Benedicte Alexandra Lie

• Hjorthaug, Hanne Sagsveen; Heimli, Marte; Flåm, Siri Tennebø & Lie, Benedicte Alexandra (2026). Multimodal single-cell profiling identifies nclTECs and links chromatin remodeling to TEC differentiation and self-antigen expression modes. iScience. 29(8). doi: 10.1016/j.isci.2026.116916. Full text in Research Archive
• Ramadan, Donia Jamal; Kichula, Katherine M.; Tao, Sudan; Porfilio, Timothy; Lande, Asgeir & Fluge, Øystein [Show all 12 contributors for this article] (2025). Killer cell immunoglobulin-like receptor (KIR) alleles suggested to be associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Brain, Behavior, and Immunity. ISSN 0889-1591. 130. doi: 10.1016/j.bbi.2025.106098. Full text in Research Archive Show summary

  Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic and debilitating disease with unknown cause. Involvement of infection and immune dysregulation has been suggested, including changes in immune cell subsets and abnormal functions of natural killer (NK) cells. The regulatory NK cell receptors, killer cell immunoglobulin-like receptors (KIR) have previously been investigated in small cohorts of ME/CFS patients with conflicting results regarding gene content. Here, we studied KIR genes also at the allelic level using high-resolution sequencing, in 418 ME/CFS patients and 473 healthy controls. Human leukocyte antigen (HLA) class I genotype data were included for KIR ligand annotation. Our healthy control data represent KIR frequencies for a Norwegian population, which have not previously been reported. We found no association between ME/CFS and KIR gene content or copy number variations. However, our data suggested that specific KIR alleles at loci encoding inhibitory receptors were associated with ME/CFS, which was further supported by allelic haplotype analyses. Three alleles were more frequent in patients, i.e. KIR3DL3*002 (OR = 1.43, 95 % CI (1.09–1.86), p = 0.009), KIR3DL1*020 (OR = 2.20, 95 % CI (1.19–4.06), p = 0.01) and KIR3DL2*009 (OR = 1.56, 95 % CI (1.09–2.23), p = 0.01), while two alleles had a reduced patient frequency, i.e. KIR3DL3*013 (OR = 0.60, 95 % CI (0.42–0.86), p = 0.005) and KIR3DL2*010 (OR = 0.46, 95 % CI (0.30–0.71), p = 0.0005). Our data support an involvement of NK cells in ME/CFS.

• Rydland, Anne; Heinicke, Fatima; Nyman, Tuula Anneli; Siebke, Anne-Marie; Flåm, Siri Tennebø & Stensland, Maria [Show all 11 contributors for this article] (2025). Newly-diagnosed rheumatoid arthritis patients have elevated levels of plasma extracellular vesicles with protein cargo altered towards inflammatory processes. Scientific Reports. 15(1). doi: 10.1038/s41598-025-96325-8. Full text in Research Archive Show summary

  Extracellular vesicles (EVs) are implicated in rheumatoid arthritis (RA) but have mainly been assessed in RA patients taking disease modifying anti-rheumatic drugs. EVs are nanoparticles important in cell-cell communication and their molecular cargo are biomarker candidates. We characterized the protein profiles of EVs from blood plasma from newly diagnosed, treatment naïve RA patients (N = 32) and compared them to healthy controls (N = 20), by size exclusion chromatography-based EV enrichment coupled with high-resolution quantitative proteomics. The RA patients had higher EV concentration and larger EVs than controls. A total of 682 EV proteins were reliably quantified, and the overall profiles were distinctly different between patients and controls. Specifically, 26 proteins were significantly upregulated and 31 downregulated in RA patients, with several proteins acting in inflammatory networks and with immunologically important upstream regulators. The RA associated EVs appear, based on the tissue expression of their cargo proteins, to originate mainly from hepatocytes or immune cells, like neutrophils. Interestingly, the strongest RA associated EV proteins were inflammatory molecules, like SAA1 and S100A9, already suggested as biomarkers in RA. Furthermore, the RA associated EV proteins were generally not correlated with total serum protein levels, stressing the importance of EV transport of inflammatory proteins in RA pathogenesis.

• Vigeland, Maria Dehli; Flåm, Siri Tennebø; Vigeland, Magnus Dehli; Zucknick, Manuela; Wigemyr, Monica & Bråten, Lars Christian Haugli [Show all 11 contributors for this article] (2025). Gene Expression Correlates with Disability and Pain Intensity in Patients with Chronic Low Back Pain and Modic Changes in a Sex-Specific Manner. International Journal of Molecular Sciences. ISSN 1661-6596. 26(2). doi: 10.3390/ijms26020800. Full text in Research Archive Show summary

  Chronic low back pain (cLBP) lacks clear physiological explanations, and the treatment options are of limited effect. We aimed to elucidate the underlying biology of cLBP in a subgroup of patients with Modic changes type I (suggestive of inflammatory vertebral bone marrow lesions) by correlating gene expression in blood with patient-reported outcomes on disability and pain intensity and explore sex differences. Patients were included from the placebo group of a clinical study on patients with cLBP and Modic changes. Blood was collected at the time of inclusion, after three months, and after one year, and gene expression was measured at all time points by high-throughput RNA sequencing. The patients reported disability using the Roland–Morris Disability Questionnaire, and pain intensity was assessed as a mean of three scores on a 0–10 numeric rating scale: current LBP, worst LBP within the last two weeks, and mean LBP within the last two weeks. The gene expression profiles were then correlated to the reported outcomes. Changes in gene expression over time correlated significantly with changes in both disability and pain. The findings showed distinct patterns in men and women, with negligible overlap in correlated genes between the sexes. The genes involved were enriched in immunological pathways, particularly T cell receptor complex and immune responses related to neutrophils. Several of the genes harbour polymorphisms that previously have been found to be associated with chronic pain. Taken together, our results indicate gender differences in the underlying biology of disability and pain intensity in patients with low back pain.

• Vigeland, Maria Dehli; Flåm, Siri Tennebø; Vigeland, Magnus Dehli; Espeland, Ansgar; Zucknick, Manuela & Wigemyr, Monica [Show all 14 contributors for this article] (2023). Long-Term Use of Amoxicillin Is Associated with Changes in Gene Expression and DNA Methylation in Patients with Low Back Pain and Modic Changes. Antibiotics. 12(7). doi: 10.3390/antibiotics12071217. Full text in Research Archive Show summary

  Long-term antibiotics are prescribed for a variety of medical conditions, recently including low back pain with Modic changes. The molecular impact of such treatment is unknown. We conducted longitudinal transcriptome and epigenome analyses in patients (n = 100) receiving amoxicillin treatment or placebo for 100 days in the Antibiotics in Modic Changes (AIM) study. Gene expression and DNA methylation were investigated at a genome-wide level at screening, after 100 days of treatment, and at one-year follow-up. We identified intra-individual longitudinal changes in gene expression and DNA methylation in patients receiving amoxicillin, while few changes were observed in patients receiving placebo. After 100 days of amoxicillin treatment, 28 genes were significantly differentially expressed, including the downregulation of 19 immunoglobulin genes. At one-year follow-up, the expression levels were still not completely restored. The significant changes in DNA methylation (n = 4548 CpGs) were mainly increased methylation levels between 100 days and one-year follow-up. Hence, the effects on gene expression occurred predominantly during treatment, while the effects on DNA methylation occurred after treatment. In conclusion, unrecognized side effects of long-term amoxicillin treatment were revealed, as alterations were observed in both gene expression and DNA methylation that lasted long after the end of treatment.

• Brun, Marthe Kirkesæther; Hammersbøen, Kristin Reine; Viken, Marte Kathrine; Stenvik, Grethe-Elisabeth; Klaasen, Rolf & Gehin, Johanna [Show all 18 contributors for this article] (2023). HLA-DQ2 is associated with anti-drug antibody formation to infliximab in patients with immune-mediated inflammatory diseases. Journal of Internal Medicine. ISSN 0954-6820. 293(5), p. 648–655. doi: 10.1111/joim.13616. Full text in Research Archive Show summary

  Abstract Background Immunogenicity to tumour necrosis factor inhibitors is a significant clinical problem leading to treatment failure and adverse events. The study aimed to assess human leukocyte antigen (HLA) associations with anti‐drug antibody (ADAb) formation to infliximab. Methods Immune‐mediated inflammatory disease patients on infliximab therapy ( n  = 612) were included. Neutralising ADAb were assessed with a drug‐sensitive assay. Next generation sequencing‐based HLA typing was performed. Results Overall, 147 (24%) patients developed ADAb. Conditional analyses indicated HLA‐DQB1 ( p  = 1.4 × 10 −6 ) as a primary risk locus. Highest risk of ADAb was seen when carrying at least one of the HLA‐DQ2 haplotypes; DQB1*02:01–DQA1*05:01 or DQB1*02:02–DQA1*02:01 (OR 3.18, 95% CI 2.15–4.69 and p  = 5.9 × 10 −9 ). Results were consistent across diseases and when adjusting for concomitant immunomodulator. Computational predictions indicated that these HLA‐DQ2 haplotypes bind to peptide motifs from infliximab light chain. Conclusion A genome‐wide significant association between two HLA‐DQ2 haplotypes and the risk of ADAb formation to infliximab was identified, suggesting that HLA‐DQ2 testing may facilitate personalised treatment decisions.

• Rydland, Anne; Heinicke, Fatima; Flåm, Siri Tennebø; Mjaavatten, Maria Dahl & Lie, Benedicte Alexandra (2023). Small extracellular vesicles have distinct CD81 and CD9 tetraspanin expression profiles in plasma from rheumatoid arthritis patients. Clinical and Experimental Medicine. ISSN 1591-8890. 23, p. 2867–2875. doi: 10.1007/s10238-023-01024-1. Full text in Research Archive Show summary

  Abstract Extracellular vesicles (EVs) are implicated in the pathogenesis of rheumatoid arthritis (RA) but little is known about the composition of specific small EV (sEV) subpopulations. This study aimed to characterize the CD63, CD81 and CD9 tetraspanin profile in the membrane of single EVs in plasma from treatment naïve RA patients and assess potential discrepancies between methotrexate (MTX) responder groups. EVs isolated from plasma were characterized using transmission electron microscopy, and detection of surface markers (CD63, CD81 and CD9) on single EVs was performed on the ExoView platform. All RA patients ( N  = 8) were newly diagnosed, treatment naïve, females, ACPA positive and former smokers. The controls ( N  = 5) were matched for age and gender. After three months of MTX treatment, responders ( N  = 4) were defined as those with ΔDAS28 > 1.2 and DAS28 ≤ 3.2 post-treatment. The isolated EVs were 50–200 nm in size. The RA patients had a higher proportion of both CD9 and CD81 single positive sEVs compared to healthy controls, while there was a decrease in CD81/CD9 double positive sEVs in patients. Stratification of RA patients into MTX responders and non-responders revealed a distinctly higher proportion of CD81 single positive sEVs in the responder group. The proportion of CD81/CD9 double positive sEVs (anti-CD9 captured) was lower in the non-responders, but increased upon 3 months of MTX treatment. Our exploratory study revealed distinct tetraspanin profiles in RA patients suggesting their implication in RA pathophysiology and MTX treatment response.

• Viste, Rannveig; Follin, Louise Frøstrup; Kornum, Birgitte R.; Lie, Benedicte Alexandra; Viken, Marte Kathrine & Thorsby, Per Medbøe [Show all 9 contributors for this article] (2023). Increased muscle activity during sleep and more RBD symptoms in H1N1-(Pandemrix)-vaccinated narcolepsy type 1 patients compared with their non-narcoleptic siblings. Sleep. ISSN 0161-8105. 46(3), p. 1–14. doi: 10.1093/sleep/zsac316. Full text in Research Archive Show summary

  Abstract Study Objectives Narcolepsy type 1 (NT1) is characterized by unstable sleep-wake and muscle tonus regulation during sleep. We characterized dream enactment and muscle activity during sleep in a cohort of post-H1N1 NT1 patients and their siblings, and analyzed whether clinical phenotypic characteristics and major risk factors are associated with increased muscle activity. Methods RBD symptoms and polysomnography m. tibialis anterior electromyographical signals [long (0.5–15 s); short (0.1–0.49 s)] were compared between 114 post-H1N1 NT1 patients and 89 non-narcoleptic siblings. Association sub-analyses with RBD symptoms, narcoleptic symptoms, CSF hypocretin-1 levels, and major risk factors [H1N1-(Pandemrix)-vaccination, HLA-DQB1*06:02-positivity] were performed. Results RBD symptoms, REM and NREM long muscle activity indices and REM short muscle activity index were significantly higher in NT1 patients than siblings (all p < 0.001). Patients with undetectable CSF hypocretin-1 levels (<40 pg/ml) had significantly more NREM periodic long muscle activity than patients with low but detectable levels (40–150 pg/ml) (p = 0.047). In siblings, REM and NREM sleep muscle activity indices were not associated with RBD symptoms, other narcolepsy symptoms, or HLA-DQB1*06:02-positivity. H1N1-(Pandemrix)-vaccination status did not predict muscle activity indices in patients or siblings. Conclusion Increased REM and NREM muscle activity and more RBD symptoms is characteristic of NT1, and muscle activity severity is predicted by hypocretin deficiency severity but not by H1N1-(Pandemrix)-vaccination status. In the patients’ non-narcoleptic siblings, neither RBD symptoms, core narcoleptic symptoms, nor the major NT1 risk factors is associated with muscle activity during sleep, hence not indicative of a phenotypic continuum.

• Heimli, Marte; Flåm, Siri Tennebø; Hjorthaug, Hanne Sagsveen; Bjørnstad, Pål Marius; Chernigovskaia, Maria & Le, Quy Khang [Show all 9 contributors for this article] (2023). Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR-seq. Scientific Reports. 13:17714(1), p. 1–13. doi: 10.1038/s41598-023-44693-4. Full text in Research Archive Show summary

  Thymic T cell development comprises T cell receptor (TCR) recombination and assessment of TCR avidity towards self-peptide-MHC complexes presented by antigen-presenting cells. Self-reactivity may lead to negative selection, or to agonist selection and differentiation into unconventional lineages such as regulatory T cells and CD8 T cells. To explore the effect of the adaptive immune receptor repertoire on thymocyte developmental decisions, we performed single cell adaptive immune receptor repertoire sequencing (scAIRR-seq) of thymocytes from human young paediatric thymi and blood. Thymic PDCD1+ cells, a putative CD8 T cell precursor population, exhibited several TCR features previously associated with thymic and peripheral ZNF683+ CD8 T cells, including enrichment of large and positively charged complementarity-determining region 3 (CDR3) amino acids. Thus, the TCR repertoire may partially explain the decision between conventional vs. agonist selected thymocyte differentiation, an aspect of importance for the development of therapies for patients with immune-mediated diseases.

