQuN are provided for Python and Matlab: https://github.com/YakhiniGroup/PyAQN.

• Rye, Inga Hansine; Huse, Kanutte; Josefsson, Sarah Elisabet; Kildal, Wanja; Danielsen, Håvard Emil Greger & Schlichting, Ellen [Show all 28 contributors for this article] (2021). Breast cancer metastasis: immune profiling of lymph nodes reveals exhaustion of effector T cells and immunosuppression. Molecular Oncology. ISSN 1574-7891. 16(1), p. 88–103. doi: 10.1002/1878-0261.13047. Full text in Research Archive Show summary

  Sentinel lymph nodes are the first nodes draining the lymph from a breast and could reveal early changes in the host immune system upon dissemination of breast cancer cells. To investigate this, we performed single-cell immune profiling of lymph nodes with and without metastatic cells. Whereas no significant changes were observed for B-cell and natural killer (NK)-cell subsets, metastatic lymph nodes had a significantly increased frequency of CD8 T cells and a skewing toward an effector/memory phenotype of CD4 and CD8 T cells, suggesting an ongoing immune response. Additionally, metastatic lymph nodes had an increased frequency of TIGIT (T-cell immunoreceptor with Ig and ITIM domains)-positive T cells with suppressed TCR signaling compared with non-metastatic nodes, indicating exhaustion of effector T cells, and an increased frequency of regulatory T cells (Tregs) with an activated phenotype. T-cell alterations correlated with the percentage of metastatic tumor cells, reflecting the presence of metastatic tumor cells driving T effector cells toward exhaustion and promoting immunosuppression by recruitment or increased differentiation toward Tregs. These results show that immune suppression occurs already in early stages of tumor progression.

• Normann, Lisa Gregusson Svartdal; Aure, Miriam Ragle; Leivonen, Suvi-Katri; Haugen, Mads Haugland; Hongisto, Vesa & Kristensen, Vessela N. [Show all 8 contributors for this article] (2021). MicroRNA in combination with HER2-targeting drugs reduces breast cancer cell viability in vitro. Scientific Reports. 11:10893, p. 1–11. doi: 10.1038/s41598-021-90385-2. Full text in Research Archive Show summary

  HER2-positive (HER2 +) breast cancer patients that do not respond to targeted treatment have a poor prognosis. The effects of targeted treatment on endogenous microRNA (miRNA) expression levels are unclear. We report that responsive HER2 + breast cancer cell lines had a higher number of miRNAs with altered expression after treatment with trastuzumab and lapatinib compared to poorly responsive cell lines. To evaluate whether miRNAs can sensitize HER2 + cells to treatment, we performed a high-throughput screen of 1626 miRNA mimics and inhibitors in combination with trastuzumab and lapatinib in HER2 + breast cancer cells. We identified eight miRNA mimics sensitizing cells to targeted treatment, miR-101-5p, mir-518a-5p, miR-19b-2-5p, miR-1237-3p, miR-29a-3p, miR-29c-3p, miR-106a-5p, and miR-744-3p. A higher expression of miR-101-5p predicted better prognosis in patients with HER2 + breast cancer (OS: p = 0.039; BCSS: p = 0.012), supporting the tumor-suppressing role of this miRNA. In conclusion, we have identified miRNAs that sensitize HER2 + breast cancer cells to targeted therapy. This indicates the potential of combining targeted drugs with miRNAs to improve current treatments for HER2 + breast cancers.

• Hovda, Tone; Hoff, Solveig Roth; Larsen, Marthe; Romundstad, Linda; Sahlberg, Kristine Kleivi & Hofvind, Solveig (2021). True and Missed Interval Cancer in Organized Mammographic Screening: A Retrospective Review Study of Diagnostic and Prior Screening Mammograms. Academic Radiology. ISSN 1076-6332. 29(Supplement 1), p. S180–S191. doi: 10.1016/j.acra.2021.03.022. Full text in Research Archive Show summary

  Rationale and Objectives To explore radiological aspects of interval breast cancer in a population-based screening program. Materials and Methods We performed a consensus-based informed review of mammograms from diagnosis and prior screening from women diagnosed with interval cancer 2004-2016 in BreastScreen Norway. Cases were classified as true (no findings on prior screening mammograms), occult (no findings at screening or diagnosis), minimal signs (minor/non-specific findings) and missed (obvious findings). We analyzed mammographic findings, density, time since prior screening, and histopathological characteristics between the classification groups. Results The study included 1010 interval cancer cases. Mean age at diagnosis was 61 years (SD = 6), mean time between screening and diagnosis 14 months (SD = 7). A total of 48% (479/1010) were classified as true or occult, 28% (285/1010) as minimal signs and 24% (246/1010) as missed. We observed no differences in mammographic density between the groups, except from a higher percentage of dense breasts in women with occult cancer. Among cancers classified as missed, about 1/3 were masses and 1/3 asymmetries at prior screening. True interval cancers were diagnosed later in the screening interval than the other classification categories. No differences in histopathological characteristics were observed between true, minimal signs and missed cases. Conclusion In an informed review, 24% of the interval cancers were classified as missed based on visibility and mammographic findings on prior screening mammograms. Three out of four true interval cancers were diagnosed in the second year of the screening interval. We observed no statistical differences in histopathological characteristics between true and missed interval cancers.

• Johnson, Nichola; Maguire, Sarah; Morra, Anna; Kapoor, Pooja Middha; Tomczyk, Katarzyna & Kristensen, Vessela N. [Show all 50 contributors for this article] (2021). CYP3A7*1C allele: linking premenopausal oestrone and progesterone levels with risk of hormone receptor-positive breast cancers. British Journal of Cancer. ISSN 0007-0920. 124, p. 842–854. doi: 10.1038/s41416-020-01185-w. Full text in Research Archive Show summary

  Abstract Background Epidemiological studies provide strong evidence for a role of endogenous sex hormones in the aetiology of breast cancer. The aim of this analysis was to identify genetic variants that are associated with urinary sex-hormone levels and breast cancer risk. Methods We carried out a genome-wide association study of urinary oestrone-3-glucuronide and pregnanediol-3-glucuronide levels in 560 premenopausal women, with additional analysis of progesterone levels in 298 premenopausal women. To test for the association with breast cancer risk, we carried out follow-up genotyping in 90,916 cases and 89,893 controls from the Breast Cancer Association Consortium. All women were of European ancestry. Results For pregnanediol-3-glucuronide, there were no genome-wide significant associations; for oestrone-3-glucuronide, we identified a single peak mapping to the CYP3A locus, annotated by rs45446698. The minor rs45446698-C allele was associated with lower oestrone-3-glucuronide (−49.2%, 95% CI −56.1% to −41.1%, P  = 3.1 × 10 –18 ); in follow-up analyses, rs45446698-C was also associated with lower progesterone (−26.7%, 95% CI −39.4% to −11.6%, P  = 0.001) and reduced risk of oestrogen and progesterone receptor-positive breast cancer (OR = 0.86, 95% CI 0.82–0.91, P  = 6.9 × 10 –8 ). Conclusions The CYP3A7*1C allele is associated with reduced risk of hormone receptor-positive breast cancer possibly mediated via an effect on the metabolism of endogenous sex hormones in premenopausal women.

• Park, JooYong; Choi, Ji-Yeob; Choi, Jaesung; Chung, Seokang; Song, Nan & Park, Sue K [Show all 50 contributors for this article] (2021). Gene-Environment Interactions Relevant to Estrogen and Risk of Breast Cancer: Can Gene-Environment Interactions Be Detected Only among Candidate SNPs from Genome-Wide Association Studies? Cancers. 13:2370(10), p. 1–21. doi: 10.3390/cancers13102370. Full text in Research Archive Show summary

  In this study we aim to examine gene–environment interactions (GxEs) between genes involved with estrogen metabolism and environmental factors related to estrogen exposure. GxE analyses were conducted with 1970 Korean breast cancer cases and 2052 controls in the case-control study, the Seoul Breast Cancer Study (SEBCS). A total of 11,555 SNPs from the 137 candidate genes were included in the GxE analyses with eight established environmental factors. A replication test was conducted by using an independent population from the Breast Cancer Association Consortium (BCAC), with 62,485 Europeans and 9047 Asians. The GxE tests were performed by using two-step methods in GxEScan software. Two interactions were found in the SEBCS. The first interaction was shown between rs13035764 of NCOA1 and age at menarche in the GE|2df model (p-2df = 1.2 × 10−3). The age at menarche before 14 years old was associated with the high risk of breast cancer, and the risk was higher when subjects had homozygous minor allele G. The second GxE was shown between rs851998 near ESR1 and height in the GE|2df model (p-2df = 1.1 × 10−4). Height taller than 160 cm was associated with a high risk of breast cancer, and the risk increased when the minor allele was added. The findings were not replicated in the BCAC. These results would suggest specificity in Koreans for breast cancer risk.

