Siri Sæterstad

• Walaas, Gunnar Andreas Enerhaug; Sridhar, Arun; Kuraas, Lusie Frostvoll; Sæterstad, Siri; Schioldborg, Amanda Yin & Granlund, Atle van Beelen [Show all 10 contributors for this article] (2026). Patient-matched transcriptomics of in vivo and in vitro colonic epithelium substantiate organoids as a translational model for ulcerative colitis. Scientific Reports. doi: 10.1038/s41598-026-54857-7. Full text in Research Archive Show summary

  Abstract Ulcerative colitis (UC) is characterized by cytokine-driven inflammation and barrier disruption in the colon, making epithelial dysfunction central to disease pathology. Intestinal epithelial organoids (IEOs) preserve donor-specific genetics and architecture, offering a promising model, but their ability to replicate patient-specific epithelial inflammation remains undetermined. To directly compare in vivo epithelial transcriptional states with defined cytokine-induced responses in vitro, we analyzed patient-matched transcriptomics from laser microdissected inflamed and uninflamed colonic epithelium and IEOs derived from uninflamed biopsies of the same UC patients. IEOs were stimulated with UC-relevant cytokines (TNF, IFNγ, IFNλ1, or TNF + IFNγ) or a cytokine cocktail (TNF, IL17, IL1β, IL22, Poly(I:C), IFNγ). Key inflammatory genes were validated by immunoblotting and immunostaining. Cytokine-stimulated IEOs recapitulated key in vivo epithelial inflammation, including interferon signaling, antigen presentation, and unfolded protein response pathways. Among the tested conditions, TNF + IFNγ combination and the cytokine cocktail most closely replicated UC epithelial inflammation, with concordance for over 350 UC-relevant genes and protein-level validation of IRF1, ERAP2, NOS2, DUOX2 confirmed patient-dependent expression between inflamed epithelium and cytokine-stimulated IEOs. Our study shows that cytokine-stimulated IEOs provide a robust, personalized platform for modeling epithelial inflammation, enabling discovery of epithelial-specific disease mechanisms and therapeutic targets.

• Rodríguez, Rocío Rivera; Sæterstad, Siri; Ali, Ann-Therese Chattergoon; Selvik, Linn-Karina M.; Bakke, Ingunn & Bruland, Torunn [Show all 7 contributors for this article] (2025). The dietary phytochemicals carnosic acid and sulforaphane regulate inflammatory markers in ulcerative colitis patient-derived colonoids. Frontiers in Pharmacology. 16. doi: 10.3389/fphar.2025.1696576. Full text in Research Archive Show summary

  Introduction The inflammatory bowel disease (IBD) ulcerative colitis (UC) is characterized by continuous inflammation of the colon with erosion and ulcers. Diagnosis typically occurs in patients between their late teens and mid-30s with no cure. Available therapeutics are efficient at controlling symptoms however, they have many serious adverse effects. Thus, additional therapies with limited adverse effects are needed to complement these drugs. In this study, we evaluated the anti-inflammatory potential of carnosic acid (CA), the most abundant diterpene in rosemary ( Salvia rosmarinus ) and sulforaphane (SFN), an isothiocyanate found in cruciferous vegetables. Methods We used colonic epithelial organoids (colonoids) derived from non-IBD and UC patients as a physiologically relevant testing platform for both phytochemicals. These patient-derived colonoids are a representative model that recapitulates the parent epithelial tissue including its cellular composition and 3D structure. Moreover, we cultured the colonoids at 2% O 2 to better approximate the low oxygen level (physioxia) observed in the colon crypts. To assess the effects of CA and SFN in the nuclear factor erythroid 2-related factor 2 (NRF2) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways, we studied modulation of inflammatory cytokines through a 40-plex chemokine assay and ELISA, as well as gene and protein expression of target genes with qPCR and western blot, respectively. Results Through these techniques, we observed that CA and SFN decreased inflammatory markers and promoted NRF2 activity in patient-derived colonoids. Additionally, SFN and CA modulated the expression and secretion of the NF-κB promoted antibacterial peptide neutrophil gelatinase-associated lipocalin which is highly expressed in the inflamed colonic epithelium and has been suggested as a biomarker for active UC. Discussion Together, the results validated the use of colonoids as a pharmacological testing platform for phytochemicals, and that CA and SFN promote NRF2 activation and decrease inflammation in a human physiologically relevant UC model.