• Heimli, Marte; Flåm, Siri Tennebø; Hjorthaug, Hanne Sagsveen; Don, Trinh; Frisk, Michael & Dumont, Karl-Andreas [Show all 10 contributors for this article] (2023). Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection. Frontiers in Immunology. 13. doi: 10.3389/fimmu.2022.1092028. Full text in Research Archive Show summary

  To prevent autoimmunity, thymocytes expressing self-reactive T cell receptors (TCRs) are negatively selected, however, divergence into tolerogenic, agonist selected lineages represent an alternative fate. As thymocyte development, selection, and lineage choices are dependent on spatial context and cell-to-cell interactions, we have performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) and spatial transcriptomics on paediatric human thymu​​s. Thymocytes expressing markers of strong TCR signalling diverged from the conventional developmental trajectory prior to CD4 + or CD8 + lineage commitment, while markers of different agonist selected T cell populations (CD8αα(I), CD8αα(II), T (agonist) , T reg (diff), and T reg ) exhibited variable timing of induction. Expression profiles of chemokines and co-stimulatory molecules, together with spatial localisation, supported that dendritic cells, B cells, and stromal cells contribute to agonist selection, with different subsets influencing thymocytes at specific developmental stages within distinct spatial niches. Understanding factors influencing agonist T cells is needed to benefit from their immunoregulatory effects in clinical use.

• Saevarsdottir, Saedis; Stefansdottir, Lilja; Sulem, Patrick; Thorleifsson, Gudmar; Ferkingstad, Egil & Rutsdottir, Gudrun [Show all 78 contributors for this article] (2022). Multiomics analysis of rheumatoid arthritis yields sequence variants that have large effects on risk of the seropositive subset. Annals of the Rheumatic Diseases. ISSN 0003-4967. 81(8), p. 1085–1095. doi: 10.1136/annrheumdis-2021-221754. Full text in Research Archive Show summary

  Objectives To find causal genes for rheumatoid arthritis (RA) and its seropositive (RF and/or ACPA positive) and seronegative subsets. Methods We performed a genome-wide association study (GWAS) of 31 313 RA cases (68% seropositive) and ~1 million controls from Northwestern Europe. We searched for causal genes outside the HLA-locus through effect on coding, mRNA expression in several tissues and/or levels of plasma proteins (SomaScan) and did network analysis (Qiagen). Results We found 25 sequence variants for RA overall, 33 for seropositive and 2 for seronegative RA, altogether 37 sequence variants at 34 non-HLA loci, of which 15 are novel. Genomic, transcriptomic and proteomic analysis of these yielded 25 causal genes in seropositive RA and additional two overall. Most encode proteins in the network of interferon-alpha/beta and IL-12/23 that signal through the JAK/STAT-pathway. Highlighting those with largest effect on seropositive RA, a rare missense variant in STAT4 (rs140675301-A) that is independent of reported non-coding STAT4-variants, increases the risk of seropositive RA 2.27-fold (p=2.1×10−9), more than the rs2476601-A missense variant in PTPN22 (OR=1.59, p=1.3×10−160). STAT4 rs140675301-A replaces hydrophilic glutamic acid with hydrophobic valine (Glu128Val) in a conserved, surface-exposed loop. A stop-mutation (rs76428106-C) in FLT3 increases seropositive RA risk (OR=1.35, p=6.6×10−11). Independent missense variants in TYK2 (rs34536443-C, rs12720356-C, rs35018800-A, latter two novel) associate with decreased risk of seropositive RA (ORs=0.63–0.87, p=10−9–10−27) and decreased plasma levels of interferon-alpha/beta receptor 1 that signals through TYK2/JAK1/STAT4. Conclusion Sequence variants pointing to causal genes in the JAK/STAT pathway have largest effect on seropositive RA, while associations with seronegative RA remain scarce.

• Ueland, Marthe; Hajdarevic, Riad; Mella, Olav; Strand, Elin Bolle; Duarte, Sosa Daysi & Saugstad, Ola Didrik [Show all 9 contributors for this article] (2022). No replication of previously reported association with genetic variants in the T cell receptor alpha (TRA) locus for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Translational Psychiatry. 12:277, p. 1–5. doi: 10.1038/s41398-022-02046-1. Full text in Research Archive Show summary

  Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disease with a variety of symptoms such as post-exertional malaise, fatigue, and pain, but where aetiology and pathogenesis are unknown. An increasing number of studies have implicated the involvement of the immune system in ME/CFS. Furthermore, a hereditary component is suggested by the reported increased risk for disease in relatives, and genetic association studies are being performed to identify potential risk variants. We recently reported an association with the immunologically important human leucocyte antigen (HLA) genes HLA-C and HLA-DQB1 in ME/ CFS. Furthermore, a genome-wide genetic association study in 42 ME/CFS patients reported significant association signals with two variants in the T cell receptor alpha (TRA) locus (P value <5 × 10−8 ). As the T cell receptors interact with the HLA molecules, we aimed to replicate the previously reported findings in the TRA locus using a large Norwegian ME/CFS cohort (409 cases and 810 controls) and data from the UK biobank (2105 cases and 4786 controls). We investigated numerous SNPs in the TRA locus, including the two previously ME/CFS-associated variants, rs11157573 and rs17255510. No associations were observed in the Norwegian cohort, and there was no significant association with the two previously reported SNPs in any of the cohorts. However, other SNPs showed signs of association (P value <0.05) in the UK Biobank cohort and meta-analyses of Norwegian and UK biobank cohorts, but none survived correction for multiple testing. Hence, our research did not identify any reliable associations with variants in the TRA locus.

• Li, Jin; Li, Yun R.; Glessner, Joseph T.; Yang, Jie; March, Michael E. & Kao, Charlly [Show all 28 contributors for this article] (2022). Identification of Novel Loci Shared by Juvenile Idiopathic Arthritis Subtypes Through Integrative Genetic Analysis. Arthritis & Rheumatology. ISSN 2326-5191. 74(8), p. 1420–1429. doi: 10.1002/art.42129. Full text in Research Archive Show summary

  Objective.Juvenile idiopathic arthritis (JIA) is the most common chronic immune-mediated joint disease amongchildren and encompasses a heterogeneous group of immune-mediated joint disorders classified into 7 subtypes according to clinical presentation. However, phenotype overlap and biologic evidence suggest a shared mechanistic basisbetween subtypes. This study was undertaken to systematicallyinvestigate shared genetic underpinnings of JIA subtypes.Methods.We performed a heterogeneity-sensitive genome-wide association study encompassing a total of 1,245JIA cases (classified into 7 subtypes) and 9,250 controls, followed byfine-mapping of candidate causal variants at eachgenome-wide significant locus, functional annotation, and pathway and network analysis. We further identified candi-date drug targets and drug repurposing opportunities by in silico analyses.Results.In addition to the major histocompatibility complex locus, we identified 15 genome-wide significant loci shared between at least 2 JIA subtypes, including 10 novel loci. Functional annotation indicated that candidate genesat these loci were expressed in diverse immune cell types. Conclusion.This study identified novel genetic loci shared by JIA subtypes. Ourfindings identified candidatemechanisms underlying JIA subtypes and candidate targets with drug repurposing opportunities for JIA treatment.

• Vigeland, Maria Dehli; Flåm, Siri Tennebø; Vigeland, Magnus Dehli; Espeland, Ansgar; Kristoffersen, Per Martin & Vetti, Nils [Show all 17 contributors for this article] (2022). Correlation between gene expression and MRI STIR signals in patients with chronic low back pain and Modic changes indicates immune involvement. Scientific Reports. 12(1), p. 1–12. doi: 10.1038/s41598-021-04189-5. Full text in Research Archive Show summary

  Disability and distress caused by chronic low back pain (LBP) lacking clear pathoanatomical explanations cause huge problems both for patients and society. A subgroup of patients has Modic changes (MC), identifiable by MRI as vertebral bone marrow lesions. The cause of such changes and their relationship to pain are not yet understood. We explored the pathobiology of these lesions using profiling of gene expression in blood, coupled with an edema-sensitive MRI technique known as short tau inversion recovery (STIR) imaging. STIR images and total RNA from blood were collected from 96 patients with chronic LBP and MC type I, the most inflammatory MC state. We found the expression of 37 genes significantly associated with STIR signal volume, ten genes with edema abundancy (a constructed combination of STIR signal volume, height, and intensity), and one gene with expression levels significantly associated with maximum STIR signal intensity. Gene sets related to interferon signaling, mitochondrial metabolism and defense response to virus were identified as significantly enriched among the upregulated genes in all three analyses. Our results point to inflammation and immunological defense as important players in MC biology in patients with chronic LBP.

• Langton, David J.; Bhalekar, Rohan M.; Joyce, Thomas J.; Rushton, Stephen P.; Wainwright, Benjamin J. & Nargol, Matthew E. [Show all 17 contributors for this article] (2022). The influence of HLA genotype on the development of metal hypersensitivity following joint replacement. Communications Medicine. 2(1), p. 1–12. doi: 10.1038/s43856-022-00137-0. Full text in Research Archive Show summary

  Background Over five million joint replacements are performed across the world each year. Cobalt chrome (CoCr) components are used in most of these procedures. Some patients develop delayed-type hypersensitivity (DTH) responses to CoCr implants, resulting in tissue damage and revision surgery. DTH is unpredictable and genetic links have yet to be definitively established. Methods At a single site, we carried out an initial investigation to identify HLA alleles associated with development of DTH following metal-on-metal hip arthroplasty. We then recruited patients from other centres to train and validate an algorithm incorporating patient age, gender, HLA genotype, and blood metal concentrations to predict the development of DTH. Accuracy of the modelling was assessed using performance metrics including time-dependent receiver operator curves. Results Using next-generation sequencing, here we determine the HLA genotypes of 606 patients. 176 of these patients had experienced failure of their prostheses; the remaining 430 remain asymptomatic at a mean follow up of twelve years. We demonstrate that the development of DTH is associated with patient age, gender, the magnitude of metal exposure, and the presence of certain HLA class II alleles. We show that the predictive algorithm developed from this investigation performs to an accuracy suitable for clinical use, with weighted mean survival probability errors of 1.8% and 3.1% for pre-operative and post-operative models respectively. Conclusions The development of DTH following joint replacement appears to be determined by the interaction between implant wear and a patient’s genotype. The algorithm described in this paper may improve implant selection and help direct patient surveillance following surgery. Further consideration should be given towards understanding patient-specific responses to different biomaterials.

• Harrison, Genelle F.; Leaton, Laura Ann; Harrison, Erica A.; Kichula, Katherine M.; Viken, Marte Kathrine & Shortt, Jonathan [Show all 11 contributors for this article] (2022). Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1. PLoS Computational Biology. ISSN 1553-734X. 18:e1009059(2), p. 1–22. doi: 10.1371/journal.pcbi.1009059. Full text in Research Archive Show summary

  Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping KIR3DL1/S1 alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles &gt;1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 with HLA-A and -B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.

• Hajdarevic, Riad; Lande, Asgeir; Mehlsen, Jesper; Rydland, Anne; Sosa, Daysi Duarte & Strand, Elin Bolle [Show all 11 contributors for this article] (2022). Genetic association study in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) identifies several potential risk loci. Brain, Behavior, and Immunity. ISSN 0889-1591. 102, p. 362–369. doi: 10.1016/j.bbi.2022.03.010. Full text in Research Archive Show summary

  Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disease of unknown etiology and pathogenesis, which manifests in a variety of symptoms like post-exertional malaise, brain fog, fatigue and pain. Hereditability is suggested by an increased disease risk in relatives, however, genome-wide association studies in ME/CFS have been limited by small sample sizes and broad diagnostic criteria, therefore no established risk loci exist to date. In this study, we have analyzed three ME/CFS cohorts: a Norwegian discovery cohort (N = 427), a Danish replication cohort (N = 460) and a replication dataset from the UK biobank (N = 2105). To the best of our knowledge, this is the first ME/CFS genome-wide association study of this magnitude incorporating 2532 patients for the genome-wide analyses and 460 patients for a targeted analysis. Even so, we did not find any ME/ CFS risk loci displaying genome-wide significance. In the Norwegian discovery cohort, the TPPP gene region showed the most significant association (rs115523291, P = 8.5 × 10− 7 ), but we could not replicate the top SNP. However, several other SNPs in the TPPP gene identified in the Norwegian discovery cohort showed modest association signals in the self-reported UK biobank CFS cohort, which was also present in the combined analysis of the Norwegian and UK biobank cohorts, TPPP (rs139264145; P = 0.00004). Interestingly, TPPP is expressed in brain tissues, hence it will be interesting to see whether this association, with time, will be verified in even larger cohorts. Taken together our study, despite being the largest to date, could not establish any ME/CFS risk loci, but comprises data for future studies to accumulate the power needed to reach genome-wide significance.

• Langton, David J.; Bourke, Stephen C.; Lie, Benedicte Alexandra; Reiff, Gabrielle; Natu, Shonali & Darlay, Rebecca [Show all 8 contributors for this article] (2021). The influence of HLA genotype on the severity of COVID-19 infection. HLA. ISSN 2059-2302. 98(1), p. 14–22. doi: 10.1111/tan.14284. Full text in Research Archive Show summary

  The impact of COVID-19 varies markedly, not only between individual patients but also between different populations. We hypothesised that differences in HLA genes might influence this variation. Using next generation sequencing, we analysed the class I and class II classical HLA genes of 147 individuals of European descent experiencing variable clinical outcomes following COVID-19 infection. Forty-nine of these patients were admitted to hospital with severe respiratory disease. They had no significant pre-existing comorbidities. We compared the results to those obtained from a group of 69 asymptomatic hospital workers who evidence of COVID exposure based on blood antibody testing. Allele frequencies in both the severe and asymptomatic groups were compared to local and national healthy controls with adjustments made for age and sex. With the inclusion of hospital staff who had reported localised symptoms only (limited to loss of smell/taste, n = 13) or systemic symptoms not requiring hospital treatment (n = 16), we carried out ordinal logistic regression modelling to determine the relative influence of age, BMI, sex and the presence of specific HLA genes on symptomatology. We found a significant difference in the allele frequency of HLA-DRB1*04:01 in the severe patient compared to the asymptomatic staff group (5.1% vs. 16.7%, P = .003 after adjustment for age and sex). There was a significantly lower frequency of the haplotype DQA1*01:01-DQB1*05:01-DRB1*01:01 in the asymptomatic group compared to the background population (P = .007). Ordinal logistic regression modelling confirmed the significant influence of DRB1*04:01 on the clinical severity of COVID-19 observed in the cohorts. These alleles are found in greater frequencies in the North Western European population. This regional study provides evidence that HLA genotype influences clinical outcome in COVID-19 infection. Validation studies must take account of the complex genetic architecture of the immune system across different geographies and ethnicities.