• Egeland, Nina Gran; Jonsdottir, Kristin; Aure, Miriam Ragle; Sahlberg, Kristine Kleivi; Kristensen, Vessela N. & Cronin-Fenton, Deirdre [Show all 10 contributors for this article] (2020). MiR-18a and miR-18b are expressed in the stroma of oestrogen receptor alpha negative breast cancers. BMC Cancer. 20. doi: 10.1186/s12885-020-06857-7. Full text in Research Archive Show summary

  Background Previously, we have shown that miR-18a and miR-18b gene expression strongly correlates with high proliferation, oestrogen receptor -negativity (ER−), cytokeratin 5/6 positivity and basal-like features of breast cancer. Methods We investigated the expression and localization of miR-18a and -18b in formalin fixed paraffin embedded (FFPE) tissue from lymph node negative breast cancers (n = 40), by chromogenic in situ hybridization (CISH). The expression level and in situ localization of miR-18a and -18b was assessed with respect to the presence of tumour infiltrating lymphocytes (TILs) and immunohistochemical markers for ER, CD4, CD8, CD20, CD68, CD138, PAX5 and actin. Furthermore, in two independent breast cancer cohorts (94 and 377 patients) the correlation between miR-18a and -18b expression and the relative quantification of 22 immune cell types obtained from the CIBERSORT tool was assessed. Results CISH demonstrated distinct and specific cytoplasmic staining for both miR-18a and miR-18b, particularly in the intratumoural stroma and the stroma surrounding the tumour margin. Staining by immunohistochemistry revealed some degree of overlap of miR-18a and -18b with CD68 (monocytes/macrophages), CD138 (plasma cells) and the presence of high percentages of TILs. CIBERSORT analysis showed a strong correlation between M1-macrophages and CD4+ memory activated T-cells with mir-18a and -18b. Conclusions Our study demonstrates that miR-18a and miR-18b expression is associated with ER- breast tumours that display a high degree of inflammation. This expression is potentially associated specifically with macrophages. These results suggest that miR-18a and miR-18b may play a role in the systemic immunological response in ER− tumours

• Tinholt, Mari; Stavik, Benedicte; Tekpli, Xavier; Garred, Øystein; Borgen, Elin & Kristensen, Vessela N. [Show all 9 contributors for this article] (2020). Coagulation factor V is a marker of tumor-infiltrating immune cells in breast cancer. Oncoimmunology. ISSN 2162-4011. 9:e1824644(1), p. 1–12. doi: 10.1080/2162402X.2020.1824644. Full text in Research Archive Show summary

  Background Factor (F) V is an essential cofactor in blood coagulation, however, F5 expression in breast tumors has also been linked to tumor aggressiveness and overall survival. The specific role of FV in breast cancer is yet unknown. We therefore aimed at dissecting the biological relevance of FV in breast cancer. Methods Gene expression data from a Scandinavian breast cancer cohort (n = 363) and the cancer genome atlas (TCGA) (n = 981) and 12 replication cohorts were used to search for F5 co-expressed genes, followed by gene ontology analysis. Pathological and bioinformatic tools were used to evaluate immune cell infiltration and tumor purity. T cell activation, proliferation and migration were studied in FV treated Jurkat T cells. Results F5 co-expressed genes were mainly associated with immune system processes and cell activation. Tumors with high expression of F5 were more infiltrated with both lymphoid (T cells, NK cells, and B cells) and myeloid cells (macrophages and dendritic cells), and F5 expression was negatively correlated with tumor purity (ρ = −0.32). Confirming a prognostic role, data from the Kaplan-Meier plotter showed that high F5 expression was associated with improved relapse-free survival. The strongest association was observed in basal-like breast cancer (HR = 0.55; 95% CI, 0.42–0.71). Exogenous FV did not substantially affect activation, proliferation or migration of human T cells. Conclusions F5 was identified as a novel marker of immune cell infiltration in breast cancer, and the prognostic role of F5 was verified. FV emerge as an interesting immunological biomarker with potential therapeutic relevance for the cancer-inflammation-thrombosis circuit.

• Liu, Jingjing; Smissen, Wendy J. C. Prager van der; Collee, Margriet J.; Bolla, Manjeet K.; Wang, Qin & Kristensen, Vessela N. [Show all 82 contributors for this article] (2020). Germline HOXB13 mutations p.G84E and p.R217C do not confer an increased breast cancer risk. Scientific Reports. 10:9688(1), p. 1–14. doi: 10.1038/s41598-020-65665-y. Full text in Research Archive Show summary

  In breast cancer, high levels of homeobox protein Hox-B13 (HOXB13) have been associated with disease progression of ER-positive breast cancer patients and resistance to tamoxifen treatment. Since HOXB13 p.G84E is a prostate cancer risk allele, we evaluated the association between HOXB13 germline mutations and breast cancer risk in a previous study consisting of 3,270 familial non-BRCA1/2 breast cancer cases and 2,327 controls from the Netherlands. Although both recurrent HOXB13 mutations p.G84E and p.R217C were not associated with breast cancer risk, the risk estimation for p.R217C was not very precise. To provide more conclusive evidence regarding the role of HOXB13 in breast cancer susceptibility, we here evaluated the association between HOXB13 mutations and increased breast cancer risk within 81 studies of the international Breast Cancer Association Consortium containing 68,521 invasive breast cancer patients and 54,865 controls. Both HOXB13 p.G84E and p.R217C did not associate with the development of breast cancer in European women, neither in the overall analysis (OR=1.035, 95% CI=0.859–1.246, P=0.718 and OR=0.798, 95% CI=0.482–1.322, P=0.381 respectively), nor in specifc high-risk subgroups or breast cancer subtypes. Thus, although involved in breast cancer progression, HOXB13 is not a material breast cancer susceptibility gene.

• Skjerven, Helle; Danielsen, Anders Skyrud; Schlichting, Ellen; Sahlberg, Kristine Kleivi & Hofvind, Solveig (2020). Kirurgisk behandling av brystkreft i Norge 2003–18. Tidsskrift for Den norske legeforening (Tidsskriftet). ISSN 0029-2001. doi: 10.4045/tidsskr.20.0090. Full text in Research Archive Show summary

  BAKGRUNN Brystbevarende kirurgi er anbefalt i Norge og internasjonalt ved brystkreft påvist i et tidlig stadium. Vi har analysert operasjonsmetode for brystkreftpasienter etter behandlende sykehus, alder ved diagnose, deteksjonsmetode og svulstenes histopatologiske karakteristikk for perioden fra 2003 til 2018. MATERIALE OG METODE Informasjon om kvinner i alle aldre diagnostisert med infiltrerende brystkreft (n = 47 004) ble hentet fra Kreftregisterets databaser. Vi ekskluderte kvinner med fjernmetastaser ved diagnose (n = 1 773) og de uten registrert operasjonsmetode (n = 2 638). Deteksjonsmetode ble definert som screeningoppdaget brystkreft, intervallkreft eller brystkreft påvist utenfor Mammografiprogrammet. Valg av operasjonsmetode ble sammenlignet ved deskriptive analyser. RESULTATER Noe over halvparten (23 661 av 42 593, dvs. 55,6 %) av kvinnene som fikk påvist brystkreft i studieperioden, ble operert med brystbevarende kirurgi. Andelen økte fra 1 189/2 423 (49,1 %) i 2003 til 2 070/2 958 (70,0 %) i 2018. Det var store forskjeller mellom sykehusene. I perioden 2015–18 fant vi den høyeste andelen brystbevarende kirurgi, 175/187 (93,6 %), ved screeningoppdaget brystkreft operert på Ålesund sjukehus, mens vi fant den laveste andelen, 121/351 (34,5 %), blant kvinner med brystkreft påvist utenfor Mammografiprogrammet, operert på Radiumhospitalet. Brystbevarende kirurgi ble oftest benyttet hos kvinner med små svulster uten spredning til lymfeknuter i armhulen. FORTOLKNING Vi fant betydelige forskjeller i operasjonsmetode for brystkreft mellom sykehusene og mellom ulike deteksjonsmetodene.