• Sæterstad, Siri; Østvik, Ann Elisabeth; Hansen, Marianne Dore; Bruland, Torunn & Granlund, Atle van Beelen (2024). The effect of rs2910686 on ERAP2 expression in IBD and epithelial inflammatory response. Journal of Translational Medicine. 22(1). doi: 10.1186/s12967-024-05532-w. Full text in Research Archive Show summary

  Background: ERAP2 is an aminopeptidase involved in antigen processing and presentation, and harbor genetic variants linked to several inflammatory diseases such as Inflammatory Bowel Disease (IBD). The lack of an ERAP2 gene homologue in mice has hampered functional studies, and most human studies have focused on cells of hematopoietic origin. Using an IBD biobank as vantage point, this study explores how genetic variation in ERAP2 affects gene expression in human-derived epithelial organoids upon proinflammatory stimulation. Methods: An IBD patient cohort was genotyped with regards to two single nucleotide polymorphisms (SNP) (rs2910686/rs2248374) associated with ERAP2 expression levels, and we examined the correlation between colon gene expression and genotype, specifically aiming to establish a relationship with ERAP2 expression proficiency. Human-derived colon organoids (colonoids) with known ERAP2 genotype were established and used to explore differences in whole genome gene expression between ERAP2-deficient (n = 4) and -proficient (n = 4) donors upon pro-inflammatory encounter. Results: When taking rs2910686 genotype into account, ERAP2 gene expression is upregulated in the inflamed colon of IBD patients. Colonoids upregulate ERAP2 upon IFNɣ stimulation, and ERAP2 expression proficiency is dependent on rs2910686 genotype. Colonoid genotyping confirms that mechanisms independent of the frequently studied SNP rs2248374 can cause ERAP2-deficiency. A total of 586 genes involved in various molecular mechanisms are differentially expressed between ERAP2 proficient- and deficient colonoids upon proinflammatory stimulation, including genes encoding proteins with the following molecular function: catalytic activity (AOC1, CPE, ANPEP and MEP1A), regulator activity (TNFSF9, MDK, GDF15, ILR6A, LGALS3 and FLNA), transmembrane transporter activity (SLC40A1 and SLC5A1), and extracellular matrix structural constituents (FGL2, HMCN2, and MUC17). Conclusions: ERAP2 is upregulated in the inflamed IBD colon mucosa, and expression proficiency is highly correlated with genotype of rs2910686. While the SNP rs2248374 is commonly used to determine ERAP2 expressional proficiency, our data confirms that mechanisms independent of this SNP can lead to ERAP2 deficiency. Our data demonstrates that epithelial ERAP2 presence affects the inflammatory response in colonoids, suggesting a pleiotropic role of ERAP2 beyond MHC class I antigen processing.

• Sæterstad, Siri; Østvik, Ann Elisabet; Røyset, Elin Synnøve; Bakke, Ingunn; Sandvik, Arne Kristian & Granlund, Atle van Beelen (2022). Profound gene expression changes in the epithelial monolayer of active ulcerative colitis and Crohn's disease. PLOS ONE. 11(17). doi: 10.1371/journal.pone.0265189. Full text in Research Archive Show summary

  In recent years it has become apparent that the epithelium is highly involved in inflammatory bowel disease (IBD) pathophysiology. The majority of gene expression studies of IBD are generated from heterogeneous biopsies, providing no distinction between immune cells, the epithelium and other mucosal cells. By using laser capture microdissection (LCM) coupled with RNA sequencing, we aimed to characterize the expressional changes of the isolated colonic epithelial monolayer from ulcerative colitis (UC) and Crohn’s disease (CD) patients compared to healthy controls (HC). The analysis identified 3706 genes as differentially expressed between active IBD epithelium and HC. Weighted gene co-expression network analysis was used to stratify genes into modules, which were subsequently characterized using enrichment analysis. Our data show a distinct upregulation of the antigen presentation machinery during inflammation, including major histocompatibility complex class II molecules (e.g. HLA-DPA1, HLA-DPB1, HLA-DRA) and key transcription factors/activators (STAT1, IRF1, CIITA). We also see an epithelial downregulation of retinoic acid-responsive nuclear receptors (RARA, RARB, RXRA), but upregulation of retinoid-metabolizing enzymes (RDH11, ALDH1A2, ALDH1A3), which together suggest a perturbation of epithelial vitamin A signaling during active IBD. Lastly, we identified a cluster of stress-related genes, including activator protein 1 components JUNB and ATF3, as significantly upregulated in active UC but not in CD, revealing an interesting aspect of IBD heterogeneity. The results represent a unique resource for enhanced understanding of epithelial involvement in IBD inflammation and is a valuable tool for further studies on these processes.