• Creary, Lisa E.; Gangavarapu, Sridevi; Caillier, Stacy J.; Cavalcante, Paola; Frangiamore, Rita & Lie, Benedicte Alexandra [Show all 16 contributors for this article] (2021). Next-Generation Sequencing Identifies Extended HLA Class I and II Haplotypes Associated With Early-Onset and Late-Onset Myasthenia Gravis in Italian, Norwegian, and Swedish Populations. Frontiers in Immunology. 12, p. 1–14. doi: 10.3389/fimmu.2021.667336. Full text in Research Archive Show summary

  Genetic susceptibility to myasthenia gravis (MG) associates with specific HLA alleles and haplotypes at the class I and II regions in various populations. Previous studies have only examined alleles at a limited number of HLA loci that defined only broad serotypes or alleles defined at the protein sequence level. Consequently, genetic variants in noncoding and untranslated HLA gene segments have not been fully explored but could also be important determinants for MG. To gain further insight into the role of HLA in MG, we applied next-generation sequencing to analyze sequence variation at eleven HLA genes in early-onset (EO) and late-onset (LO) non-thymomatous MG patients positive for the acetylcholine receptor (AChR) antibodies and ethnically matched controls from Italy, Norway, and Sweden. For all three populations, alleles and haplotype blocks present on the ancestral haplotype AH8.1 were associated with risk in AChR-EOMG patients. HLA-B*08:01:01:01 was the dominant risk allele in Italians (OR = 3.28, P = 1.83E−05), Norwegians (OR = 3.52, P = 4.41E−16), and in Swedes HLA-B*08:01 was the primary risk allele (OR = 4.24, P <2.2E-16). Protective alleles and haplotype blocks were identified on the HLA-DRB7, and HLA-DRB13.1 class II haplotypes in Italians and Norwegians, whereas in Swedes HLA-DRB7 exhibited the main protective effect. For AChR-LOMG patients, the HLA-DRB15.1 haplotype and associated alleles were significantly associated with susceptibility in all groups. The HLA-DR13–HLA-DR–HLA-DQ haplotype was associated with protection in all AChR-LOMG groups. This study has confirmed and extended previous findings that the immunogenetic predisposition profiles for EOMG and LOMG are distinct. In addition, the results are consistent with a role for non-coding HLA genetic variants in the pathogenesis of MG.

• Guderud, Kari; Sunde, Line Hagen; Flåm, Siri Tennebø; Mæhlen, Marthe Thoresen; Mjaavatten, Maria Dahl & NORLI, ELLEN SAUAR [Show all 13 contributors for this article] (2021). Methotrexate Treatment of Newly Diagnosed RA Patients Is Associated With DNA Methylation Differences at Genes Relevant for Disease Pathogenesis and Pharmacological Action. Frontiers in Immunology. 12, p. 1–11. doi: 10.3389/fimmu.2021.713611. Full text in Research Archive Show summary

  Background: Methotrexate (MTX) is the first line treatment of rheumatoid arthritis (RA), and methylation changes in bulk T cells have been reported after treatment with MTX. We have investigated cell-type specific DNA methylation changes across the genome in naïve and memory CD4+ T cells before and after MTX treatment of RA patients. DNA methylation profiles of newly diagnosed RA patients (N=9) were assessed by reduced representation bisulfite sequencing. Results: We found that MTX treatment significantly influenced DNA methylation levels at multiple CpG sites in both cell populations. Interestingly, we identified differentially methylated sites annotated to two genes; TRIM15 and SORC2, previously reported to predict treatment outcome in RA patients when measured in bulk T cells. Furthermore, several of the genes, including STAT3, annotated to the significant CpG sites are relevant for RA susceptibility or the action of MTX. Conclusion: We detected CpG sites that were associated with MTX treatment in CD4+ naïve and memory T cells isolated from RA patients. Several of these sites overlap genetic regions previously associated with RA risk and MTX treatment outcome.

• Heinicke, Fatima; Zhong, Xiangfu; Flåm, Siri Tennebø; Breidenbach, Johannes; Leithaug, Magnus & Mæhlen, Marthe Thoresen [Show all 14 contributors for this article] (2021). MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients. Frontiers in Immunology. 12. doi: 10.3389/fimmu.2021.663736. Full text in Research Archive Show summary

  Rheumatoid arthritis (RA) is a complex disease with a wide range of underlying susceptibility factors. Recently, dysregulation of microRNAs (miRNAs) in RA have been reported in several immune cell types from blood. However, B cells have not been studied in detail yet. Given the autoimmune nature of RA with the presence of autoantibodies, CD19+ B cells are a key cell type in RA pathogenesis and alterations in CD19+ B cell subpopulations have been observed in patient blood. Therefore, we aimed to reveal the global miRNA repertoire and to analyze miRNA expression profile differences in homogenous RA patient phenotypes in blood-derived CD19+ B cells. Small RNA sequencing was performed on CD19+ B cells of newly diagnosed untreated RA patients (n=10), successfully methotrexate (MTX) treated RA patients in remission (MTX treated RA patients, n=18) and healthy controls (n=9). The majority of miRNAs was detected across all phenotypes. However, significant expression differences between MTX treated RA patients and controls were observed for 27 miRNAs, while no significant differences were seen between the newly diagnosed patients and controls. Several of the differentially expressed miRNAs were previously found to be dysregulated in RA including miR-223-3p, miR-486-3p and miR-23a-3p. MiRNA target enrichment analysis, using the differentially expressed miRNAs and miRNA-target interactions from miRTarBase as input, revealed enriched target genes known to play important roles in B cell activation, differentiation and B cell receptor signaling, such as STAT3, PRDM1 and PTEN. Interestingly, many of those genes showed a high degree of correlated expression in CD19+ B cells in contrast to other immune cell types. Our results suggest important regulatory functions of miRNAs in blood-derived CD19+ B cells of MTX treated RA patients and motivate for future studies investigating the interactive mechanisms between miRNA and gene targets, as well as the possible predictive power of miRNAs for RA treatment response.

• Ali, Muhammad; Giannakopoulou, Eirini Chrysovalantou; Li, Yingqian; Lehander, Madeleine; Culleton, Stina Virding & Yang, Weiwen [Show all 33 contributors for this article] (2021). T cells targeted to TdT kill leukemic lymphoblasts while sparing normal lymphocytes. Nature Biotechnology. ISSN 1087-0156. doi: 10.1038/s41587-021-01089-x. Full text in Research Archive Show summary

  Abstract Unlike chimeric antigen receptors, T-cell receptors (TCRs) can recognize intracellular targets presented on human leukocyte antigen (HLA) molecules. Here we demonstrate that T cells expressing TCRs specific for peptides from the intracellular lymphoid-specific enzyme terminal deoxynucleotidyl transferase (TdT), presented in the context of HLA-A*02:01, specifically eliminate primary acute lymphoblastic leukemia (ALL) cells of T- and B-cell origin in vitro and in three mouse models of disseminated B-ALL. By contrast, the treatment spares normal peripheral T- and B-cell repertoires and normal myeloid cells in vitro, and in vivo in humanized mice. TdT is an attractive cancer target as it is highly and homogeneously expressed in 80–94% of B- and T-ALLs, but only transiently expressed during normal lymphoid differentiation, limiting on-target toxicity of TdT-specific T cells. TCR-modified T cells targeting TdT may be a promising immunotherapy for B-ALL and T-ALL that preserves normal lymphocytes.

• Gansmo, Liv Beathe; Lie, Benedicte Alexandra; Mæhlen, Marthe Thoresen; Vatten, Lars Johan; Romundstad, Pål Richard & Hveem, Kristian [Show all 8 contributors for this article] (2021). Polymorphisms in the TP53-MDM2-MDM4-axis in patients with rheumatoid arthritis. Gene. ISSN 0378-1119. 793. doi: 10.1016/j.gene.2021.145747. Full text in Research Archive Show summary

  Background In addition to being a tumour suppressor, TP53 is a suppressor of inflammation, and dysfunction of this gene has been related to autoimmune diseases. Patients with autoimmunity, such as rheumatoid arthritis (RA) have an increased risk of certain cancers, like lymphomas, indicating that some underlying mechanisms may modulate risk of both cancers and autoimmunity. Methods We genotyped 5 common genetic variants in TP53 and its main regulators MDM2 and MDM4 in a sample of 942 RA patients and 3,747 healthy controls, and mined previously published GWAS-data, to assess the potential impact of these variants on risk of RA. Results For the TP53 Arg72Pro polymorphism (rs1042522), MDM4 SNP34091 (rs4245739) and MDM2 SNP285C (rs117039649), we found no association to risk of RA. For MDM2 SNP309 (rs2279744), the minor G-allele was associated with a reduced risk of RA (OR: 0.87; CI: 0.79–0.97). This association was also seen in genotype models (OR: 0.86; CI: 0.74–0.99 and OR: 0.79; CI 0.63–0.99; dominant and recessive model, respectively), but was not validated in a large GWAS data set. For MDM2 del1518 (rs3730485), the minor del-allele was associated with an increased risk of RA in the dominant model (OR: 1.18; CI: 1.02–1.38). Stratifying RA cases and controls into phylogenetic subgroups according to the combined genotypes of all three MDM2 polymorphism, we found individuals with the del158-285–309 genotype del/ins-G/G-T/T to have an increased risk of RA as compared to those with the ins/ins-G/G-G/G genotype (OR: 1.56; CI: 1.18–2.06) indicating opposite effects of the del1518 del-allele and the SNP309 G-allele. Conclusion We find a potential association between the MDM2 del1518 variant and RA, and indications that combinatorial genotypes and haplotypes in the MDM2 locus may be related to RA.

• Viste, Rannveig; Lie, Benedicte Alexandra; Viken, Marte Kathrine; Rootwelt, Terje; Knudsen-Heier, Stine & Kornum, Birgitte Rahbek (2021). Narcolepsy type 1 patients have lower levels of effector memory CD4+ T cells compared to their siblings when controlling for H1N1-(Pandemrix™)-vaccination and HLA DQB1∗06:02 status. Sleep Medicine. ISSN 1389-9457. 85, p. 271–279. doi: 10.1016/j.sleep.2021.07.024. Full text in Research Archive Show summary

  Study objectives Evidence suggests a cell-mediated autoimmune pathogenesis for narcolepsy type 1 (NT1), but it is not clear whether the disease is associated with overall changes in T cell subsets. The increase in NT1 incidence after H1N1 vaccination campaign with the Pandemrix™ vaccine suggests that disease-relevant changes in the immune system following this vaccination were important. In this study, we aimed to investigate differentiated T cell subsets and levels of CD25 and CD69 activation markers in a cohort of mainly Pandemrix™-vaccinated NT1 patients compared with their vaccinated and unvaccinated siblings. Methods Peripheral blood mononuclear cells were collected in parallel and analysed with flow cytometry in 31 NT1 patients with disease onset after the 2009 influenza A (H1N1) pandemic and/or Pandemrix™ vaccination and 45 of their non-narcoleptic siblings (29/31 and 34/45 vaccinated, respectively). Results We observed significantly lower effector memory CD4+ T cell levels in NT1 patients compared to their siblings, when controlling for HLA DQB1∗06:02 and vaccination status. Further, within the sibling group, vaccination status significantly affected frequencies of central memory and CD8+CD25+ T cells, and HLA DQB1∗06:02 status significantly affected frequencies of CD4+CD25+ T cells. Conclusion We confirm that NT1 is associated with lower levels of effector memory CD4+ T cells in peripheral blood. Importantly, this finding was only significant when controlling for vaccination and HLA status in both patients and controls. We thus demonstrate the importance of characterizing such factors (eg HLA and vaccination) when studying T cell subsets in NT1. This might explain earlier conflicting results.

• Viste, Rannveig; Viken, Marte Kathrine; Lie, Benedicte Alexandra; Juvodden, Hilde Therese; Nordstrand, Sebjørg E. H. & Thorsby, Per M. [Show all 9 contributors for this article] (2021). High nocturnal sleep fragmentation is associated with low T lymphocyte P2Y<inf>11</inf>protein levels in narcolepsy type 1. Sleep. ISSN 0161-8105. 44(8), p. 1–12. doi: 10.1093/sleep/zsab062. Full text in Research Archive Show summary

  Abstract Study Objectives Narcolepsy type 1 (NT1) is associated with hypocretin neuron loss. However, there are still unexplained phenotypic NT1 features. We investigated the associations between clinical and sleep phenotypic characteristics, the NT1-associated P2RY11 polymorphism rs2305795, and P2Y11 protein levels in T lymphocytes in patients with NT1, their first-degree relatives and unrelated controls. Methods The P2RY11 SNP was genotyped in 100 patients (90/100 H1N1-(Pandemrix)-vaccinated), 119 related and 123 non-related controls. CD4 and CD8 T lymphocyte P2Y11 protein levels were quantified using flow cytometry in 167 patients and relatives. Symptoms and sleep recording parameters were also collected. Results We found an association between NT1 and the rs2305795 A allele (OR = 2, 95% CI (1.3, 3.0), p = 0.001). T lymphocyte P2Y11 protein levels were significantly lower in patients and relatives homozygous for the rs2305795 risk A allele (CD4: p = 0.012; CD8: p = 0.007). The nocturnal sleep fragmentation index was significantly negatively correlated with patients’ P2Y11 protein levels (CD4: p = 0.004; CD8: p = 0.006). Mean MSLT sleep latency, REM-sleep latency, and core clinical symptoms were not associated with P2Y11 protein levels. Conclusions We confirmed that the P2RY11 polymorphism rs2305795 is associated with NT1 also in a mainly H1N1-(Pandemrix)-vaccinated cohort. We demonstrated that homozygosity for the A risk allele is associated with lower P2Y11 protein levels. A high level of nocturnal sleep fragmentation was associated with low P2Y11 levels in patients. This suggests that P2Y11 has a previously unknown function in sleep-wake stabilization that affects the severity of NT1.