• Kramer, Iris; Hooning, Maartje J.; Mavaddat, Nasim; Hauptmann, Michael; Keeman, Renske & Steyerberg, Ewout W. [Show all 54 contributors for this article] (2020). Breast Cancer Polygenic Risk Score and Contralateral Breast Cancer Risk. American Journal of Human Genetics. ISSN 0002-9297. 107(5), p. 837–848. doi: 10.1016/j.ajhg.2020.09.001. Full text in Research Archive Show summary

  Previous research has shown that polygenic risk scores (PRSs) can be used to stratify women according to their risk of developing primary invasive breast cancer. This study aimed to evaluate the association between a recently validated PRS of 313 germline variants (PRS313) and contralateral breast cancer (CBC) risk. We included 56,068 women of European ancestry diagnosed with first invasive breast cancer from 1990 onward with follow-up from the Breast Cancer Association Consortium. Metachronous CBC risk (N = 1,027) according to the distribution of PRS313 was quantified using Cox regression analyses. We assessed PRS313 interaction with age at first diagnosis, family history, morphology, ER status, PR status, and HER2 status, and (neo)adjuvant therapy. In studies of Asian women, with limited follow-up, CBC risk associated with PRS313 was assessed using logistic regression for 340 women with CBC compared with 12,133 women with unilateral breast cancer. Higher PRS313 was associated with increased CBC risk: hazard ratio per standard deviation (SD) = 1.25 (95%CI = 1.18–1.33) for Europeans, and an OR per SD = 1.15 (95%CI = 1.02–1.29) for Asians. The absolute lifetime risks of CBC, accounting for death as competing risk, were 12.4% for European women at the 10th percentile and 20.5% at the 90th percentile of PRS313. We found no evidence of confounding by or interaction with individual characteristics, characteristics of the primary tumor, or treatment. The C-index for the PRS313 alone was 0.563 (95%CI = 0.547–0.586). In conclusion, PRS313 is an independent factor associated with CBC risk and can be incorporated into CBC risk prediction models to help improve stratification and optimize surveillance and treatment strategies.

• Hovda, Tone; Tsuruda, Kaitlyn; Hoff, Solveig Roth; Sahlberg, Kristine Kleivi & Hofvind, Solveig (2020). Radiological review of prior screening mammograms of screen-detected breast cancer. European Radiology. ISSN 0938-7994. 31(4), p. 2568–2579. doi: 10.1007/s00330-020-07130-y. Full text in Research Archive Show summary

  Objective: To perform a radiological review of mammograms from prior screening and diagnosis of screen-detected breast cancer in BreastScreen Norway, a population-based screening program. Methods: We performed a consensus-based informed review of mammograms from prior screening and diagnosis for screen-detected breast cancers. Mammographic density and findings on screening and diagnostic mammograms were classified according to the Breast Imaging-Reporting and Data System®. Cases were classified based on visible findings on prior screening mammograms as true (no findings), missed (obvious findings), minimal signs (minor/non-specific findings), or occult (no findings at diagnosis). Histopathologic tumor characteristics were extracted from the Cancer Registry of Norway. The Bonferroni correction was used to adjust for multiple testing; p

• Tekpli, Xavier; Lien, Tonje Gulbrandsen; Røssevold, Andreas Hagen; Nebdal, Daniel J.H.; Borgen, Elin & Ohnstad, Hege Oma [Show all 19 contributors for this article] (2019). An independent poor-prognosis subtype of breast cancer defined by a distinct tumor immune microenvironment. Nature Communications. 10:5499, p. 1–14. doi: 10.1038/s41467-019-13329-5. Full text in Research Archive Show summary

  How mixtures of immune cells associate with cancer cell phenotype and affect pathogenesis is still unclear. In 15 breast cancer gene expression datasets, we invariably identify three clusters of patients with gradual levels of immune infiltration. The intermediate immune infiltration cluster (Cluster B) is associated with a worse prognosis independently of known clinicopathological features. Furthermore, immune clusters are associated with response to neoadjuvant chemotherapy. In silico dissection of the immune contexture of the clusters identified Cluster A as immune cold, Cluster C as immune hot while Cluster B has a pro-tumorigenic immune infiltration. Through phenotypical analysis, we find epithelial mesenchymal transition and proliferation associated with the immune clusters and mutually exclusive in breast cancers. Here, we describe immune clusters which improve the prognostic accuracy of immune contexture in breast cancer. Our discovery of a novel independent prognostic factor in breast cancer highlights a correlation between tumor phenotype and immune contexture.

• Lindholm, Evita Maria; Aure, Miriam Ragle; Haugen, Mads Haugland; Sahlberg, Kristine Kleivi; Kristensen, Vessela N. & Nebdal, Daniel J.H. [Show all 9 contributors for this article] (2019). miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer. Molecular Oncology. ISSN 1574-7891. 13(10), p. 2278–2296. doi: 10.1002/1878-0261.12561. Full text in Research Archive Show summary

  One of the hallmarks of cancer is sustained angiogenesis. Favorable results have been reported in some breast cancer (BC) patients receiving antiangiogenic therapy with bevacizumab (Bev) in combination with chemotherapy, and further knowledge on how Bev can be optimally combined with conventional treatment to increase efficacy is strongly needed. In this randomized, neoadjuvant phase II clinical trial, 132 patients with HER2‐negative, nonmetastatic BC were treated with Bev in combination with sequential chemotherapy. Biopsies were sampled before treatment, after 12 weeks with anthracycline and after taxane therapy at week 25. MicroRNA (miRNA) expression profiling was performed on biopsies from each time point. Altogether, 241 biopsies were analyzed with the aim of identifying miRNA‐based biomarkers of response to therapy. Results from the miRNA analyses were reported for the ER‐positive cohort, which were previously demonstrated to benefit from antiangiogenic therapy in this study. For both treatment arms of this cohort, significantly different expression was observed for 217 miRNAs between objective responding and nonresponding patients before treatment initiation. These miRNAs have been linked to regulation of epithelial–mesenchymal transition, metastasis, and tumor growth, among other processes. Bev in combination with chemotherapy resulted in similar miRNA changes to chemotherapy alone. However, the deregulation of miRNA expression occurred earlier in the Bev arm. In both arms, tumor suppressor miRNAs were found upregulated after treatment, while oncogenic miRNAs were downregulated in the Bev arm. Patients responding to Bev showed a strong correlation between deregulated miRNAs and decreased proliferation score during the course of treatment, with downregulation of miR‐4465 as the strongest indicator of reduced proliferation. Integrative analyses at miRNA‐, gene‐, and protein expression further indicated a longitudinal decrease in proliferation. Altogether, the results indicate that proliferation might represent a predictive factor for increased Bev sensitivity, which may aid in the identification of patients who could potentially benefit from Bev.

• Johansson, Henrik J.; Socciarelli, Fabio; Vacanti, Nathaniel M.; Haugen, Mads Haugland; Zhu, Yafeng & Siavelis, Ioannis [Show all 36 contributors for this article] (2019). Breast cancer quantitative proteome and proteogenomic landscape. Nature Communications. 10:1600, p. 1–14. doi: 10.1038/s41467-019-09018-y. Full text in Research Archive Show summary

  In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.

• Madssen, Torfinn Støve; Cao, Maria Dung; Pladsen, Arne Valebjørg; Ottestad, Lars; Sahlberg, Kristine Kleivi & Bathen, Tone Frost [Show all 7 contributors for this article] (2019). Historical Biobanks in Breast Cancer Metabolomics — Challenges and Opportunities. Metabolites. 9(11). doi: 10.3390/metabo9110278. Full text in Research Archive Show summary

  Background: Metabolomic characterization of tumours can potentially improve prediction of cancer prognosis and treatment response. Here, we describe efforts to validate previous metabolomic findings using a historical cohort of breast cancer patients and discuss challenges with using older biobanks collected with non-standardized sampling procedures. Methods: In total, 100 primary breast cancer samples were analysed by high-resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) and subsequently examined by histology. Metabolomic profiles were related to the presence of cancer tissue, hormone receptor status, T-stage, N-stage, and survival. RNA integrity number (RIN) and metabolomic profiles were compared with an ongoing breast cancer biobank. Results: The 100 samples had a median RIN of 4.3, while the ongoing biobank had a significantly higher median RIN of 6.3 (p = 5.86 × 10−7). A low RIN was associated with changes in choline-containing metabolites and creatine, and the samples in the older biobank showed metabolic differences previously associated with tissue degradation. The association between metabolomic profile and oestrogen receptor status was in accordance with previous findings, however, with a lower classification accuracy. Conclusions: Our findings highlight the importance of standardized biobanking procedures in breast cancer metabolomics studies.