• Jørandli, Jonas Woll; Thorsvik, Silje; Skovdahl, Helene Kolstad; Kornfeld, Benedikt; Sæterstad, Siri & Gustafsson, Björn [Show all 8 contributors for this article] (2020). The serotonin reuptake transporter is reduced in the epithelium of active Crohn's disease and ulcerative colitis. American Journal of Physiology - Gastrointestinal and Liver Physiology. 319(6), p. G761–G768. doi: 10.1152/ajpgi.00244.2020. Full text in Research Archive
• Zegarra, Sergio Miguel Castaneda; Xing, Mengtan; Gago-Fuentes, Raquel; Sæterstad, Siri & Oksenych, Valentyn (2019). Synthetic lethality between DNA repair factors Xlf and Paxx is rescued by inactivation of Trp53. DNA Repair. ISSN 1568-7864. 73, p. 164–169. doi: 10.1016/j.dnarep.2018.12.002. Full text in Research Archive Show summary

  Non-homologous end joining (NHEJ) is a DNA repair pathway that senses, processes and ligates DNA double-strand breaks (DSBs) throughout the cell cycle. During NHEJ, core Ku70 and Ku80 subunits bind DSBs as a heterodimer and promote further recruitment of accessory factors (e.g., PAXX, Mri, DNA-PKcs, Artemis) and downstream core subunits XRCC4 and DNA ligase 4 (Lig4). Inactivation of Ku70 or Ku80 genes in mice results in immunodeficiency and high levels of genomic instability; deletion of individual Dna-pkcs, Xlf, Paxx or Mri genes results in viable mice with no or modest DNA repair defects. However, combined inactivation of either Xlf and Dna-pkcs, or Xlf and Paxx, or Xlf and Mri, leads to synthetic lethality in mice, which correlates with increased levels of apoptosis in the central nervous system. Here, we demonstrated that inactivation of pro-apoptotic factor Trp53 rescues embryonic lethality of Xlf−/−Paxx−/− and Xlf−/−Dna-pkcs−/− double knockout mice. Moreover, combined inactivation of Paxx and Dna-pkcs results in live-born fertile Paxx−/−Dna-pkcs−/− mice indistinguishable from Dna-pkcs−/− knockout controls.

• Dewan, Alisa Elinsdatter; Xing, Mengtan; Lundbæk, Marie Benner; Gago-Fuentes, Raquel; Beck, Carole & Aas, Per Arne [Show all 11 contributors for this article] (2018). Robust DNA repair in PAXX-deficient mammalian cells. FEBS Open Bio. 8(3), p. 442–448. doi: 10.1002/2211-5463.12380. Full text in Research Archive Show summary

  To ensure genome stability, mammalian cells employ several DNA repair pathways. Nonhomologous DNA end joining (NHEJ) is the DNA repair process that fixes double-strand breaks throughout the cell cycle. NHEJ is involved in the development of B and T lymphocytes through its function in V(D)J recombination and class switch recombination (CSR). NHEJ consists of several core and accessory factors, including Ku70, Ku80, XRCC4, DNA ligase 4, DNA-PKcs, Artemis, and XLF. Paralog of XRCC4 and XLF (PAXX) is the recently described accessory NHEJ factor that structurally resembles XRCC4 and XLF and interacts with Ku70/Ku80. To determine the physiological role of PAXX in mammalian cells, we purchased and characterized a set of custom-generated and commercially available NHEJ-deficient human haploid HAP1 cells, PAXXΔ, XRCC4Δ, and XLFΔ. In our studies, HAP1 PAXXΔ cells demonstrated modest sensitivity to DNA damage, which was comparable to wild-type controls. By contrast, XRCC4Δ and XLFΔ HAP1 cells possessed significant DNA repair defects measured as sensitivity to double-strand break inducing agents and chromosomal breaks. To investigate the role of PAXX in CSR, we generated and characterized Paxx−/− and Aid−/− murine lymphoid CH12F3 cells. CSR to IgA was nearly at wild-type levels in the Paxx−/− cells and completely ablated in the absence of activation-induced cytidine deaminase (AID). In addition, Paxx−/− CH12F3 cells were hypersensitive to zeocin when compared to wild-type controls. We concluded that Paxx-deficient mammalian cells maintain robust NHEJ and CSR.