• Hajdarevic, Riad; Lande, Asgeir; Rekeland, Ingrid Gurvin; Rydland, Anne; Strand, Elin Bolle & Sosa, Daysi Duarte [Show all 13 contributors for this article] (2021). Fine mapping of the major histocompatibility complex (MHC) in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) suggests involvement of both HLA class I and class II loci. Brain, Behavior, and Immunity. ISSN 0889-1591. 98, p. 101–109. doi: 10.1016/j.bbi.2021.08.219. Full text in Research Archive Show summary

  The etiology of myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is unknown, but involvement of the immune system is one of the proposed underlying mechanisms. Human leukocyte antigen (HLA) associations are hallmarks of immune-mediated and autoimmune diseases. We have previously performed high resolution HLA genotyping and detected associations between ME/CFS and certain HLA class I and class II alleles. However, the HLA complex harbors numerous genes of immunological importance, and there is extensive and complex linkage disequilibrium across the region. In the current study, we aimed to fine map the association signals in the HLA complex by genotyping five additional classical HLA loci and 5,342 SNPs in 427 Norwegian ME/CFS patients, diagnosed according to the Canadian Consensus Criteria, and 480 healthy Norwegian controls. SNP association analysis revealed two distinct and independent association signals (p ≤ 0.001) tagged by rs4711249 in the HLA class I region and rs9275582 in the HLA class II region. Furthermore, the primary association signal in the HLA class II region was located within the HLA-DQ gene region, most likely due to HLA-DQB1, particularly the amino acid position 57 (aspartic acid/alanine) in the peptide binding groove, or an intergenic SNP upstream of HLA-DQB1. In the HLA class I region, the putative causal locus might map outside the classical HLA genes as the association signal spans several genes (DDR1, GTF2H4, VARS2, SFTA2 and DPCR1) with expression levels influenced by the ME/CFS associated SNP genotype. Taken together, our results implicate the involvement of the MHC, and in particular the HLA-DQB1 gene, in ME/CFS. These findings should be replicated in larger cohorts, particularly to verify the putative involvement of HLA-DQB1, a gene important for antigen-presentation to T cells and known to harbor alleles providing the largest risk for well–established autoimmune diseases.

• Sandling, Johanna K.; Pucholt, Pascal; Rosenberg, Lina Hultin; Farias, Fabiana H.G.; Kozyrev, Sergey V. & Eloranta, Maija-Leena [Show all 32 contributors for this article] (2021). Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing. Annals of the Rheumatic Diseases. ISSN 0003-4967. 80, p. 109–117. doi: 10.1136/annrheumdis-2020-218636. Full text in Research Archive Show summary

  Objectives Systemic lupus erythematosus (SLE) is an autoimmune disease with extensive heterogeneity in disease presentation between patients, which is likely due to an underlying molecular diversity. Here, we aimed at elucidating the genetic aetiology of SLE from the immunity pathway level to the single variant level, and stratify patients with SLE into distinguishable molecular subgroups, which could inform treatment choices in SLE. Methods We undertook a pathway-centred approach, using sequencing of immunological pathway genes. Altogether 1832 candidate genes were analysed in 958 Swedish patients with SLE and 1026 healthy individuals. Aggregate and single variant association testing was performed, and we generated pathway polygenic risk scores (PRS). Results We identified two main independent pathways involved in SLE susceptibility: T lymphocyte differentiation and innate immunity, characterised by HLA and interferon, respectively. Pathway PRS defined pathways in individual patients, who on average were positive for seven pathways. We found that SLE organ damage was more pronounced in patients positive for the T or B cell receptor signalling pathways. Further, pathway PRS-based clustering allowed stratification of patients into four groups with different risk score profiles. Studying sets of genes with priors for involvement in SLE, we observed an aggregate common variant contribution to SLE at genes previously reported for monogenic SLE as well as at interferonopathy genes. Conclusions Our results show that pathway risk scores have the potential to stratify patients with SLE beyond clinical manifestations into molecular subsets, which may have implications for clinical follow-up and therapy selection.

• Viken, Marte Kathrine; Pedersen, Alice Marie; Andersen, Menaka; Jensen, Tore; Lie, Benedicte Alexandra & Boulland, Line (2021). HLA-B*27 typing using a triplex real time PCR in routine laboratory. HLA. ISSN 2059-2302. 98(4), p. 366–369. doi: 10.1111/tan.14386. Full text in Research Archive Show summary

  We have established an in-house HLA-B*27 multiplex typing assay by using acombination of previously published, newly designed and commercial primersand probes for use with real-time PCR instruments. Hence, facilitating quickand large-scale HLA-B*27 typing.

• Guderud, Kari; Sunde, Line Hagen; Flåm, Siri Tennebø; Mæhlen, Marthe Thoresen; Mjaavatten, Maria Dahl & Lillegraven, Siri [Show all 16 contributors for this article] (2020). Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells. Frontiers in Immunology. 11:194, p. 1–14. doi: 10.3389/fimmu.2020.00194. Full text in Research Archive Show summary

  Background: Differences in DNA methylation have been reported in B and T lymphocyte populations, including CD4+ T cells, isolated from rheumatoid arthritis (RA) patients when compared to healthy controls. CD4+ T cells are a heterogeneous cell type with subpopulations displaying distinct DNA methylation patterns. In this study, we investigated DNA methylation using reduced representation bisulfite sequencing in two CD4+ T cell populations (CD4+ memory and naïve cells) in three groups: newly diagnosed, disease modifying antirheumatic drugs (DMARD) naïve RA patients (N = 11), methotrexate (MTX) treated RA patients (N = 18), and healthy controls (N = 9) matched for age, gender and smoking status. Results: Analyses of these data revealed significantly more differentially methylated positions (DMPs) in CD4+ memory than in CD4+ naïve T cells (904 vs. 19 DMPs) in RA patients compared to controls. The majority of DMPs (72%) identified in newly diagnosed and DMARD naïve RA patients with active disease showed increased DNA methylation (39 DMPs), whereas most DMPs (80%) identified in the MTX treated RA patients in remission displayed decreased DNA methylation (694 DMPs). Interestingly, we also found that about one third of the 101 known RA risk loci overlapped (±500 kb) with the DMPs. Notably, introns of the UBASH3A gene harbor both the lead RA risk SNP and two DMPs in CD4+ memory T cells. Conclusion: Our results suggest that RA associated DNA methylation differences vary between the two T cell subsets, but are also influenced by RA characteristics such as disease activity, disease duration and/or MTX treatment.

• Helgeland, Hanna; Gabrielsen, Ingvild Synnøve Matre; Akselsen, Helle; Sundaram, Arvind Yegambaram Meenakshi; Flåm, Siri Tennebø & Lie, Benedicte Alexandra (2020). Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells. BMC Genomics. 21(350). doi: 10.1186/s12864-020-6755-1. Full text in Research Archive Show summary

  Background: The thymus is a highly specialized organ of the immune system where T cell precursors develop and differentiate into self-tolerant CD4+ or CD8+ T cells. No studies to date have investigated how the human transcriptome profiles differ, between T cells still residing in the thymus and T cells in the periphery. Results: We have performed high-throughput RNA sequencing to characterize the transcriptomes of primary single positive (SP) CD4+ and CD8+ T cells from infant thymic tissue, as well as primary CD4+ and CD8+ T cells from infant and adult peripheral blood, to enable the comparisons across tissues and ages. In addition, we have assessed the expression of candidate genes related to autoimmune diseases in thymic CD4+ and CD8+ T cells. The thymic T cells showed the largest number of uniquely expressed genes, suggesting a more diverse transcription in thymic T cells. Comparing T cells of thymic and blood origin, revealed more differentially expressed genes, than between infant and adult blood. Functional enrichment analysis revealed an over-representation of genes involved in cell cycle and replication in thymic T cells, whereas infant blood T cells were dominated by immune related terms. Comparing adult and infant blood T cells, the former was enriched for inflammatory response, cytokine production and biological adhesion, while upregulated genes in infant blood T cells were associated with cell cycle, cell death and gene expression. Conclusion: This study provides valuable insight into the transcriptomes of the human primary SP T cells still residing within the thymus, and offers a unique comparison to primary blood derived T cells. Interestingly, the majority of autoimmune disease associated genes were expressed in one or more T cell subset, however ~ 11% of these were not expressed in frequently studied adult peripheral blood.

• Rekeland, Ingrid Gurvin; Fosså, Alexander; Lande, Asgeir; Ktoridou-Valen, Irini; Sørland, Kari & Holsen, Mari Helgesen [Show all 14 contributors for this article] (2020). Intravenous Cyclophosphamide in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. An Open-Label Phase II Study. Frontiers in Medicine. 7:162, p. 1–15. doi: 10.3389/fmed.2020.00162. Full text in Research Archive Show summary

  Introduction: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disease with high symptom burden, of unknown etiology, with no established treatment. We observed patients with long-standing ME/CFS who got cancer, and who reported improvement of ME/CFS symptoms after chemotherapy including cyclophosphamide, forming the basis for this prospective trial. Materials and methods: This open-label phase II trial included 40 patients with ME/CFS diagnosed by Canadian criteria. Treatment consisted of six intravenous infusions of cyclophosphamide, 600–700 mg/m2, given at four-week intervals with follow-up for 18 months, extended to 4 years. Response was defined by self-reported improvements in symptoms by Fatigue score, supported by Short Form 36 (SF-36) scores, physical activity measures and other instruments. Repeated measures of outcome variables were assessed by General linear models. Responses were correlated with specific Human Leukocyte Antigen (HLA) alleles. Results: The overall response rate by Fatigue score was 55.0% (22 of 40 patients). Fatigue score and other outcome variables showed significant improvements compared to baseline. The SF-36 Physical Function score increased from mean 33.0 at baseline to 51.5 at 18 months (all patients), and from mean 35.0 to 69.5 among responders. Mean steps per 24 h increased from mean 3,199 at baseline to 4,347 at 18 months (all patients), and from 3,622 to 5,589 among responders. At extended follow-up to 4 years 68% (15 of 22 responders) were still in remission. Patients positive for HLA-DQB1*03:03 and/or HLA-C*07:04 (n = 12) had significantly higher response rate compared to patients negative for these alleles (n = 28), 83 vs. 43%, respectively. Nausea and constipation were common grade 1–2 adverse events. There were one suspected unexpected serious adverse reaction (aggravated POTS) and 11 serious adverse events in eight patients. Conclusion: Intravenous cyclophosphamide treatment was feasible for ME/CFS patients and associated with an acceptable toxicity profile. More than half of the patients responded and with prolonged follow-up, a considerable proportion of patients reported ongoing remission. Without a placebo group, clinical response data must be interpreted with caution. We nevertheless believe a future randomized trial is warranted.

• Lande, Asgeir; Fluge, Øystein; Strand, Elin Bolle; Flåm, Siri Tennebø; Duarte, Sosa Daysi & Mella, Olav [Show all 10 contributors for this article] (2020). Human Leukocyte Antigen Alleles Associated With Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Scientific Reports. 10:5267(1), p. 1–8. doi: 10.1038/s41598-020-62157-x. Full text in Research Archive Show summary

  The etiology and pathogenesis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) are unknown, and autoimmunity is one of many proposed underlying mechanisms. Human Leukocyte Antigen (HLA) associations are hallmarks of autoimmune disease, and have not been thoroughly investigated in a large ME/CFS patient cohort. We performed high resolution HLA -A, -B, -C, -DRB1, -DQB1 and -DPB1 genotyping by next generation sequencing in 426 adult, Norwegian ME/CFS patients, diagnosed according to the Canadian Consensus Criteria. HLA associations were assessed by comparing to 4511 healthy and ethnically matched controls. Clinical information was collected through questionnaires completed by patients or relatives. We discovered two independent HLA associations, tagged by the alleles HLA-C*07:04 (OR 2.1 [95% CI 1.4–3.1]) and HLA-DQB1*03:03 (OR 1.5 [95% CI 1.1–2.0]). These alleles were carried by 7.7% and 12.7% of ME/CFS patients, respectively. The proportion of individuals carrying one or both of these alleles was 19.2% in the patient group and 12.2% in the control group (OR 1.7 [95% CI 1.3–2.2], pnc = 0.00003). ME/CFS is a complex disease, potentially with a substantial heterogeneity. We report novel HLA associations pointing toward the involvement of the immune system in ME/CFS pathogenesis.

• Heinicke, Fatima; Zhong, Xiangfu; Zucknick, Karola Manuela; Breidenbach, Johannes; Sundaram, Arvind Yegambaram Meenakshi & Flåm, Siri Tennebø [Show all 11 contributors for this article] (2020). An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biology. ISSN 1547-6286. 17(9), p. 1284–1292. doi: 10.1080/15476286.2020.1761081. Full text in Research Archive Show summary

  High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. We recently compared the performance (sensitivity, reliability, titration response and differential expression) of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. NEXTflex demonstrated the highest sensitivity, which may reflect its use of partially-randomized adapter sequences, but overall performance was lower than the QIAseq and TailorMix kits. NEBNext showed intermediate performance. We reaffirm that biases are kit specific, complicating the comparison of miRNA datasets generated using different kits.

• Tapia, German; Mortimer, Georgina; Ye, Jody; Mårild, Karl Staffan; Chipper-Keating, Saranna & Gillard, Benjamin Thomas [Show all 11 contributors for this article] (2020). Maternal microchimerism in cord blood and risk of celiac disease in childhood. Journal of Pediatric Gastroenterology and Nutrition - JPGN. ISSN 0277-2116. 71(3), p. 321–327. doi: 10.1097/MPG.0000000000002811. Full text in Research Archive Show summary

  Objectives: During pregnancy, small quantities of maternal cells are naturally transmitted to the fetus. This transmission, termed maternal microchimerism (MMc), has been implicated in autoimmune diseases but its potential role is unclear. We aimed to investigate if MMc at birth predicted childhood celiac disease (CD) risk, a common immune-mediated enteropathy often presenting in childhood. Methods: We designed a case-control study, nested in the Norwegian Mother, Father and Child Cohort. Participants were HLA class II typed to determine noninherited, nonshared maternal alleles (NIMA). Droplet digital (dd) PCR assays specific for common HLA class II NIMAs (HLA-DQB1∗03:01, ∗04:02 and ∗06:02/03) were used to estimate the quantity of maternal DNA, as a marker of maternal cells, in cord blood DNA from 124 children who later developed clinically diagnosed CD (median age at end of study 7.4 years, range 3.6–12.9) and 124 random controls. We tested whether presence of MMc was associated with CD using logistic regression, and compared ranks between cases and controls. Results: MMc, for example, maternal HLA antigens not inherited by the child, was found in 42% of cases and 43% of controls, and not associated with CD (odds ratio [OR] 0.97, 95% confidence interval [CI] 0.58–1.60). The ranks of MMc quantities in cases and controls were also similar (Mann-Whitney U-test, P = 0.71). The subgroup with HLA-DQB1:03∗01 as their NIMA had a potential association with MMc, where levels greater than median was associated with CD (OR 3.78, 95% CI 1.28–11.18). Conclusion: MMc measured in cord blood was not associated with later risk of CD.