• Hovda, Tone; Holen, åsne Sørlien; Lång, Kristina; Albertsen, Judy; Bjørndal, Hilde & Brandal, Siri Helene Bertelsen [Show all 10 contributors for this article] (2019). Interval and Consecutive Round Breast Cancer after Digital Breast Tomosynthesis and Synthetic 2D Mammography versus Standard 2D Digital Mammography in BreastScreen Norway. Radiology. ISSN 0033-8419. 294(2), p. 256–264. doi: 10.1148/radiol.2019191337. Full text in Research Archive Show summary

  Background Screening that includes digital breast tomosynthesis (DBT) with two-dimensional (2D) synthetic mammography (SM) or standard 2D digital mammography (DM) results in detection of more breast cancers than does screening with DM alone. A decrease in interval breast cancer rates is anticipated but is not reported. Purpose To compare rates and characteristics of (a) interval breast cancer in women screened with DBT and SM versus those screened with DM alone and (b) screen-detected breast cancer at consecutive screenings with DM. Materials and Methods This prospective cohort study from BreastScreen Norway included women screened with DBT and SM (study group) or DM alone (control group) between February 2014 and December 2015 (baseline). All women, except nonattendees, women with breast cancer, and those who exceeded the upper age limit, were consecutively screened with DM after 2 years. Interval breast cancer, sensitivity, and specificity were estimated for women screened at baseline. Recall, screen-detected breast cancer, and positive predictive value were analyzed for consecutively screened women. A χ2 test, t test (P < .001 after Bonferroni correction indicated a significant difference), and binomial regression model were used to analyze differences across groups. Results A total of 92 404 women who underwent baseline screening (mean age, 59 years ± 6 [standard deviation]) were evaluated; 34 641 women in the study group (mean age, 59 years ± 6) were screened with DBT and SM and 57 763 women in the control group (mean age, 59 years ± 6) were screened with DM. A total of 26 474 women in the study group (mean age, 60 years ± 5) and 45 543 women in the control group (mean age, 60 years ± 5) were consecutively screened with DM. Rates of interval breast cancer were 2.0 per 1000 screened women in the study group and 1.5 per 1000 screened women in the control group (P = .12). No differences in histopathologic characteristics of interval breast cancer were observed. In the consecutive screening round, rates of screen-detected breast cancer were 3.9 per 1000 screened women (study group) and 5.6 per 1000 screened women (control group) (P = .001). Rates of histologic grade 1 invasive cancer were 0.5 per 1000 screened women (study group) and 1.3 per 1000 screened women (control group) (P = .001). Conclusion No differences in interval breast cancer rates or tumor characteristics were observed in women screened with DBT and SM compared with women screened with DM. Higher rates of low-grade screen-detected tumors were observed in the control group at consecutive screening.

• Lindholm, Evita Maria; Leivonen, Suvi-Katri; Due, Eldri Undlien; Nebdal, Daniel J.H.; Git, Anna & Caldas, Carlos [Show all 8 contributors for this article] (2019). miR-342-5p as a Potential Regulator of HER2 Breast Cancer Cell Growth. MicroRNA. ISSN 2211-5366. 8(2), p. 155–165. doi: 10.2174/2211536608666181206124922. Full text in Research Archive
• Tinholt, Mari; Garred, Øystein; Borgen, Elin; Beraki, Else; Schlichting, Ellen & Kristensen, Vessela N. [Show all 8 contributors for this article] (2018). Subtype-specific clinical and prognostic relevance of tumor-expressed F5 and regulatory F5 variants in breast cancer: the CoCaV study. Journal of Thrombosis and Haemostasis. ISSN 1538-7933. 16(7), p. 1347–1356. doi: 10.1111/jth.14151. Full text in Research Archive
• Cui, Xue-Yan; Skretting, Grethe; Tinholt, Mari; Stavik, Benedicte; Dahm, Anders Erik A & Sahlberg, Kristine Kleivi [Show all 9 contributors for this article] (2017). A novel hypoxia response element regulates oxygen-related repression of tissue factor pathway inhibitor in the breast cancer cell line MCF-7. Thrombosis Research. ISSN 0049-3848. 157, p. 111–116. doi: 10.1016/j.thromres.2017.07.013. Full text in Research Archive
• Fleischer, Thomas; Tekpli, Xavier; Mathelier, Anthony; Wang, Shixiong; Nebdal, Daniel J.H. & Dhakal, Hari Prasad [Show all 16 contributors for this article] (2017). DNA methylation at enhancers identifies distinct breast cancer lineages. Nature Communications. 8(1379). doi: 10.1038/s41467-017-00510-x. Full text in Research Archive Show summary

  Breast cancers exhibit genome-wide aberrant DNA methylation patterns. To investigate how these affect the transcriptome and which changes are linked to transformation or progression, we apply genome-wide expression–methylation quantitative trait loci (emQTL) analysis between DNA methylation and gene expression. On a whole genome scale, in cis and in trans, DNA methylation and gene expression have remarkably and reproducibly conserved patterns of association in three breast cancer cohorts (n = 104, n = 253 and n = 277). The expression–methylation quantitative trait loci associations form two main clusters; one relates to tumor infiltrating immune cell signatures and the other to estrogen receptor signaling. In the estrogen related cluster, using ChromHMM segmentation and transcription factor chromatin immunoprecipitation sequencing data, we identify transcriptional networks regulated in a cell lineage-specific manner by DNA methylation at enhancers. These networks are strongly dominated by ERα, FOXA1 or GATA3 and their targets were functionally validated using knockdown by small interfering RNA or GRO-seq analysis after transcriptional stimulation with estrogen.

• Aure, Miriam Ragle; Vitelli, Valeria; Jernström, Sandra Johanna; Kumar, Surendra; Krohn, Marit & Due, Eldri Undlien [Show all 35 contributors for this article] (2017). Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome. Breast Cancer Research. ISSN 1465-5411. 19(44). doi: 10.1186/s13058-017-0812-y. Full text in Research Archive Show summary

  Background Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different molecular levels in order to identify integrated subtypes. Methods Tumor tissue from 425 patients with primary breast cancer from the Oslo2 study was cut and blended, and divided into fractions for DNA, RNA and protein isolation and metabolomics, allowing the acquisition of representative and comparable molecular data. Patients were stratified into groups based on their tumor characteristics from five different molecular levels, using various clustering methods. Finally, all previously identified and newly determined subgroups were combined in a multilevel classification using a “cluster-of-clusters” approach with consensus clustering. Results Based on DNA copy number data, tumors were categorized into three groups according to the complex arm aberration index. mRNA expression profiles divided tumors into five molecular subgroups according to PAM50 subtyping, and clustering based on microRNA expression revealed four subgroups. Reverse-phase protein array data divided tumors into five subgroups. Hierarchical clustering of tumor metabolic profiles revealed three clusters. Combining DNA copy number and mRNA expression classified tumors into seven clusters based on pathway activity levels, and tumors were classified into ten subtypes using integrative clustering. The final consensus clustering that incorporated all aforementioned subtypes revealed six major groups. Five corresponded well with the mRNA subtypes, while a sixth group resulted from a split of the luminal A subtype; these tumors belonged to distinct microRNA clusters. Gain-of-function studies using MCF-7 cells showed that microRNAs differentially expressed between the luminal A clusters were important for cancer cell survival. These microRNAs were used to validate the split in luminal A tumors in four independent breast cancer cohorts. In two cohorts the microRNAs divided tumors into subgroups with significantly different outcomes, and in another a trend was observed. Conclusions The six integrated subtypes identified confirm the heterogeneity of breast cancer and show that finer subdivisions of subtypes are evident. Increasing knowledge of the heterogeneity of the luminal A subtype may add pivotal information to guide therapeutic choices, evidently bringing us closer to improved treatment for this largest subgroup of breast cancer.