• Gago-Fuentes, Raquel; Xing, Mengtan; Sæterstad, Siri; Sarno, Antonio; Dewan, Alisa Elinsdatter & Beck, Carole [Show all 9 contributors for this article] (2018). Normal development of mice lacking PAXX, the paralogue of XRCC4 and XLF. FEBS Open Bio. 8(3), p. 426–434. doi: 10.1002/2211-5463.12381. Full text in Research Archive Show summary

  DNA repair consists of several cellular pathways which recognize and repair damaged DNA. The classical nonhomologous DNA end-joining (NHEJ) pathway repairs double-strand breaks in DNA. It is required for maturation of both B and T lymphocytes by supporting V(D)J recombination as well as B-cell differentiation during class switch recombination (CSR). Inactivation of NHEJ factors Ku70, Ku80, XRCC4, DNA ligase 4, DNA-PKcs, and Artemis impairs V(D)J recombination and blocks lymphocyte development. Paralogue of XRCC4 and XLF (PAXX) is an accessory NHEJ factor that has a significant impact on the repair of DNA lesions induced by ionizing radiation in human, murine, and chicken cells. However, the role of PAXX during development is poorly understood. To determine the physiological role of PAXX, we deleted part of the Paxx promoter and the first two exons in mice. Further, we compared Paxx-knockout mice with wild-type (WT) and NHEJ-deficient controls including Ku80- and Dna-pkcs-null and severe combined immunodeficiency mice. Surprisingly, Paxx-deficient mice were not distinguishable from the WT littermates; they were the same weight and size, fertility status, had normal spleen, thymus, and bone marrow. Paxx-deficient mice had the same number of chromosomal and chromatid breaks as WT mice. Moreover, Paxx-deficient primary B lymphocytes had the same level of CSR as lymphocytes isolated from WT mice. We concluded that PAXX is dispensable for normal mouse development.

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• Walaas, Gunnar Andreas Enerhaug; Sridhar, Arun; Kuraas, Lusie Frostvoll; Sæterstad, Siri; Schioldborg, Amanda Yin & Granlund, Atle van Beelen [Show all 10 contributors for this article] (2026). Can patient-derived colonic organoids faithfully recapitulate epithelial inflammation in ulcerative colitis when compared with patient-matched microdissected colonic tissue? Full text in Research Archive Show summary

  Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by continuous epithelial barrier dysfunction and cytokine-mediated inflammation in the colon. As mucosal healing in UC depends on epithelial barrier restoration, understanding the epithelial dysfunction is central to improve treatment. Patient-derived colonic epithelial organoids offer a unique opportunity to model UC pathophysiology in a personalized manner, as they preserve epithelial architecture and donor-specific genetic backgrounds. However, their ability to faithfully reproduce in vivo epithelial inflammation has not been fully established. Here, we present a patient-matched translational framework directly linking in vivo UC epithelial inflammation to defined in vitro colonic organoid responses. Using laser microdissected inflamed and uninflamed colonic epithelium and colonic organoids derived from the same UC patients, we performed integrated transcriptomic profiling to assess how closely cytokine-stimulated colonic organoids recapitulate the epithelial inflammatory state observed in the patients. Colonic organoids were exposed to clinically relevant inflammatory stimuli, including TNF, IFNg, IFNl1, or a combination of TNF+IFNg. Transcriptomes of these colonic organoids were additionally compared to an in-house dataset where colonic organoids were stimulated with a cocktail of pro- and anti-inflammatory cytokines (TNF, IL-17, IL-1b, IL-22, Poly(I:C), IFNg). We demonstrated that the combined TNF+IFN stimulation, as well as the cytokine cocktail, elicits transcriptional programs that closely mirror in vivo UC epithelial inflammation, including robust activation of interferon signaling, antigen presentation, and unfolded protein response pathways. The unique in vivo epithelial transcriptome revealed inflammation-specific programs not captured in vitro, including signatures linked to epithelial immune and -stromal interactions, chemotaxis, and platelet-endothelium-leukocyte signaling, underscoring biological processes that are exclusive to the native tissue context. Importantly, patient-matched analyses revealed strong correlations in the expression of UC-relevant genes between in vivo epithelium and in vitro stimulated colonic organoids, with conserved donor-specific expression patterns, underscoring the fidelity and reproducibility of the model. Protein verification of ERAP2, IRF1, DUOX2, and iNOS demonstrated conserved inflammatory regulation between patient epithelium and cytokine-stimulated organoids, underscoring cross-platform consistency. By uniquely integrating patient-matched in vivo and in vitro epithelial transcriptomes, our study provides compelling evidence that colonic organoids constitute a clinically relevant and personalized model system for UC. This approach establishes a robust platform for dissecting epithelial disease mechanisms, evaluating therapeutic responses, and advancing precision medicine strategies in inflammatory bowel disease.