• Gjefsen, Elisabeth; Bråten, Lars Christian Haugli; Goll, Guro Løvik; Wigemyr, Monica; Bolstad, Nils & Valberg, Morten [Show all 27 contributors for this article] (2020). The effect of infliximab in patients with chronic low back pain and Modic changes (the BackToBasic study): study protocol of a randomized, double blind, placebo-controlled, multicenter trial. BMC Musculoskeletal Disorders. 21:698, p. 1–14. doi: 10.1186/s12891-020-03720-5. Full text in Research Archive Show summary

  Low back pain is common and a significant number of patients experience chronic low back pain. Current treatment options offer small to moderate effects. Patients with vertebral bone marrow lesions visualized as Modic changes on magnetic resonance imaging may represent a subgroup within the low back pain population. There is evidence for inflammatory mediators being involved in development of Modic changes; hence, suppression of inflammation could be a treatment strategy for these patients. This study examines the effect of anti-inflammatory treatment with the TNF-α inhibitor infliximab in patients with chronic low back pain and Modic changes.Methods/design: The BackToBasic trial is a multicenter, double blind, randomized controlled trial conducted at six hospitals in Norway, comparing intravenous infusions with infliximab with placebo. One hundred twenty-six patients aged 18–65 with chronic low back pain and type 1 Modic changes will be recruited from secondary care outpatients’ clinics. The primary outcome is back pain-specific disability at day 154 (5 months). The study is designed to detect a difference in change of 10 (SD 18) in the Oswestry Disability Index at day 154/ 5 months. The study also aims to refine MRI-assessment, investigate safety and cost-effectiveness and explore the underlying biological mechanisms of Modic changes..Discussion: Finding treatments that target underlying mechanisms could pose new treatment options for patients with low back pain. Suppression of inflammation could be a treatment strategy for patients with low back pain and Modic changes. This paper presents the design of the BackToBasic study, where we will assess the effect of an anti-inflammatory treatment versus placebo in patients with chronic low back pain and type 1 Modic changes.

• Juvodden, Hilde Therese; Viken, Marte Kathrine; Nordstrand, Sebjørg Elizabeth Hesla; Viste, Rannveig; Westlye, Lars Tjelta & Thorsby, Per Medbøe [Show all 8 contributors for this article] (2020). HLA and sleep parameter associations in post-H1N1 narcolepsy type 1 patients and first-degree relatives. Sleep. ISSN 0161-8105. 43(3), p. 1–11. doi: 10.1093/sleep/zsz239. Full text in Research Archive Show summary

  Abstract Study Objectives To explore HLA (human leukocyte antigen) in post-H1N1 narcolepsy type 1 patients (NT1), first-degree relatives and healthy controls, and assess HLA associations with clinical and sleep parameters in patients and first-degree relatives. Methods Ninety post-H1N1 NT1 patients and 202 of their first-degree relatives were HLA-genotyped (next generation sequencing) and phenotyped (semistructured interviews, Stanford Sleep Questionnaire, polysomnography, and multiple sleep latency test). HLA allele distributions were compared between DQB1*06:02-heterozygous individuals (77 patients, 59 parents, 1230 controls). A subsample (74 patients, 114 relatives) was investigated for associations between HLA-loci and continuous sleep variables using logistic regression. Identified candidate HLA-loci were explored for HLA allele associations with hypnagogic hallucinations and sleep paralysis in 90 patients, and patient allele findings were checked for similar associations in 202 relatives. Results DQB1*06:02 heterozygous post-H1N1 NT1 patients (84.4% H1N1-vaccinated) showed several significant HLA associations similar to those reported previously in samples of mainly sporadic NT1, i.e. DQB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:07, DRB1*11:04, A*25:01, B*35:03, and B*51:01, and novel associations, i.e. B*14:02, C*01:02, and C*07:01. Parents HLA alleles did not deviate significantly from controls. The HLA-C locus was associated with sleep parameters in patients and relatives. In patients C*02:02 seems to be associated with protective effects against sleep paralysis and hypnagogic hallucinations. Conclusions Our findings of similar risk/protective HLA-alleles in post-H1N1 as in previous studies of mainly sporadic narcolepsy support similar disease mechanisms. We also report novel allelic associations. Associations between HLA-C and sleep parameters were seen independent of NT1 diagnosis, supporting involvement of HLA-C in sleep subphenotypes.

• Bråten, Lars Christian Haugli; Rolfsen, Mads Peder; Espeland, Ansgar; Wigemyr, Monica; Assmus, Jörg & Froholdt, Anne [Show all 28 contributors for this article] (2019). Efficacy of antibiotic treatment in patients with chronic low back pain and Modic changes (the AIM study): double blind, randomised, placebo controlled, multicentre trial. The BMJ. 367. doi: 10.1136/bmj.l5654. Full text in Research Archive Show summary

  Objective To assess the efficacy of three months of antibiotic treatment compared with placebo in patients with chronic low back pain, previous disc herniation, and vertebral endplate changes (Modic changes). Design Double blind, parallel group, placebo controlled, multicentre trial. Setting Hospital outpatient clinics at six hospitals in Norway. Participants 180 patients with chronic low back pain, previous disc herniation, and type 1 (n=118) or type 2 (n=62) Modic changes enrolled from June 2015 to September 2017. Interventions Patients were randomised to three months of oral treatment with either 750 mg amoxicillin or placebo three times daily. The allocation sequence was concealed by using a computer generated number on the prescription. Main outcome measures The primary outcome was the Roland-Morris Disability Questionnaire (RMDQ) score (range 0-24) at one year follow-up in the intention to treat population. The minimal clinically important between group difference in mean RMDQ score was predefined as 4. Results In the primary analysis of the total cohort at one year, the difference in the mean RMDQ score between the amoxicillin group and the placebo group was −1.6 (95% confidence interval −3.1 to 0.0, P=0.04). In the secondary analysis, the difference in the mean RMDQ score between the groups was −2.3 (−4.2 to−0.4, P=0.02) for patients with type 1 Modic changes and −0.1 (−2.7 to 2.6, P=0.95) for patients with type 2 Modic changes. Fifty patients (56%) in the amoxicillin group experienced at least one drug related adverse event compared with 31 (34%) in the placebo group. Conclusions In this study on patients with chronic low back pain and Modic changes at the level of a previous disc herniation, three months of treatment with amoxicillin did not provide a clinically important benefit compared with placebo. Secondary analyses and sensitivity analyses supported this finding. Therefore, our results do not support the use of antibiotic treatment for chronic low back pain and Modic changes.

• López-Isac, Elena; Acosta-Herrera, Marialbert; Kerick, Martin; Assassi, Shervin; Satpathy, Ansuman T. & Granja, Jeffrey [Show all 42 contributors for this article] (2019). GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. Nature Communications. 10:4955, p. 1–14. doi: 10.1038/s41467-019-12760-y. Full text in Research Archive Show summary

  Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previous GWASs, in 26,679 individuals and identify 27 independent genome-wide associated signals, including 13 new risk loci. The novel associations nearly double the number of genome-wide hits reported for SSc thus far. We define 95% credible sets of less than 5 likely causal variants in 12 loci. Additionally, we identify specific SSc subtype-associated signals. Functional analysis of high-priority variants shows the potential function of SSc signals, with the identification of 43 robust target genes through HiChIP. Our results point towards molecular pathways potentially involved in vasculopathy and fibrosis, two main hallmarks in SSc, and highlight the spectrum of critical cell types for the disease. This work supports a better understanding of the genetic basis of SSc and provides directions for future functional experiments.

• Zhong, Xiangfu; Heinicke, Fatima; Lie, Benedicte Alexandra & Rayner, Simon (2019). Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies. Non-coding RNA. doi: 10.3390/ncrna5040049. Full text in Research Archive Show summary

  A necessary pre-processing data analysis step is the removal of adapter sequences from the raw reads. While most adapter trimming tools require adapter sequence as an essential input, adapter information is often incomplete or missing. This can impact quantification of features, reproducibility of the study and might even lead to erroneous conclusions. Here, we provide examples to highlight the importance of specifying the adapter sequence by demonstrating the effect of using similar but different adapter sequences and identify additional potential sources of errors in the adapter trimming step. Finally, we propose solutions by which users can ensure their small RNA-seq data is fully annotated with adapter information.

• Heinicke, Fatima; Zhong, Xiangfu; Zucknick, Manuela; Breidenbach, Johannes; Sundaram, Arvind Yegambaram Meenakshi & Flåm, Siri Tennebø [Show all 21 contributors for this article] (2019). Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biology. ISSN 1547-6286. 17(1), p. 75–86. doi: 10.1080/15476286.2019.1667741. Full text in Research Archive Show summary

  High-throughput sequencing is increasingly favoured to assay the presence and abundance of microRNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. Although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling <100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers (UMI) sequence tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of synthetic miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the relative levels of the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.

• Tapia, German; Mortimer, Georgina; Ye, Jody; Gillard, Benjamin Thomas; Chipper-Keating, Saranna & Mårild, Karl Staffan [Show all 14 contributors for this article] (2019). Maternal microchimerism in cord blood and risk of childhood-onset type 1 diabetes. Pediatric Diabetes. ISSN 1399-543X. 20(6), p. 728–735. doi: 10.1111/pedi.12875. Full text in Research Archive Show summary

  Background: Maternal microchimerism (MMc), the transmission of small quantities of maternal cells to the fetus, is relatively common and persistent. MMc has been detected with increased frequency in the circulation and pancreas of type 1 diabetes (T1D) patients. We investigated for the first time whether MMc levels at birth predict future T1D risk. We also tested whether cord blood MMc predicted MMc in samples taken at T1D diagnosis. Methods: Participants in the Norwegian Mother and Child Cohort study were human leukocyte antigen (HLA) class II typed to determine non‐inherited, non‐shared maternal alleles (NIMA). Droplet digital (dd) polymerase chain reaction (PCR) assays specific for common HLA class II NIMA (HLADQB1*03:01, *04:02, and *06:02/03) were developed and validated. MMc was estimated as maternal DNA quantity in the fetal circulation, by NIMA specific ddPCR, measured in cord blood DNA from 71 children who later developed T1D and 126 controls within the cohort. Results: We found detectable quantities of MMc in 34/71 future T1D cases (48%) and 53/126 controls (42%) (adjusted odds ratio [aOR] 1.27, 95% confidence interval (CI) 0.68‐2.36), and no significant difference in ranks of MMc quantities between cases and controls (Mann‐Whitney P = .46). There was a possible association in the NIMA HLA‐DQB1*03:01subgroup with later T1D (aOR 3.89, 95%CI 1.05‐14.4). MMc in cord blood was not significantly associated with MMc at T1D diagnosis. Conclusions: Our findings did not support the hypothesis that the degree of MMc in cord blood predict T1D risk. The potential subgroup association with T1D risk should be replicated in a larger cohort.

• Tapia, German; Mårild, Karl Staffan; Dahl, Sandra Rinne; Lund-Blix, Nicolai Andre; Viken, Marte K & Lie, Benedicte Alexandra [Show all 12 contributors for this article] (2019). Maternal and Newborn Vitamin D-Binding Protein, Vitamin D Levels, Vitamin D Receptor Genotype, and Childhood Type 1 Diabetes. Diabetes Care. ISSN 0149-5992. 42(4), p. 553–559. doi: 10.2337/dc18-2176. Full text in Research Archive Show summary

  OBJECTIVE Circumstantial evidence links 25-hydroxy vitamin D [25(OH)D], vitamin D–binding protein (DBP), vitamin D–associated genes, and type 1 diabetes (T1D), but no studies have jointly analyzed these. We aimed to investigate whether DBP levels during pregnancy or at birth were associated with offspring T1D and whether vitamin D pathway genetic variants modified associations between DBP, 25(OH)D, and T1D. RESEARCH DESIGN AND METHODS From a cohort of >100,000 mother/child pairs, we analyzed 189 pairs where the child later developed T1D and 576 random control pairs. We measured 25(OH)D using liquid chromatography–tandem mass spectrometry, and DBP using polyclonal radioimmunoassay, in cord blood and maternal plasma samples collected at delivery and midpregnancy. We genotyped mother and child for variants in or near genes involved in vitamin D metabolism (GC, DHCR7, CYP2R1, CYP24A1, CYP27B1, and VDR). Logistic regression was used to estimate odds ratios (ORs) adjusted for potential confounders. RESULTS Higher maternal DBP levels at delivery, but not in other samples, were associated with lower offspring T1D risk (OR 0.86 [95% CI 0.74–0.98] per μmol/L increase). Higher cord blood 25(OH)D levels were associated with lower T1D risk (OR = 0.87 [95% CI 0.77–0.98] per 10 nmol/L increase) in children carrying the VDR rs11568820 G/G genotype (Pinteraction = 0.01 between 25(OH)D level and rs11568820). We did not detect other gene-environment interactions. CONCLUSIONS Higher maternal DBP level at delivery may decrease offspring T1D risk. Increased 25(OH)D levels at birth may decrease T1D risk, depending on VDR genotype. These findings should be replicated in other studies. Future studies of vitamin D and T1D should include VDR genotype and DBP levels.