• Jernström, Sandra Johanna; Hongisto, Vesa; Leivonen, Suvi-Katri; Due, Eldri Undlien; Tadele, Dagim Shiferaw & Edgren, Henrik [Show all 10 contributors for this article] (2017). Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. Breast Cancer: Targets and Therapy. 9, p. 185–198. doi: 10.2147/BCTT.S115600. Full text in Research Archive Show summary

  Background<br> Approximately 15%–20% of all diagnosed breast cancers are characterized by amplified and overexpressed HER2 (= ErbB2). These breast cancers are aggressive and have a poor prognosis. Although improvements in treatment have been achieved after the introduction of trastuzumab and lapatinib, many patients do not benefit from these drugs. Therefore, in-depth understanding of the mechanisms behind the treatment responses is essential to find alternative therapeutic strategies.<p> Materials and methods<br> Thirteen HER2 positive breast cancer cell lines were screened with 22 commercially available compounds, mainly targeting proteins in the ErbB2-signaling pathway, and molecular mechanisms related to treatment sensitivity were sought. Cell viability was measured, and treatment responses between the cell lines were compared. To search for response predictors and genomic and transcriptomic profiling, PIK3CA mutations and PTEN status were explored and molecular features associated with drug sensitivity sought.<p> Results<br> The cell lines were divided into three groups according to the growth-retarding effect induced by trastuzumab and lapatinib. Interestingly, two cell lines insensitive to trastuzumab (KPL4 and SUM190PT) showed sensitivity to an Akt1/2 kinase inhibitor. These cell lines had mutation in PIK3CA and loss of PTEN, suggesting an activated and druggable Akt-signaling pathway. Expression levels of five genes (CDC42, MAPK8, PLCG1, PTK6, and PAK6) were suggested as predictors for the Akt1/2 kinase-inhibitor response.<p> Conclusion<br> Targeting the Akt-signaling pathway shows promise in cell lines that do not respond to trastuzumab. In addition, our results indicate that several molecular features determine the growth-retarding effects induced by the drugs, suggesting that parameters other than HER2 amplification/expression should be included as markers for therapy decisions.

• Cui, Xue-Yan; Tinholt, Mari; Stavik, Benedicte; Dahm, Anders Erik A; Kanse, Sandip & Jin, Yang [Show all 11 contributors for this article] (2016). Effect of hypoxia on tissue factor pathway inhibitor expression in breast cancer. Journal of Thrombosis and Haemostasis. ISSN 1538-7933. 14(2), p. 387–396. doi: 10.1111/jth.13206. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Lamichhane, Santosh; Krohn, Marit & Jernström, Sandra Johanna [Show all 15 contributors for this article] (2016). Metabolic clusters of breast cancer in relation to gene- and protein expression subtypes. Cancer & Metabolism. 4(12). doi: 10.1186/s40170-016-0152-x. Full text in Research Archive Show summary

  Background: The heterogeneous biology of breast cancer leads to high diversity in prognosis and response to treatment, even for patients with similar clinical diagnosis, histology, and stage of disease. Identifying mechanisms contributing to this heterogeneity may reveal new cancer targets or clinically relevant subgroups for treatment stratification. In this study, we have merged metabolite, protein, and gene expression data from breast cancer patients to examine the heterogeneity at a molecular level. Methods: The study included primary tumor samples from 228 non-treated breast cancer patients. High-resolution magic-angle spinning magnetic resonance spectroscopy (HR MAS MRS) was performed to extract the tumors metabolic profiles further used for hierarchical cluster analysis resulting in three significantly different metabolic clusters (Mc1, Mc2, and Mc3). The clusters were further combined with gene and protein expression data. Results: Our result revealed distinct differences in the metabolic profile of the three metabolic clusters. Among the most interesting differences, Mc1 had the highest levels of glycerophosphocholine (GPC) and phosphocholine (PCho), Mc2 had the highest levels of glucose, and Mc3 had the highest levels of lactate and alanine. Integrated pathway analysis of metabolite and gene expression data uncovered differences in glycolysis/gluconeogenesis and glycerophospholipid metabolism between the clusters. All three clusters had significant differences in the distribution of protein subtypes classified by the expression of breast cancer-related proteins. Genes related to collagens and extracellular matrix were downregulated in Mc1 and consequently upregulated in Mc2 and Mc3, underpinning the differences in protein subtypes within the metabolic clusters. Genetic subtypes were evenly distributed among the three metabolic clusters and could therefore contribute to additional explanation of breast cancer heterogeneity. Conclusions: Three naturally occurring metabolic clusters of breast cancer were detected among primary tumors from non-treated breast cancer patients. The clusters expressed differences in breast cancer-related protein as well as genes related to extracellular matrix and metabolic pathways known to be aberrant in cancer. Analyses of metabolic activity combined with gene and protein expression provide new information about the heterogeneity of breast tumors and, importantly, the metabolic differences infer that the clusters may be susceptible to different metabolically targeted drugs.

• Sas-Chen, Aldema; Aure, Miriam Ragle; Leibovich, Limor; Carvalho, Silvia; Enuka, Yehoshua & Körner, Cindy [Show all 38 contributors for this article] (2016). LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer. EMBO Molecular Medicine. ISSN 1757-4676. 8(9), p. 1052–1064. doi: 10.15252/emmm.201606198. Full text in Research Archive Show summary

  Long noncoding RNAs (lncRNAs) are emerging as regulators of gene expression in pathogenesis, including cancer. Recently, lncRNAs have been implicated in progression of specific subtypes of breast cancer. One aggressive, basal‐like subtype associates with increased EGFR signaling, while another, the HER2‐enriched subtype, engages a kin of EGFR. Based on the premise that EGFR‐regulated lncRNAs might control the aggressiveness of basal‐like tumors, we identified multiple EGFR‐inducible lncRNAs in basal‐like normal cells and overlaid them with the transcriptomes of over 3,000 breast cancer patients. This led to the identification of 11 prognostic lncRNAs. Functional analyses of this group uncovered LINC01089 (here renamed LncRNA Inhibiting Metastasis; LIMT), a highly conserved lncRNA, which is depleted in basal‐like and in HER2‐positive tumors, and the low expression of which predicts poor patient prognosis. Interestingly, EGF rapidly downregulates LIMT expression by enhancing histone deacetylation at the respective promoter. We also find that LIMT inhibits extracellular matrix invasion of mammary cells in vitro and tumor metastasis in vivo. In conclusion, lncRNAs dynamically regulated by growth factors might act as novel drivers of cancer progression and serve as prognostic biomarkers.

• Tinholt, Mari; Sandset, Per Morten; Mowinckel, Marie-Christine; Garred, Øystein; Sahlberg, Kristine Kleivi & Kristensen, Vessela N. [Show all 10 contributors for this article] (2016). Determinants of acquired activated protein C resistance and D-dimer in breast cancer. Thrombosis Research. ISSN 0049-3848. 145, p. 78–83. doi: 10.1016/j.thromres.2016.08.003. Full text in Research Archive
• Nunes-Xavier, Caroline Elisabeth; Karlsen, Karine Flem; Tekle, Christina; Pedersen, Cathrine; Øyjord, Tove Ragnhild & Hongisto, Vesa [Show all 10 contributors for this article] (2016). Decreased expression of B7-H3 reduces the glycolytic capacity and sensitizes breast cancer cells to AKT/mTOR inhibitors. OncoTarget. 7(6), p. 6891–6901. doi: 10.18632/oncotarget.6902. Full text in Research Archive Show summary

  B7 family proteins are important immune response regulators, and can mediate oncogenic signaling and cancer development. We have used human triple-negative breast cancer cell lines with different expression levels of B7-H3 to evaluate its effects on the sensitivity to 22 different anticancer compounds in a drug screen. API-2 (triciribidine) and everolimus (RAD-001), two inhibitors that target the PI3K/AKT/mTOR pathway, showed enhanced inhibition of cell viability and proliferation in B7-H3 knockdown tumor cells compared to their B7-H3 expressing counterparts. Similar inhibition was seen in control cells treated with an anti-B7-H3 monoclonal antibody. In B7-H3 overexpressing cells, the effects of the two drugs were reduced, supported also by in vivo experiments in which B7-H3 overexpressing xenografts were less sensitive to everolimus than control tumors. In API-2 and everolimus-treated B7-H3 overexpressing cells, phospho-mTOR levels were decreased. However, phosphorylation of p70S6K was differentially regulated in B7-H3 cells treated with API-2 or everolimus, suggesting a different B7-H3-mediated mechanism downstream of mTOR. Both API-2 and everolimus decreased the glycolysis of the cells, whereas knockdown of B7-H3 decreased and B7-H3 overexpression increased the glycolytic capacity. In conclusion, we have unveiled a previously unknown relationship between B7-H3 expression and glycolytic capacity in tumor cells, and found that B7-H3 confers resistance to API-2 and everolimus. The results provide novel insights into the function of B7-H3 in cancer, and suggest that targeting of B7-H3 may be a novel alternative to improve current anticancer therapies.