• Walaas, Gunnar Andreas Enerhaug; Sridhar, Arun; Kuraas, Lusie Frostvoll; Sæterstad, Siri; Schioldborg, Amanda Yin & Granlund, Atle van Beelen [Show all 10 contributors for this article] (2025). Organoids as translational tools: Patient-matched transcriptomics reveals similarities between in vitro and in vivo epithelial responses in ulcerative colitis. Full text in Research Archive
• Sridhar, Arun; Walaas, Gunnar Andreas Enerhaug; Sæterstad, Siri; Myrmehl, Johan Pierre Durand; Cermakova, Romana & Myrseth, Marte Gisvold [Show all 11 contributors for this article] (2025). Approved and investigational JAK/TYK2 inhibitors attenuate inflammatory pathways and promote mucosal homeostasis in IBD patient-derived organoids. Full text in Research Archive
• Sridhar, Arun; Walaas, Gunnar Andreas Enerhaug; Sæterstad, Siri; Hansen, Marianne Dore; Østvik, Ann Elisabeth & Bakke, Ingunn [Show all 7 contributors for this article] (2025). Investigating the effects of JAK-inhibitors on inflammatory responses in intestinal epithelial cells using IBD patient-derived colonoids. Full text in Research Archive
• Nakstad, Vu To; Sigfúsdóttir, Margrét Sylvía; Chahal, Aman Singh; Haukaas, Tonje Husby; Ringers, Christa & Bwanika, Henri Colyn Harry [Show all 14 contributors for this article] (2025). Miniaturization of patient- and stem cell derived organoids – increasing throughput and reproducibility. Full text in Research Archive
• Sæterstad, Siri; Østvik, Ann Elisabeth; Hansen, Marianne Dore; Bruland, Torunn & Granlund, Atle van Beelen (2024). Utilizing patient-derived colon organoids to explore the effect of genetically determined ERAP2-proficiency upon proinflammatory stimulation. Full text in Research Archive
• Sæterstad, Siri; Østvik, Ann Elisabeth; Hansen, Marianne Dore; Bruland, Torunn & Granlund, Atle van Beelen (2024). Utilizing patient-derived colon organoids to explore the effect of genetically determined ERAP2-proficiency upon proinflammatory stimulation. Full text in Research Archive
• Sæterstad, Siri; Østvik, Ann Elisabeth; Hansen, Marianne Dore; Bruland, Torunn & Granlund, Atle van Beelen (2024). Correction to: The effect of rs2910686 on ERAP2 expression in IBD and epithelial inflammatory response(Journal of Translational Medicine, (2024), 22, 1, (750), 10.1186/s12967-024-05532-w). Journal of Translational Medicine. 22(1). doi: 10.1186/s12967-024-05645-2. Full text in Research Archive
• Sæterstad, Siri; Østvik, Ann Elisabet; Sandvik, Arne Kristian & Granlund, Atle van Beelen (2020). Gene expression landscape of epithelial monolayer in inflammatory bowel disease. Full text in Research Archive
• Sæterstad, Siri; Østvik, Ann Elisabet; Sandvik, Arne Kristian & Granlund, Atle van Beelen (2020). Gene expression landscape of epithelial monolayer in inflammatory bowel disease. Journal of Crohn`s and Colitis. 14(Jan.2020), p. S087–S087. doi: 10.1093/ecco-jcc/jjz203.087. Full text in Research Archive

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