• Gabrielsen, Ingvild Synnøve Matre; Helgeland, Hanna; Akselsen, Helle; Aass, Hans Christian Dalsbotten; Sundaram, Arvind Yegambaram Meenakshi & Snowhite, Isaac V. [Show all 9 contributors for this article] (2019). Transcriptomes of antigen presenting cells in human thymus. PLOS ONE. 14:e0218858(7), p. 1–18. doi: 10.1371/journal.pone.0218858. Full text in Research Archive Show summary

  Antigen presenting cells (APCs) in the thymus play an essential role in the establishment of central tolerance, i.e. the generation of a repertoire of functional and self-tolerant T cells to prevent autoimmunity. In this study, we have compared the transcriptomes of four primary APCs from human thymus (mTECs, CD19+ B cells, CD141+ and CD123+ DCs). We investigated a set of genes including the HLA genes, genes encoding transcriptional regulators and finally, tissue-enriched genes, i.e, genes with a five-fold higher expression in a particular human tissue. We show that thymic CD141+ DCs express the highest levels of all classical HLA genes and 67% (14/21) of the HLA class I and II pathway genes investigated in this study. CD141+ DCs also expressed the highest levels of the transcriptional regulator DEAF1, whereas AIRE and FEZF2 expression were mainly found in primary human mTECs. We found expression of “tissue enriched genes” from the Human Protein Atlas (HPA) in all four APC types, but the mTECs were clearly dominating in the number of uniquely expressed tissue enriched genes (20% in mTECs, 7% in CD19+ B cells, 4% in CD123+ DCs and 2% in CD141+ DCs). The tissue enriched genes also overlapped with reported human autoantigens. This is, to our knowledge, the first study that performs RNA sequencing of mTECs, CD19+ B cells, CD141+ and CD123+ DCs isolated from the same individuals and provides insight into the transcriptomes of these human thymic APCs.

• Kjeldsen-Kragh, Jens; Titze, Thomas Larsen; Lie, Benedicte Alexandra; Vaage, John T. & Kjær, Mette (2019). HLA-DRB3*01:01 exhibits a dose-dependent impact on HPA-1a antibody levels in HPA-1a-immunized women. Blood Advances. ISSN 2473-9529. 3(7), p. 945–951. doi: 10.1182/bloodadvances.2019032227. Full text in Research Archive Show summary

  HLA-DRB3*01:01 is a predisposing factor for human platelet antigen 1a (HPA-1a) immunization, which is responsible for most cases of fetal and neonatal alloimmune thrombocytopenia. The aim of this study was to investigate if the HLA-DRB3*01:01 allele imposes a dose-dependent effect on anti-HPA-1a levels and neonatal platelet counts. One hundred and thirty HPA-1a–immunized women were divided into 3 groups: HLA-DRB3*01:01 negative, HLA-DRB3*01:01 hemizygous or heterozygous, and HLA-DRB3*01:01 homozygous. The dose of the HLA-DRB3*01:01 allele was determined by sequencing exon 2 of the HLA-DRB3 gene followed by HLA-DRB3 and HLA-DRB1 typing of selected samples. Anti-HPA-1a levels at time of delivery and neonatal platelet counts were compared among groups. There was a significant dose-dependent effect of the HLA-DRB3*01:01 allele on anti-HPA-1a levels (global P value [Pglobal] = .0032). Median (range) anti-HPA-1a levels were 1.5 IU/mL (0.0-19.0 IU/mL), 21.1 IU/mL (0.0-1967 IU/mL), and 43.7 IU/mL (1.0-980 IU/mL) in women with 0, 1, and 2 copies of the HLA-DRB3*01:01 allele, respectively. There was also a significant, but opposite, dose-dependent effect of the mother’s HLA-DRB3*01:01 allele on the platelet count of the newborn (Pglobal = .0155). Median (range) neonatal platelet counts were 241 × 109/L (59 × 109/L to 393 × 109/L), 107 × 109/L (4 × 109/L to 387 × 109/L) and 32 × 109/L (4 × 109/L to 352 × 109/L) for newborns of mothers with 0, 1, and 2 copies of the HLA-DRB3*01:01 allele, respectively. Thus, the HLA-DRB3*01:01 allele exhibits a dose-dependent impact on maternal anti-HPA-1a levels in HPA-1a–immunized women.

• Guderud, Kari; Mæhlen, Marthe Thoresen; Namløs, Gry Beate; Viken, Marte K; Kulle, Bettina & Molberg, Øyvind [Show all 8 contributors for this article] (2018). Lack of association among peptidyl arginine deiminase type 4 autoantibodies, PADI4 polymorphisms, and clinical characteristics in rheumatoid arthritis. Journal of Rheumatology. ISSN 0315-162X. 45(9), p. 1211–1219. doi: 10.3899/jrheum.170769. Full text in Research Archive Show summary

  Objective.We aimed to jointly investigate the role of antipeptidyl arginine deiminase type 4 antibodies (anti-PAD4) and polymorphisms in the PADI4 gene together with clinical variables in rheumatoid arthritis (RA). Methods. Serum IgG autoantibodies to human recombinant PAD4 were identified by DELFIA technique in 745 patients with RA (366 available from previous studies). Genotyping of PADI4 was performed using TaqMan assays in 945 patients and 1118 controls. Clinical data, anticitrullinated protein antibodies (ACPA) status, shared epitope status, and a combined genetic risk score were also available. Results. Anti-PAD4 antibodies were detected in 193 (26%) of 745 patients with RA; 149 (77%) of these were also ACPA-positive. No association was observed between anti-PAD4 status and clinical characteristics, PADI4 polymorphisms, or genetic risk scores after stratification for ACPA status. Conclusion. Taken together, the results from these combined serological, genetic, and clinical analyses suggest that anti-PAD4 appears to be a bystander autoantibody with no current clinical utility in RA. (First Release June 1 2018; J Rheumatol 2018;45:1211–19; doi:10.3899/jrheum.170769)

• Størdal, Ketil; McArdle, Harry J.; Hayes, Helen; Tapia, German; Viken, Marte K & Lund-Blix, Nicolai Andre [Show all 17 contributors for this article] (2018). Prenatal iron exposure and childhood type 1 diabetes. Scientific Reports. 8. doi: 10.1038/s41598-018-27391-4. Full text in Research Archive Show summary

  Iron overload due to environmental or genetic causes have been associated diabetes. We hypothesized that prenatal iron exposure is associated with higher risk of childhood type 1 diabetes. In the Norwegian Mother and Child cohort study (n = 94,209 pregnancies, n = 373 developed type 1 diabetes) the incidence of type 1 diabetes was higher in children exposed to maternal iron supplementation than unexposed (36.8/100,000/year compared to 28.6/100,000/year, adjusted hazard ratio 1.33, 95%CI: 1.06–1.67). Cord plasma biomarkers of high iron status were non-significantly associated with higher risk of type 1 diabetes (ferritin OR = 1.05 [95%CI: 0.99–1.13] per 50 mg/L increase; soluble transferrin receptor: OR = 0.91 [95%CI: 0.81–1.01] per 0.5 mg/L increase). Maternal but not fetal HFE genotypes causing high/intermediate iron stores were associated with offspring diabetes (odds ratio: 1.45, 95%CI: 1.04, 2.02). Maternal anaemia or non-iron dietary supplements did not significantly predict type 1 diabetes. Perinatal iron exposures were not associated with cord blood DNA genome-wide methylation, but fetal HFE genotype was associated with differential fetal methylation near HFE. Maternal cytokines in mid-pregnancy of the pro-inflammatory M1 pathway differed by maternal iron supplements and HFE genotype. Our results suggest that exposure to iron during pregnancy may be a risk factor for type 1 diabetes in the offspring.

• Lande, Asgeir; Andersen, Irene; Egeland, Torstein; Lie, Benedicte Alexandra & Viken, Marte K (2018). HLA -A, -C, -B, -DRB1, -DQB1 and -DPB1 allele and haplotype frequencies in 4514 healthy Norwegians. Human Immunology. ISSN 0198-8859. 79(7), p. 527–529. doi: 10.1016/j.humimm.2018.04.012. Full text in Research Archive
• Mitrovic, Mitja; Patsopoulos, Nikolaos A.; Beecham, Ashley H.; Dankowski, Theresa; Goris, An & Dubois, Benedicte [Show all 52 contributors for this article] (2018). Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk. Cell. ISSN 0092-8674. 175(6), p. 1679–1687. doi: 10.1016/j.cell.2018.09.049. Full text in Research Archive Show summary

  Multiple sclerosis is a complex neurological disease, with ∼20% of risk heritability attributable to common genetic variants, including >230 identified by genome-wide association studies. Multiple strands of evidence suggest that much of the remaining heritability is also due to additive effects of common variants rather than epistasis between these variants or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that up to 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common-variant signals, highlighting key pathogenic roles for regulatory T cell homeostasis and regulation, IFNγ biology, and NFκB signaling. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS.

• Mårild, Karl; Tapia, German; Haugen, Margaretha; Dahl, Sandra Rinne; Cohen, Arieh S. & Lundqvist, Marika [Show all 9 contributors for this article] (2017). Maternal and neonatal vitamin D status, genotype and childhood celiac disease. PLOS ONE. 12(7). doi: 10.1371/journal.pone.0179080. Full text in Research Archive Show summary

  Background: Low concentration of 25-hydroxyvitamin D during pregnancy may be associated with offspring autoimmune disorders. Little is known about environmental triggers except gluten for celiac disease, a common immune-mediated disorder where seasonality of birth has been reported as a risk factor. We therefore aimed to test whether low maternal and neonatal 25-hydroxyvitamin D predicted higher risk of childhood celiac disease. Methods and Findings: In this Norwegian nationwide pregnancy cohort (n = 113,053) and nested case-control study, we analyzed 25-hydroxyvitamin D in maternal blood from mid-pregnancy, postpartum and cord plasma of 416 children who developed celiac disease and 570 randomly selected controls. Mothers and children were genotyped for established celiac disease and vitamin D metabolism variants. We used mixed linear regression models and logistic regression to study associations. There was no significant difference in average 25-hydroxyvitamin D between cases and controls (63.1 and 62.1 nmol/l, respectively, p = 0.28), and no significant linear trend (adjusted odds ratio per 10 nM increase 1.05, 95% CI: 0.93–1.17). Results were similar when analyzing the mid-pregnancy, postpartum or cord plasma separately. Genetic variants for vitamin D deficiency were not associated with celiac disease (odds ratio per risk allele of the child, 1.00; 95% CI, 0.90 to 1.10, odds ratio per risk allele of the mother 0.94; 95% CI 0.85 to 1.04). Vitamin D intake in pregnancy or by the child in early life did not predict later celiac disease. Adjustment for established genetic risk markers for celiac disease gave similar results. Conclusions: We found no support for the hypothesis that maternal or neonatal vitamin D status is related to the risk of childhood celiac disease.

• Popperud, Trine Haug; Viken, Marte K; Kerty, Emilia & Lie, Benedicte Alexandra (2017). Juvenile myasthenia gravis in Norway: HLA-DRB1*04:04 is positively associated with prepubertal onset. PLOS ONE. 12:e0186383(10), p. 1–9. doi: 10.1371/journal.pone.0186383. Full text in Research Archive
• Witoelar, Aree; Jansen, Iris E.; Wang, Yunpeng; Desikan, Rahul S.; Gibbs, J. Raphael & Thompson, Wesley Kurt [Show all 26 contributors for this article] (2017). Genome-wide pleiotropy between Parkinson disease and autoimmune diseases. JAMA Neurology. ISSN 2168-6149. 74(7), p. 780–792. doi: 10.1001/jamaneurol.2017.0469. Full text in Research Archive
• Viken, Marte K; Flåm, Siri Tennebø; Skrivarhaug, Torild; Amundsen, Silja Svanstrøm; Sollid, Ludvig Magne & Drivvoll, Ann Kristin [Show all 9 contributors for this article] (2017). HLA class II alleles in Norwegian patients with coexisting type 1 diabetes and celiac disease. HLA. ISSN 2059-2302. 89(5), p. 278–284. doi: 10.1111/tan.12986. Full text in Research Archive
• Henriksen, Eva Kristine Klemsdal; Viken, Marte K; Wittig, Michael; Holm, Kristian; Folseraas, Trine & Mucha, Sören [Show all 29 contributors for this article] (2017). HLA haplotypes in primary sclerosing cholangitis patients of admixed and non-European ancestry. HLA. ISSN 2059-2302. 90(4), p. 228–233. doi: 10.1111/tan.13076. Full text in Research Archive
• Størdal, Ketil; Mårild, Karl; Tapia, German; Haugen, Margaretha; Cohen, Arieh S & Lie, Benedicte Alexandra [Show all 7 contributors for this article] (2017). Fetal and maternal genetic variants influencing neonatal vitamin D status. Journal of Clinical Endocrinology and Metabolism (JCEM). ISSN 0021-972X. 102(11), p. 4072–4079. doi: 10.1210/jc.2017-00827. Full text in Research Archive
• Hov, Johannes Espolin Roksund; Boberg, Kirsten Muri; Taraldsrud, Eli; Vesterhus, Mette; Boyadzhieva, Maria & Solberg, Inger Camilla [Show all 11 contributors for this article] (2017). Antineutrophil antibodies define clinical and genetic subgroups in primary sclerosing cholangitis. Liver international (Print). ISSN 1478-3223. 37(3), p. 458–465. doi: 10.1111/liv.13238. Full text in Research Archive
• Valentin, Mev Dominguez; Navarro, Andrea Gras; Rahman, Mohummad Aminur; Kumar, Surendra; Retière, Christèle & Ulvestad, Elling [Show all 14 contributors for this article] (2016). Identification of a natural killer cell receptor allele that prolongs survival of cytomegalovirus-positive glioblastoma patients. Cancer Research. ISSN 0008-5472. 76(18), p. 5326–5336. doi: 10.1158/0008-5472.CAN-16-1162. Full text in Research Archive
• Carmona, David; Vaglio, Augusto; Mackie, Sarah L; Hernández-Rodríguez, José; Monarch, Paul A & Castaneda, Santos [Show all 46 contributors for this article] (2016). A genome-wide association study identifies risk alleles in plasminogen and P4HA2 associated with giant cell arteritis. American Journal of Human Genetics. ISSN 0002-9297. 100(1), p. 64–74. doi: 10.1016/j.ajhg.2016.11.013. Full text in Research Archive
• Wang, Yunpeng; Bos, Steffan Daniel; Harbo, Hanne Flinstad; Thompson, Wesley K.; Schork, Andrew J. & Bettella, Francesco [Show all 14 contributors for this article] (2016). Genetic overlap between multiple sclerosis and several cardiovascular disease risk factors. Multiple Sclerosis. ISSN 1352-4585. 22(14), p. 1783–1793. doi: 10.1177/1352458516635873. Full text in Research Archive
• Gustavsen, Marte Wendel; Celius, Elisabeth Gulowsen; Winsvold, Bendik K S; Moen, Stine Marit; Nygaard, Gro Owren & Berg-Hansen, Pål [Show all 9 contributors for this article] (2016). Migraine and frequent tension-type headache are not associated with multiple sclerosis in a Norwegian case-control study. Multiple Sclerosis Journal, Experimental, Translational and Clinical. 2, p. 1–4. doi: 10.1177/2055217316682976. Full text in Research Archive Show summary

  Background Inconsistent results have been obtained with regard to headache comorbidity in multiple sclerosis (MS). Objective Investigate the one-year prevalence of migraine and tension-type headache (TTH) in Norwegian MS patients and relate this to clinical parameters. Methods A questionnaire concerning headache was administered to 756 MS patients and 1090 controls and used to determine the one-year prevalence of migraine and frequent TTH. Results No significant differences were seen between patients and controls or between patients with different disease course. Less migraine was observed in patients with Expanded Disability Status Scale score (EDSS) ≥4.0. Conclusions This case-control study does not support an association between migraine or TTH and MS.