• Aure, Miriam Ragle; Jernström, Sandra Johanna; Krohn, Marit; Vollan, Hans Kristian Moen; Due, Eldri Undlien & Rødland, Einar Andreas [Show all 14 contributors for this article] (2015). Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer. Genome Medicine. 7:21. doi: 10.1186/s13073-015-0135-5. Full text in Research Archive Show summary

  Background The role played by microRNAs in the deregulation of protein expression in breast cancer is only partly understood. To gain insight, the combined effect of microRNA and mRNA expression on protein expression was investigated in three independent data sets. Methods Protein expression was modeled as a multilinear function of powers of mRNA and microRNA expression. The model was first applied to mRNA and protein expression for 105 selected cancer-associated genes and to genome-wide microRNA expression from 283 breast tumors. The model considered both the effect of one microRNA at a time and all microRNAs combined. In the latter case the Lasso penalized regression method was applied to detect the simultaneous effect of multiple microRNAs. Results An interactome map for breast cancer representing all direct and indirect associations between the expression of microRNAs and proteins was derived. A pattern of extensive coordination between microRNA and protein expression in breast cancer emerges, with multiple clusters of microRNAs being associated with multiple clusters of proteins. Results were subsequently validated in two independent breast cancer data sets. A number of the microRNA-protein associations were functionally validated in a breast cancer cell line. Conclusions A comprehensive map is derived for the co-expression in breast cancer of microRNAs and 105 proteins with known roles in cancer, after filtering out the in-cis effect of mRNA expression. The analysis suggests that group action by several microRNAs to deregulate the expression of proteins is a common modus operandi in breast cancer.

• Tinholt, Mari; Vollan, Hans Kristian Moen; Sahlberg, Kristine Kleivi; Jernström, Sandra Johanna; Kaveh, Fatemeh & Lingjærde, Ole Christian [Show all 12 contributors for this article] (2015). Tumor expression, plasma levels and genetic polymorphisms of the coagulation inhibitor TFPI are associated with clinicopathological parameters and survival in breast cancer, in contrast to the coagulation initiator TF. Breast Cancer Research. ISSN 1465-5411. 17(44), p. 1–15. doi: 10.1186/s13058-015-0548-5. Full text in Research Archive Show summary

  Introduction Hypercoagulability in malignancy increases the risk of thrombosis, but is also involved in cancer progression. Experimental studies suggest that tissue factor (TF) and tissue factor pathway inhibitor (TFPI) are involved in cancer biology as a tumor- promoter and suppressor, respectively, but the clinical significance is less clear. Here, we aimed to investigate the clinical relevance of TF and TFPI genetic and phenotypic diversity in breast cancer. Methods The relationship between tumor messenger RNA (mRNA) expression and plasma levels of TF and TFPI (α and β), tagging single nucleotide polymorphisms (tagSNPs) in F3 (TF) (n = 6) and TFPI (n = 18), and clinicopathological characteristics and molecular tumor subtypes were explored in 152 treatment naive breast cancer patients. The effect of tumor expressed TF and TFPIα and TFPIβ on survival was investigated in a merged breast cancer dataset of 1881 patients. Results Progesterone receptor negative patients had higher mRNA expression of total TFPI (α + β) (P = 0.021) and TFPIβ (P = 0.014) in tumors. TF mRNA expression was decreased in grade 3 tumors (P = 0.003). In plasma, total TFPI levels were decreased in patients with larger tumors (P = 0.013). SNP haplotypes of TFPI, but not TF, were associated with specific clinicopathological characteristics like tumor size (odds ratio (OR) 3.14, P = 0.004), triple negativity (OR 2.4, P = 0.004), lymph node spread (OR 3.34, P = 0.006), and basal-like (OR 2.3, P = 0.011) and luminal B (OR 3.5, P = 0.005) molecular tumor subtypes. Increased expression levels of TFPIα and TFPIβ in breast tumors were associated with better outcome in all tumor subtypes combined (P = 0.007 and P = 0.005) and in multiple subgroups, including lymph node positive subjects (P = 0.006 and P = 0.034). Conclusions This study indicates that genetic and phenotypic variation of both TFPIα and TFPIβ, more than TF, are markers of cancer progression. Together with the previously demonstrated tumor suppressor effects of TFPI, the beneficial effect of tumor expressed TFPI on survival, renders TFPI as a potential anticancer agent, and the clinical significance of TFPI in cancer deserves further investigation.

• Cui, Xueyan; Tinholt, Mari; Stavik, Benedicte; Dahm, Anders Erik A; Kanse, Sandip & Seidl, Sebastian [Show all 11 contributors for this article] (2015). Effect of hypoxia on tissue factor pathway inhibitor expression in breast cancer cell lines and tissues. Journal of Thrombosis and Haemostasis. ISSN 1538-7933. 13, p. 303–303. Full text in Research Archive
• Hongisto, Vesa; Aure, Miriam Ragle; Mäkelä, Rami & Sahlberg, Kristine Kleivi (2014). The HER2 ampicon includes several genes required for the growth and survival of HER2 positive breast cancer cells - A data description. Genomics Data. 2, p. 249–253. doi: 10.1016/j.gdata.2014.06.025. Full text in Research Archive
• Sahlberg, Kristine Kleivi; Bottai, Giulia; Naume, Bjørn; Burwinkel, Barbara; Calin, George A. & Børresen-Dale, Anne-Lise [Show all 7 contributors for this article] (2014). A Serum MicroRNA Signature Predicts Tumor Relapse and Survival in Triple-Negative Breast Cancer Patients. Clinical Cancer Research. ISSN 1078-0432. 21, p. 1207–1214. doi: 10.1158/1078-0432.CCR-14-2011. Full text in Research Archive
• Nygren, Marit; Tekle, Christina; Ingebrigtsen, Vibeke Anett; Mäkelä, Rami; Krohn, Marit & Aure, Miriam Ragle [Show all 17 contributors for this article] (2014). Identifyinig microRNAs regulating B7-H3 in breast cancer: the clinical impact of microRNA-29c. British Journal of Cancer. ISSN 0007-0920. 15. doi: 10.1038/bjc.2014.113. Full text in Research Archive
• Tinholt, Mari; Viken, Marte K; Dahm, Anders Erik A; Vollan, Hans Kristian Moen; Sahlberg, Kristine Kleivi & Garred, Øystein [Show all 16 contributors for this article] (2014). Increased coagulation activity and genetic polymorphisms in the F5, F10 and EPCR genes are associated with breast cancer: a case-control study. BMC Cancer. 14. doi: 10.1186/1471-2407-14-845. Full text in Research Archive Show summary

  Background The procoagulant state in cancer increases the thrombotic risk, but also supports tumor progression. To investigate the molecular mechanisms controlling cancer and hemostasis, we conducted a case-control study of genotypic and phenotypic variables of the tissue factor (TF) pathway of coagulation in breast cancer. Methods 366 breast cancer patients and 307 controls were genotyped for SNPs (n = 41) in the F2, F3 (TF), F5, F7, F10, TFPI and EPCR genes, and assayed for plasma coagulation markers (thrombin generation, activated protein C (APC) resistance, D-dimer, antithrombin, protein C, protein S, and TF pathway inhibitor (TFPI)). Associations with breast cancer were evaluated using logistic regression to obtain odds ratios (ORs) and 95% confidence intervals (CIs), or the chi-square test. Results Four SNPs in F5 (rs12120605, rs6427202, rs9332542 and rs6427199), one in F10 (rs3093261), and one in EPCR (rs2069948) were associated with breast cancer. EPCR rs2069948 was associated with estrogen receptor (ER) and progesterone receptor (PR) positivity, while the SNPs in F5 appeared to follow hormone receptor negative and triple negative patients. The prothrombotic polymorphisms factor V Leiden (rs6025) and prothrombin G20210A (rs1799963) were not associated with breast cancer. High APC resistance was associated with breast cancer in both factor V Leiden non-carriers (OR 6.5, 95% CI 4.1-10.4) and carriers (OR 38.3, 95% CI 6.2-236.6). The thrombin parameters short lag times (OR 5.8, 95% CI 3.7-9.2), short times to peak thrombin (OR 7.1, 95% CI 4.4-11.3), and high thrombin peak (OR 6.1, 95% CI 3.9-9.5) predicted presence of breast cancer, and high D-dimer also associated with breast cancer (OR 2.0, 95% CI 1.3-3.3). Among the coagulation inhibitors, low levels of antithrombin associated with breast cancer (OR 5.7, 95% CI 3.6-9.0). The increased coagulability was not explained by the breast cancer associated SNPs, and was unaffected by ER, PR and triple negative status. Conclusions A procoagulant phenotype was found in the breast cancer patients. Novel associations with SNPs in F5, F10 and EPCR to breast cancer susceptibility were demonstrated, and the SNPs in F5 were confined to hormone receptor negative and triple negative patients. The study supports the importance of developing new therapeutic strategies targeting coagulation processes in cancer.

• Aure, Miriam Ragle; Leivonen, Suvi-Katri; Fleischer, Thomas; Zhu, Qian; Overgaard, Jens & Alsner, Jan [Show all 19 contributors for this article] (2013). Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biology. ISSN 1465-6906. doi: 10.1186/gb-2013-14-11-r126. Full text in Research Archive
• Leivonen, Suvi-Katri; Sahlberg, Kristine Kleivi; Mäkelä, Rami; Due, Eldri Undlien; Kallioniemi, Olli & Børresen-Dale, Anne-Lise [Show all 7 contributors for this article] (2013). High-throughput screens identify microRNAs essential for HER2 positive breast cancer cell growth. Molecular Oncology. ISSN 1574-7891. 8(1), p. 93–104. doi: 10.1016/j.molonc.2013.10.001. Full text in Research Archive
• Hongisto, Vesa; Jernström, Sandra Johanna; Fey, Vidal; Mpindi, John-Patrick; Sahlberg, Kristine Kleivi & Kallioniemi, Olli [Show all 7 contributors for this article] (2013). High-Throughput 3D Screening Reveals Differences in Drug Sensitivities between Culture Models of JIMT1 Breast Cancer Cells. PLOS ONE. 8(10). doi: 10.1371/journal.pone.0077232. Full text in Research Archive
• Tahiri, Andliena; Leivonen, Suvi-Katri; Luders, Torben; Stenfeld, Israel; Aure, Miriam Ragle & Geisler, Jürgen [Show all 15 contributors for this article] (2013). Deregulation of cancer-related miRNAs is a common event in both benign and malignant human breast tumors. Carcinogenesis. ISSN 0143-3334. 35(1), p. 76–85. doi: 10.1093/carcin/bgt333. Full text in Research Archive
• Aure, Miriam Ragle; Steinfeld, I; Baumbusch, Lars Oliver; Liestøl, Knut; Lipson, Doron & Nyberg, Sandra Johanna [Show all 12 contributors for this article] (2013). Identifying In-Trans Process Associated Genes in Breast Cancer by Integrated Analysis of Copy Number and Expression Data. PLOS ONE. 8(1). doi: 10.1371/journal.pone.0053014. Full text in Research Archive
• Sahlberg, Kristine Kleivi; Hongisto, Vesa; Edgren, Henrik; Makela, R; Hellstrøm, Kirsi & Due, Eldri Undlien [Show all 12 contributors for this article] (2013). The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells. Molecular Oncology. ISSN 1574-7891. 7(3), p. 392–401. doi: 10.1016/j.molonc.2012.10.012. Full text in Research Archive
• Enerly, Espen; Steinfeld, Israel; Kleivi, Kristine; Leivonen, Suvi-Katri; Aure, Miriam Ragle & Russnes, Hege Elisabeth Giercksky [Show all 17 contributors for this article] (2011). miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in Primary Breast Tumors. PLOS ONE. 6(2). doi: 10.1371/journal.pone.0016915. Full text in Research Archive
• Westbury, Charlotte B.; Sahlberg, Kristine Kleivi; Børresen-Dale, Anne-Lise; Isacke, Clare M. & Yarnold, John R. (2011). Gene expression profiling of human dermal fibroblasts exposed to bleomycin sulphate does not differentiate between radiation sensitive and control patients. Radiation Oncology. 6. doi: 10.1186/1748-717X-6-42. Full text in Research Archive Show summary

  Background Gene expression profiling of the transcriptional response of human dermal fibroblasts to in vitro radiation has shown promise as a predictive test of radiosensitivity. This study tested if treatment with the radiomimetic drug bleomycin sulphate could be used to differentiate radiation sensitive patients and controls in patients who had previously received radiotherapy for early breast cancer. Findings Eight patients who developed marked late radiation change assessed by photographic breast appearance and 8 matched patients without any change were selected from women entered in a prospective randomised trial of breast radiotherapy fractionation. Gene expression profiling of primary skin fibroblasts exposed in vitro to bleomycin sulphate and mock treated fibroblast controls was performed. 973 genes were up-regulated and 923 down-reguated in bleomycin sulphate treated compared to mock treated control fibroblasts. Gene ontology analysis revealed enriched groups were cellular localisation, apoptosis, cell cycle and DNA damage response for the deregulated genes. No transcriptional differences were identified between fibroblasts from radiation sensitive cases and control patients; subgroup analysis using cases exhibiting severe radiation sensitivity or with high risk alleles present in TGF β1 also showed no difference. Conclusions The transcriptional response of human dermal fibroblasts to bleomycin sulphate has been characterised. No differences between clinically radiation sensitive and control patients were detected using this approach.

• Edgren, Henrik; Murumagi, Astrid; Kangaspeska, Sara; Nicorici, Daniel; Hongisto, Vesa & Kleivi, Kristine [Show all 11 contributors for this article] (2011). Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biology. ISSN 1465-6906. 12(1). doi: 10.1186/gb-2011-12-1-r6. Full text in Research Archive Show summary

  Background Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements. Results We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival. Conclusions In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.

• Rantala, Juha K.; Edgren, Henrik; Lehtinen, Laura; Wolf, Maija; Kleivi, Kristine & Vollan, Hans Kristian Moen [Show all 12 contributors for this article] (2010). Integrative Functional Genomics Analysis of Sustained Polyploidy Phenotypes in Breast Cancer Cells Identifies an Oncogenic Profile for GINS2. Neoplasia. ISSN 1522-8002. 12(11), p. 877–U50. doi: 10.1593/neo.10548. Full text in Research Archive
• Muggerud, Aslaug; Hallett, Michael; Johnsen, Hilde; Kleivi, Kristine; Zhou, Wenjing & Tahmasebpoor, Simin [Show all 11 contributors for this article] (2010). Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer. Molecular Oncology. ISSN 1574-7891. 4(4), p. 357–368. doi: 10.1016/j.molonc.2010.06.007. Full text in Research Archive
• Muggerud, Aslaug Aamodt; Edgren, H; Wolf, M; Kleivi, Kristine; Dejeux, E & Tost, J [Show all 8 contributors for this article] (2009). Data integration from two microarray platforms identifies bi-allelic genetic inactivation of RIC8A in a breast cancer cell line. BMC Medical Genomics. 2. doi: 10.1186/1755-8794-2-26. Full text in Research Archive
• Leivonen, SK; Makela, R; Ostling, P; Kohonen, P; Haapa-Paananen, S & Kleivi, Kristine [Show all 15 contributors for this article] (2009). Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines. Oncogene. ISSN 0950-9232. 28(44), p. 3926–3936. doi: 10.1038/onc.2009.241. Full text in Research Archive
• Kleivi, Kristine; Lind, Guro E; Diep, Chieu B; Meling, Gunn I; Brandal, Lin Thorstensen & Nesland, Jahn M [Show all 11 contributors for this article] (2007). Gene expression profiles of primary colorectal carcinomas, liver metastases, and carcinomatoses. Molecular Cancer. 6. doi: 10.1186/1476-4598-6-2. Full text in Research Archive Show summary

  Background Despite the fact that metastases are the leading cause of colorectal cancer deaths, little is known about the underlying molecular changes in these advanced disease stages. Few have studied the overall gene expression levels in metastases from colorectal carcinomas, and so far, none has investigated the peritoneal carcinomatoses by use of DNA microarrays. Therefore, the aim of the present study is to investigate and compare the gene expression patterns of primary carcinomas (n = 18), liver metastases (n = 4), and carcinomatoses (n = 4), relative to normal samples from the large bowel. Results Transcriptome profiles of colorectal cancer metastases independent of tumor site, as well as separate profiles associated with primary carcinomas, liver metastases, or peritoneal carcinomatoses, were assessed by use of Bayesian statistics. Gains of chromosome arm 5p are common in peritoneal carcinomatoses and several candidate genes (including PTGER4, SKP2, and ZNF622) mapping to this region were overexpressed in the tumors. Expression signatures stratified on TP53 mutation status were identified across all tumors regardless of stage. Furthermore, the gene expression levels for the in vivo tumors were compared with an in vitro model consisting of cell lines representing all three tumor stages established from one patient. Conclusion By statistical analysis of gene expression data from primary colorectal carcinomas, liver metastases, and carcinomatoses, we are able to identify genetic patterns associated with the different stages of tumorigenesis.