• Finkel, Terri H.; Li, Jin; Wei, Zhi; Wang, Wei; Zhang, Haitao & Behrens, Edward M. [Show all 33 contributors for this article] (2016). Variants in CXCR4 associate with juvenile idiopathic arthritis susceptibility. BMC Medical Genetics. 17(1). doi: 10.1186/s12881-016-0285-3. Full text in Research Archive
• Gabrielsen, Ingvild; Viken, Marte K; Amundsen, Svanstrøm Silja; Helgeland, Hanna; Holm, Kristian & Flåm, Siri Tennebø [Show all 7 contributors for this article] (2016). Autoimmune risk variants in ERAP2 are associated with gene-expression levels in thymus. Genes and Immunity. ISSN 1466-4879. 17(7), p. 406–411. doi: 10.1038/gene.2016.39. Full text in Research Archive
• Gabrielsen, Ingvild; Amundsen, Svanstrøm Silja; Helgeland, Hanna; Flåm, Siri Tennebø; Hatinoor, Nimo & Holm, Kristian [Show all 8 contributors for this article] (2016). Genetic risk variants for autoimmune diseases that influence gene expression in thymus. Human Molecular Genetics. ISSN 0964-6906. 25(14), p. 3117–3124. doi: 10.1093/hmg/ddw152. Full text in Research Archive Show summary

  Genome-wide association studies (GWAS) have boosted our knowledge of genetic risk variants in autoimmune diseases (AIDs). Most risk variants are located within or near genes with immunological functions, and the majority is found to be non-coding, pointing towards a regulatory role. In this study, we performed a cis expression quantitative trait locus (eQTL) screen restricted to 353 AID associated risk variants selected from the GWAS catalog to investigate whether these single nucleotide polymorphisms (SNPs) influence gene expression in thymus. Genotypes were obtained by Immunochip (Ichip) and tested against expression of surrounding genes (±1 Mb) in human thymic tissue (n = 42). We identified eight significant eQTLs located within seven genetic regions (FCRL3, RNASET2, C2orf74, NPIPB8, SIRPG, SYS1 and AJ006998.2) where the expression was associated with AID risk SNPs at a study-wide level of significance (P < 2.7 × 10-5). In NPIPB8 and AJ006998.2, the eQTL signals appeared to be thymus-specific. Furthermore, many AID risk SNPs from GWAS have been subsequently fine-mapped in recent Ichip projects, and fine-mapped AID SNPs overlapped with the thymic eQTLs within RNASET2 and SIRPG Finally, in all the eQTL regions, except C2orf74, SNPs underlying the thymic eQTLs were predicted to interfere with transcription factors important in T cell development. Our study therefore reveals autoimmune risk variants that act as eQTLs in thymus, and suggest that thymic gene regulation may play a functional role at some AID risk loci.

• Flåm, Siri Tennebø; Gunnarsson, Ragnar; Garen, Torhild Oddveig; Lie, Benedicte Alexandra & Molberg, Øyvind (2015). The HLA profiles of mixed connective tissue disease differ distinctly from the profiles of clinically related connective tissue diseases. Rheumatology. ISSN 1462-0324. 54(3), p. 528–535. doi: 10.1093/rheumatology/keu310. Full text in Research Archive
• Chiaroni-Clarke, Rachel C.; Li, Yun R.; Munro, Jane E.; Chavez, Raul A.; Scurrah, Katrina J. & Pezic, Angela [Show all 21 contributors for this article] (2015). The association of PTPN22 rs2476601 with juvenile idiopathic arthritis is specific to females. Genes and Immunity. ISSN 1466-4879. 16(7), p. 495–498. doi: 10.1038/gene.2015.32. Full text in Research Archive
• Li, Yun R.; Li, Jin; Zhao, Sihai D.; Bradfield, Jonathan P.; Mentch, Frank D. & Maggadóttir, Sólrún Melkorka [Show all 66 contributors for this article] (2015). Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nature Medicine. ISSN 1078-8956. 21(9), p. 1018–1027. doi: 10.1038/nm.3933. Full text in Research Archive
• Gustavsen, Marte Wendel; Celius, Elisabeth Gulowsen; Moen, Stine Marit; Bjølgerud, Anja; Berg-Hansen, Pål & Nygaard, Gro Owren [Show all 9 contributors for this article] (2015). No association between multiple sclerosis and periodontitis after adjusting for smoking habits. European Journal of Neurology. ISSN 1351-5101. 22(3), p. 588–590. doi: 10.1111/ene.12520. Full text in Research Archive
• Ellis, Justine A.; Scurrah, Katrina J.; Li, Yun R.; Ponsonby, Anne-Louise; Chavez, Raul A. & Pezic, Angela [Show all 19 contributors for this article] (2015). Epistasis amongst PTPN2 and genes of the vitamin D pathway contributes to risk of juvenile idiopathic arthritis. Journal of Steroid Biochemistry and Molecular Biology. ISSN 0960-0760. 145, p. 113–120. doi: 10.1016/j.jsbmb.2014.10.012. Full text in Research Archive
• Bossini-Castillo, Lara; Kovel, Carolien G.F. de; Källberg, Henrik; Slot, Ruben van't; Italiaander, Annet & Coenen, Marieke J.H. [Show all 36 contributors for this article] (2015). A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides. Annals of the Rheumatic Diseases. ISSN 0003-4967. 74(e15). doi: 10.1136/annrheumdis-2013-204591. Full text in Research Archive
• Seldin, Michael F.; Alkhairy, Omar K; Lee, Annette T.; Lamb, Janine; Sussman, Jon & Pirskanen-Matell, Ritva [Show all 19 contributors for this article] (2015). Genome-wide association study of late-onset myasthenia gravis: Confirmation of TNFRSF11A and identification of ZBTB10 and three distinct HLA associations. Molecular medicine (Cambridge, Mass. Print). ISSN 1076-1551. 21, p. 769–781. doi: 10.2119/molmed.2015.00232. Full text in Research Archive Show summary

  To investigate the genetics of late-onset myasthenia gravis (LOMG), we conducted a genome-wide association study imputation of >6 million single nucleotide polymorphisms (SNPs) in 532 LOMG cases (anti–acetylcholine receptor [AChR] antibody positive; onset age ≥50 years) and 2,128 controls matched for sex and population substructure. The data confirm reported TNFRSF11A associations (rs4574025, P = 3.9 × 10–7, odds ratio [OR] 1.42) and identify a novel candidate gene, ZBTB10, achieving genome-wide significance (rs6998967, P = 8.9 × 10–10, OR 0.53). Several other SNPs showed suggestive significance including rs2476601 (P = 6.5 × 10–6, OR 1.62) encoding the PTPN22 R620W variant noted in early-onset myasthenia gravis (EOMG) and other autoimmune diseases. In contrast, EOMG-associated SNPs in TNIP1 showed no association in LOMG, nor did other loci suggested for EOMG. Many SNPs within the major histocompatibility complex (MHC) region showed strong associations in LOMG, but with smaller effect sizes than in EOMG (highest OR ~2 versus ~6 in EOMG). Moreover, the strongest associations were in opposite directions from EOMG, including an OR of 0.54 for DQA1*05:01 in LOMG (P = 5.9 × 10–12) versus 2.82 in EOMG (P = 3.86 × 10–45). Association and conditioning studies for the MHC region showed three distinct and largely independent association peaks for LOMG corresponding to (a) MHC class II (highest attenuation when conditioning on DQA1), (b) HLA-A and (c) MHC class III SNPs. Conditioning studies of human leukocyte antigen (HLA) amino acid residues also suggest potential functional correlates. Together, these findings emphasize the value of subgrouping myasthenia gravis patients for clinical and basic investigations and imply distinct predisposing mechanisms in LOMG.

• Andreassen, Ole Andreas; Harbo, Hanne Flinstad; Wang, Yunpeng; Thompson, WK; Schork, AJ & Mattingsdal, Morten [Show all 18 contributors for this article] (2015). Genetic pleiotropy between multiple sclerosis and schizophrenia but not bipolar disorder: differential involvement of immune-related gene loci. Molecular Psychiatry. ISSN 1359-4184. 20(2), p. 207–214. doi: 10.1038/mp.2013.195. Full text in Research Archive Show summary

  Converging evidence implicates immune abnormalities in schizophrenia (SCZ), and recent genome-wide association studies (GWAS) have identified immune-related single-nucleotide polymorphisms (SNPs) associated with SCZ. Using the conditional false discovery rate (FDR) approach, we evaluated pleiotropy in SNPs associated with SCZ (n=21 856) and multiple sclerosis (MS) (n=43 879), an inflammatory, demyelinating disease of the central nervous system. Because SCZ and bipolar disorder (BD) show substantial clinical and genetic overlap, we also investigated pleiotropy between BD (n=16 731) and MS. We found significant genetic overlap between SCZ and MS and identified 21 independent loci associated with SCZ, conditioned on association with MS. This enrichment was driven by the major histocompatibility complex (MHC). Importantly, we detected the involvement of the same human leukocyte antigen (HLA) alleles in both SCZ and MS, but with an opposite directionality of effect of associated HLA alleles (that is, MS risk alleles were associated with decreased SCZ risk). In contrast, we found no genetic overlap between BD and MS. Considered together, our findings demonstrate genetic pleiotropy between SCZ and MS and suggest that the MHC signals may differentiate SCZ from BD susceptibility.

• Cortes, Adrian; Pulit, Sara L.; Leo, Paul J.; Pointon, Jenny J.; Robinson, Philip C. & Weisman, Michael H. [Show all 48 contributors for this article] (2015). Major histocompatibility complex associations of ankylosing spondylitis are complex and involve further epistasis with ERAP1. Nature Communications. 6. doi: 10.1038/ncomms8146. Full text in Research Archive Show summary

  Abstract Ankylosing spondylitis (AS) is a common, highly heritable, inflammatory arthritis for which HLA-B*27 is the major genetic risk factor, although its role in the aetiology of AS remains elusive. To better understand the genetic basis of the MHC susceptibility loci, we genotyped 7,264 MHC SNPs in 22,647 AS cases and controls of European descent. We impute SNPs, classical HLA alleles and amino-acid residues within HLA proteins, and tested these for association to AS status. Here we show that in addition to effects due to HLA-B*27 alleles, several other HLA-B alleles also affect susceptibility. After controlling for the associated haplotypes in HLA-B , we observe independent associations with variants in the HLA-A , HLA-DPB1 and HLA-DRB1 loci. We also demonstrate that the ERAP1 SNP rs30187 association is not restricted only to carriers of HLA-B*27 but also found in HLA-B*40:01 carriers independently of HLA-B*27 genotype.

• Hov, Johannes Espolin Roksund; Zhong, Huanzi; Qin, Bincai; Anmarkrud, Jarl Andreas; Holm, Kristian & Franke, Andre [Show all 8 contributors for this article] (2015). The influence of the autoimmunity-associated ancestral HLA haplotype AH8.1 on the human gut microbiota: A cross-sectional study. PLOS ONE. 10:e0133804(7). doi: 10.1371/journal.pone.0133804. Full text in Research Archive
• Andreassen, Ole Andreas; Desikan, Rahul S.; Wang, Yunpeng; Thompson, Wesley K.; Schork, Andrew J. & Zuber, Verena [Show all 18 contributors for this article] (2015). Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms. PLOS ONE. 10:e 0123057(4). doi: 10.1371/journal.pone.0123057. Full text in Research Archive Show summary

  Epidemiological studies suggest a relationship between blood lipids and immune-mediated diseases, but the nature of these associations is not well understood. We used genome-wide association studies (GWAS) to investigate shared single nucleotide polymorphisms (SNPs) between blood lipids and immune-mediated diseases. We analyzed data from GWAS (n~200,000 individuals), applying new False Discovery Rate (FDR) methods, to investigate genetic overlap between blood lipid levels [triglycerides (TG), low density lipoproteins (LDL), high density lipoproteins (HDL)] and a selection of archetypal immune-mediated diseases (Crohn’s disease, ulcerative colitis, rheumatoid arthritis, type 1 diabetes, celiac disease, psoriasis and sarcoidosis). We found significant polygenic pleiotropy between the blood lipids and all the investigated immune-mediated diseases. We discovered several shared risk loci between the immune-mediated diseases and TG (n = 88), LDL (n = 87) and HDL (n = 52). Three-way analyses differentiated the pattern of pleiotropy among the immune-mediated diseases. The new pleiotropic loci increased the number of functional gene network nodes representing blood lipid loci by 40%. Pathway analyses implicated several novel shared mechanisms for immune pathogenesis and lipid biology, including glycosphingolipid synthesis (e.g. FUT2) and intestinal host-microbe interactions (e.g. ATG16L1). We demonstrate a shared genetic basis for blood lipids and immune-mediated diseases independent of environmental factors. Our findings provide novel mechanistic insights into dyslipidemia and immune-mediated diseases and may have implications for therapeutic trials involving lipid-lowering and anti-inflammatory agents.