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• Fjermeros, Kamilla; Ghannoum, Salim; Geisler, Stephanie; Bhargava, Sameer; Tahiri, Andliena & Klajic, Jovana [Show all 32 contributors for this article] (2024). The NEOLETRIB trial: neoadjuvant treatment with Letrozole and Ribociclib in ER-positive, HER2-negative breast cancer. Future Oncology. ISSN 1479-6694. 20(32), p. 2457–2466. doi: 10.1080/14796694.2024.2377531. Full text in Research Archive Show summary

  Chemotherapy is used as neoadjuvant therapy for all subgroups of breast cancer, including ER-positive, and HER2-negative cases. However, studies have suggested that using aromatase inhibitors combined with CDK4/6-inhibitors might be an appropriate alternative in selected patients. Thus, the NEOLETRIB trial evaluates the response of ER-positive, HER2-negative luminal A/B breast cancer to the combination of letrozole and ribociclib in the neoadjuvant setting. Comprehensive molecular biology procedures, including sequential single-cell RNA-sequencing of tumor biopsies, are performed during 6 months of treatment with extensive biobanking of blood samples, tumor biopsies and gut microbiome specimens. Our findings will hopefully contribute to an improved selection of patients who may benefit from this drug combination and give new insights into the intra-tumoral changes during this treatment.

• Tinholt, Mari; Stavik, Benedicte; Sletten, Marit; Garred, Øystein; Tekpli, Xavier & Kristensen, Vessela N. [Show all 9 contributors for this article] (2019). Coagulation factor V is associated with immune response and tumor lymphocyte recruitment in breast cancer. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Lamichhane, Santosh; Krohn, Marit & Jernström, Sandra [Show all 15 contributors for this article] (2016). Metabolic clusters of breast cancer in relation to gene- and protein expression subtypes. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Schlichting, Ellen; Kåresen, Rolf & Sauer, Torill [Show all 9 contributors for this article] (2016). Prediction of clinical prognostic markers in breast cancer using MR-based metabolic profiles. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Schlichting, Ellen; Kåresen, Rolf & Sauer, Torill [Show all 9 contributors for this article] (2016). Prediction of clinical prognostic markers in breast cancer using MR-based metabolic profiles. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Schlichting, Ellen; Kåresen, Rolf & Sauer, Torill [Show all 9 contributors for this article] (2016). Prediction of clinical prognostic markers in breast cancer using MR-based metabolic profiles. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Krohn, Marit; Schlichting, Ellen & Kåresen, Rolf [Show all 10 contributors for this article] (2015). Combining ‘omics’; metabolic breast cancer clusters correlation with protein and gene expression subtypes. Full text in Research Archive
• Haukaas, Tonje Husby; Euceda, Leslie R.; Giskeødegård, Guro F.; Krohn, Marit; Schlichting, Ellen & Kåresen, Rolf [Show all 10 contributors for this article] (2015). Combining ‘omics’; metabolic breast cancer clusters correlation with protein and gene expression subtypes. Full text in Research Archive
• Haukaas, Tonje Husby; Wood, Leslie Euceda; Giskeødegård, Guro F.; Lamichhane, Santosh; Krohn, Marit & Schlichting, Ellen [Show all 14 contributors for this article] (2015). Interpreting the clinical relevance of metabolic subgroups in breast cancer in combination with gene- and protein- expression subtypes. Full text in Research Archive
• Aure, Miriam Ragle; Jernstrøm, Sandra; Krohn, Marit; Due, Eldri Undlien; consortium, OSBREAC & Mills, Gordon B. [Show all 11 contributors for this article] (2014). Integrative analysis reveals extensive association between microRNA expression and mRNA−protein translation. European Journal of Cancer. ISSN 0959-8049. 50, p. 79–79. Full text in Research Archive
• Wood, Leslie Euceda; Haukaas, Tonje Husby; Giskeødegård, Guro F.; Krohn, Marit; Schlichting, Ellen & Kåresen, Rolf [Show all 10 contributors for this article] (2014). Metabolic subgrouping of breast cancer using HR MAS MRS and hierarchical cluster analysis; correlation with molecular subtypes. Full text in Research Archive
• Haukaas, Tonje Husby; Wood, Leslie Euceda; Giskeødegård, Guro F.; Krohn, Marit; Schlichting, Ellen & Kåresen, Rolf [Show all 10 contributors for this article] (2014). Metabolic subgrouping of breast cancer using HR MAS MRS and hierarchical cluster analysis; correlation with molecular subtypes. Full text in Research Archive
• Hongisto, Vesa; Sahlberg, Kristine Kleivi; Edgren, H; Mäkelä, Rami; Due, Eldri Undlien & Vollan, Hans Kristian Moen [Show all 10 contributors for this article] (2012). The HER2 Amplicon Includes Several Genes Required for the Growth and Survival of HER2 Positive Breast Cancer Cells. European Journal of Cancer. ISSN 0959-8049. 48(Supp. 5), p. S82–S83. Full text in Research Archive
• Sørlie, Therese; Muggerud, Aslaug; Hallett, Michael; Johnsen, Hilde; Sahlberg, Kristine Kleivi & Botling, Johan [Show all 8 contributors for this article] (2010). Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 200–201. Full text in Research Archive
• Enerly, Espen; Steinfeld, Israel; Sahlberg, Kristine Kleivi; Aure, Miriam Ragle; Leivonen, Suvi-Katri & Johnsen, Hilde [Show all 10 contributors for this article] (2010). Molecular characterization of breast cancer subtypes derived from joint analysis of high throughput miRNA and mRNA data. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 164–164. Full text in Research Archive
• Torland, Lilly Anne & Sahlberg, Guro Kristine Kleivi (2026). Subtype-specific immune microenvironments and molecular features in benign and malignant breast tumors. Universitetet i Oslo. ISSN 9788234808807. Full text in Research Archive Show summary

  This doctoral thesis investigates how molecular characteristics and the tumor microenvironment differ across benign breast lesions, molecular subtypes of breast cancer, and interval breast cancers, with the aim of improving the understanding of breast cancer heterogeneity and progression. The thesis comprises three studies using molecular and histopathological approaches. Gene expression profiling, pathway analysis, multiplex immunohistochemistry, single-cell RNA sequencing, transcriptomic deconvolution, cytokine profiling, and regulatory network analyses were applied to characterize immune and molecular features in multiple breast cancer cohorts. The results demonstrate that benign breast tumors exhibit distinct immune related pathway activity and immune cell compositions compared with normal breast tissue and breast cancer. Suggesting that immune alterations are established early in breast disease. Furthermore, differences in immune infiltration were identified across the intrinsic PAM50 breast cancer subtypes, with Basal-like and HER2-enriched tumors displaying greater infiltration of lymphocytes, macrophages, and B cells than Luminal tumors. Interval breast cancers were characterized by enhanced proliferative signaling, altered transcriptional regulatory networks, and distinct immune cell infiltration patterns, providing biological insight into their aggressive clinical behavior. Overall, the findings demonstrate that the breast tumor microenvironment differs substantially across benign and malignant breast lesions and contributes to breast cancer heterogeneity. The work advances our understanding of the biological and immunological mechanisms underlying breast cancer development and progression.

• Muggerud, Aslaug Aamodt; Sørlie, Therese; Kleivi, Kristine & Børresen-Dale, Anne-Lise (2009). Genetic and epigenetic alterations in breast tumour progression: The transition from in situ to invasive cancer. Universitetet i Oslo. ISSN 9788280723369. Full text in Research Archive

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