• Mæhlen, Marthe Thoresen; Olsen, Inge Christoffer; Andreassen, Bettina Kulle; Viken, Marte K; Jiang, Xia & Alfredsson, Lars [Show all 22 contributors for this article] (2015). Genetic risk scores and number of autoantibodies in patients with rheumatoid arthritis. Annals of the Rheumatic Diseases. ISSN 0003-4967. 74(4), p. 762–768. doi: 10.1136/annrheumdis-2013-204173. Full text in Research Archive
• Li, Yun R.; Zhao, Sihai D.; Li, Jin; Bradfield, Jonathan P.; Mohebnasab, Maede & Steel, Laura [Show all 63 contributors for this article] (2015). Genetic sharing and heritability of paediatric age of onset autoimmune diseases. Nature Communications. 6:8442. doi: 10.1038/ncomms9442. Full text in Research Archive
• Omair, Ahmad; Mannion, Anne F.; Holden, Marit; Fairbank, Jeremy; Lie, Benedicte Alexandra & Hägg, Olle [Show all 8 contributors for this article] (2015). Catechol-O-methyltransferase (COMT) gene polymorphisms are associated with baseline disability but not long-term treatment outcome in patients with chronic low back pain. European spine journal. ISSN 0940-6719. 24(11), p. 2425–2431. doi: 10.1007/s00586-015-3866-5. Full text in Research Archive Show summary

  Purpose: To examine the association between COMT and OPRM1 gene polymorphisms and pain and disability at baseline and long-term follow-up in patients treated for chronic low back pain (LBP). Methods: 371 of 767 unrelated European patients recruited from four randomised trials underwent genetic analyses at mean 11.4 years follow-up. 274 patients had fusion and 97 had non-operative treatment. Association analyses included disability, pain, five single nucleotide polymorphisms (SNPs) in the COMT gene, and one SNP in the OPRM1 gene. Analyses were adjusted for age, gender, smoking, analgesics and treatment. Results: Disability at baseline was significantly associated with COMT SNPs rs4818 (p = 0.02), rs6269 (p = 0.007), rs4633 (p = 0.04) rs2075507 (p = 0.009), two haplotypes (p < 0.002), age, gender and smoking (p ≤ 0.002). No significant associations with clinical variables were observed for OPRM1, or for COMT at long-term follow-up. Conclusions: Results suggest that genetic factors are partly responsible for the variation in disability levels in patients presenting with chronic LBP being considered for surgery; in contrast, genetics has no influence on the long-term outcome of treatment.

• Næss, Sigrid; Björnsson, Einar; Anmarkrud, Jarl Andreas; Mamari, Said Al; Juran, Brian D. & Lazaridis, Konstantinos N. [Show all 15 contributors for this article] (2014). Small duct primary sclerosing cholangitis without inflammatory bowel disease is genetically different from large duct disease. Liver international (Print). ISSN 1478-3223. 34(10), p. 1488–1495. doi: 10.1111/liv.12492. Full text in Research Archive
• Avidan, Nili; Panse, Rozen Le; Harbo, Hanne Flinstad; Bernasconi, Pia; Poulas, Konstantinos & Ginzburg, Elizabeta [Show all 28 contributors for this article] (2014). VAV1 and BAFF, via NFκB pathway, are genetic risk factors for myasthenia gravis. Annals of clinical and translational neurology. 1(5), p. 329–339. doi: 10.1002/acn3.51. Full text in Research Archive
• Næss, Sigrid; Lie, Benedicte Alexandra; Melum, Espen; Olsson, Marita; Hov, Johannes Espolin Roksund & Croucher, PJP [Show all 15 contributors for this article] (2014). Refinement of the MHC risk map in a Scandinavian primary sclerosing cholangitis population. PLOS ONE. 9:e0114486(12). doi: 10.1371/journal.pone.0114486. Full text in Research Archive Show summary

  Background Genetic variants within the major histocompatibility complex (MHC) represent the strongest genetic susceptibility factors for primary sclerosing cholangitis (PSC). Identifying the causal variants within this genetic complex represents a major challenge due to strong linkage disequilibrium and an overall high physical density of candidate variants. We aimed to refine the MHC association in a geographically restricted PSC patient panel. Methodology/Principal Findings A total of 365 PSC cases and 368 healthy controls of Scandinavian ancestry were included in the study. We incorporated data from HLA typing (HLA-A, -B, -C, -DRB3, -DRB1, -DQB1) and single nucleotide polymorphisms across the MHC (n = 18,644; genotyped and imputed) alongside previously suggested PSC risk determinants in the MHC, i.e. amino acid variation of DRβ, a MICA microsatellite polymorphism and HLA-C and HLA-B according to their ligand properties for killer immunoglobulin-like receptors. Breakdowns of the association signal by unconditional and conditional logistic regression analyses demarcated multiple PSC associated MHC haplotypes, and for eight of these classical HLA class I and II alleles represented the strongest association. A novel independent risk locus was detected near NOTCH4 in the HLA class III region, tagged by rs116212904 (odds ratio [95% confidence interval] = 2.32 [1.80, 3.00], P = 1.35×10−11). Conclusions/Significance Our study shows that classical HLA class I and II alleles, predominantly at HLA-B and HLA-DRB1, are the main risk factors for PSC in the MHC. In addition, the present assessments demonstrated for the first time an association near NOTCH4 in the HLA class III region.

• Moreno-Mayar, J. Victor; Rasmussen, Simon; Seguin-Orlando, Andaine; Rasmussen, Morten; Liang, Mason & Flåm, Siri Tennebø [Show all 12 contributors for this article] (2014). Genome-wide ancestry patterns in rapanui suggest pre-european admixture with native americans. Current Biology. ISSN 0960-9822. 24(21), p. 2518–2525. doi: 10.1016/j.cub.2014.09.057. 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.

• Amundsen, Svanstrøm Silja; Viken, Marte K; Sollid, Ludvig Magne & Lie, Benedicte Alexandra (2014). Coeliac disease-associated polymorphisms influence thymic gene expression. Genes and Immunity. ISSN 1466-4879. 15(6), p. 355–360. doi: 10.1038/gene.2014.26. Full text in Research Archive
• Gustavsen, Marte Wendel; Page, Christian; Moen, Stine Marit; Bjølgerud, Anja; Berg-Hansen, Pål & Nygaard, Gro Owren [Show all 10 contributors for this article] (2014). Environmental exposures and the risk of multiple sclerosis investigated in a Norwegian case-control study. BMC Neurology. 14(1). doi: 10.1186/s12883-014-0196-x. Full text in Research Archive Show summary

  Background: Several environmental exposures, including infection with Epstein-Barr virus, low levels of vitamin D and smoking are established risk factors for multiple sclerosis (MS). Also, high hygienic standard and infection with parasites have been proposed to influence MS risk. The aim of this study was to investigate the influence of various environmental exposures on MS risk in a Norwegian cohort, focusing on factors during childhood related to the hygiene hypothesis. Methods: A questionnaire concerning environmental exposures, lifestyle, demographics and comorbidity was administrated to 756 Norwegian MS patients and 1090 healthy controls. Logistic regression was used to calculate odds ratio (OR) with 95% confidence interval (CI) for the risk of MS associated with the variables infectious mononucleosis, severe infection during childhood, vaccination and animals in the household during childhood. Age, gender, HLA-DRB1*15:01, smoking and infectious mononucleosis were included as covariates. General environmental exposures, including tobacco use, were also evaluated. Results: Infectious mononucleosis was confirmed to be significantly associated with increased MS risk, also after adjusting for the covariates (OR?=?1.79, 95% CI: 1.12-2.87, p?=?0.016). The controls more often reported growing up with a cat and/or a dog in the household, and this was significant for ownership of cat also after adjusting for the covariates (OR?=?0.56, 95% CI: 0.40-0.78, p?=?0.001). More patients than controls reported smoking and fewer patients reported snuff use. Conclusions: In this Norwegian MS case-control study of environmental exposures, we replicate that infectious mononucleosis and smoking are associated with increased MS risk. Our data also indicate a protective effect on MS of exposure to cats during childhood, in accordance with the hypothesis that risk of autoimmune diseases like MS may increase with high hygienic standard.

• Gustavsen, Marte Wendel; Viken, Marte K; Celius, Elisabeth Gulowsen; Berge, Tone; Mero, Inger-Lise & Berg-Hansen, Pål [Show all 17 contributors for this article] (2014). Oligoclonal band phenotypes in MS differ in their HLA class II association, while specific KIR ligands at HLA class I show association to MS in general. Journal of Neuroimmunology. ISSN 0165-5728. 274(1-2), p. 174–179. doi: 10.1016/j.jneuroim.2014.06.024. Full text in Research Archive
• Andersen, Ina Marie Riise; Tengesdal, Guro; Lie, Benedicte Alexandra; Boberg, Kirsten Muri; Karlsen, Tom Hemming & Hov, Johannes Espolin Roksund (2014). Effects of Coffee Consumption, Smoking, and Hormones on Risk for Primary Sclerosing Cholangitis. Clinical Gastroenterology and Hepatology. ISSN 1542-3565. 12(6), p. 1019–1028. doi: 10.1016/j.cgh.2013.09.024. Full text in Research Archive
• Elbarbary, Nancy S.; Tjora, Erling; Molnes, Janne; Lie, Benedicte Alexandra; Habib, Mohammad A. & Salem, Mona A. [Show all 7 contributors for this article] (2013). An Egyptian family with H syndrome due to a novel mutation in SLC29A3 illustrating overlapping features with pigmented hypertrichotic dermatosis with insulin-dependent diabetes and Faisalabad histiocytosis. Pediatric Diabetes. ISSN 1399-543X. 14(6), p. 466–472. doi: 10.1111/j.1399-5448.2012.00925.x. Full text in Research Archive
• Serrano, A.; Márquez, Arturo; Mackie, SL; Carmona, Francisco David; Solans, R. & Miranda-Filloy, JA [Show all 31 contributors for this article] (2013). Identification of the PTPN22 functional variant R620W as susceptibility genetic factor for giant cell arteritis. Annals of the Rheumatic Diseases. ISSN 0003-4967. 72(11), p. 1882–1886. doi: 10.1136/annrheumdis-2013-203641. Full text in Research Archive
• Mero, Inger-Lise; Gustavsen, Marte Wendel; Sæther, Hanne Skarpodde; Flåm, Siri Tennebø; Berg-Hansen, Pål & Søndergaard, Helle Bach [Show all 22 contributors for this article] (2013). Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles. PLOS ONE. 8(3). doi: 10.1371/journal.pone.0058352. Full text in Research Archive
• Teruel, Maria; McKinney, Cushla; Balsa, Alejandro; Pascual-Salcedo, Dora; Rodríguez-Rodríguez, Luis & Ortiz, Ana M. [Show all 13 contributors for this article] (2013). Association of CD247 polymorphisms with rheumatoid athritis: a replication study and a meta-analysis. PLOS ONE. 8(7:e68295). doi: 10.1371/journal.pone.0068295. Full text in Research Archive
• Leikfoss, Ingvild Sørum; Mero, Inger-Lise; Dahle, Maria Krudtaa; Lie, Benedicte Alexandra; Harbo, Hanne Flinstad & Spurkland, Anne [Show all 7 contributors for this article] (2013). Multiple sclerosis-associated single-nucleotide polymorphisms in CLEC16A correlate with reduced SOCS1 and DEXI expression in the thymus. Genes and Immunity. ISSN 1466-4879. 14(1), p. 62–66. doi: 10.1038/gene.2012.52. Full text in Research Archive
• Beecham, Ashley H.; Patsopoulos, NA; Xifara, DK; Davis, MF; Kemppinen, A & Cotsapas, C [Show all 193 contributors for this article] (2013). Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nature Genetics. ISSN 1061-4036. 45(11), p. 1353–1360. doi: 10.1038/ng.2770. Full text in Research Archive
• Cortes, Adrian; Hadler, Johanna; Pointon, JP; Robinson, Philip; Karaderi, Kudce & Leo, Paul [Show all 66 contributors for this article] (2013). Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nature Genetics. ISSN 1061-4036. 45(7), p. 730–738. doi: 10.1038/ng.2667. Full text in Research Archive
• Nordang, Gry Beate Namløs; Flåm, Siri Tennebø; Mæhlen, Marthe Thoresen; Kvien, Tore Kristian; Viken, Marte K & Lie, Benedicte Alexandra (2013). HLA-C alleles confer risk for anti-citrullinated peptide antibody-positive rheumatoid arthritis independent of HLA-DRB1 alleles. Rheumatology. ISSN 1462-0324. 52(11), p. 1973–1982. doi: 10.1093/rheumatology/ket252. Full text in Research Archive
• Vang, Torkel; Landskron, Johannes; Viken, Marte K; Oberprieler, Nikolaus; Torgersen, Knut Martin & Mustelin, Tomas [Show all 10 contributors for this article] (2013). The autoimmune-predisposing variant of lymphoid tyrosine phosphatase favors T helper 1 responses. Human Immunology. ISSN 0198-8859. 74(5), p. 574–585. doi: 10.1016/j.humimm.2012.12.017. Full text in Research Archive

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• Vigeland, Maria Dehli & Lie, Benedicte Alexandra (2023). Kvinner er i unødvendig mye smerte, mener forsker. [Journal]. Morgenbladet. Full text in Research Archive
• Langton, David J.; Bhalekar, Rohan M.; Joyce, Thomas J.; Rushton, Stephen P.; Wainwright, Benjamin J. & Nargol, Matthew E. [Show all 17 contributors for this article] (2022). Author Correction: The influence of HLA genotype on the development of metal hypersensitivity following joint replacement (Communications Medicine, (2022), 2, 1, (73), 10.1038/s43856-022-00137-0). Communications Medicine. 2(1). doi: 10.1038/s43856-022-00158-9. Full text in Research Archive
• Robinson, Philip C.; Costello, Mary-Ellen; Leo, Paul; Bradbury, Linda A.; Hollis, Kelly & Cortes, Adrian [Show all 52 contributors for this article] (2015). ERAP2 is associated with ankylosing spondylitis in HLA-B27-positive and HLA-B27-negative patients. Annals of the Rheumatic Diseases. ISSN 0003-4967. 74(8), p. 1627–1629. doi: 10.1136/annrheumdis-2015-207416. Full text in Research Archive
• Tinholt, Mari; Viken, MK; Borresen-Dale, AL; Kristensen, V; Karesen, R & Schlichting, E [Show all 12 contributors for this article] (2013). The link between the hemostatic system and cancer: A genotype-phenotype study in breast cancer patients. Thrombosis Research. ISSN 0049-3848. 131, p. S75–S76. Full text in Research Archive
• Sanchez-Mazas, Alicia; Buhler, Stéphane; Bekmane, Uma; Buus, Søren; Claas, Frans H.J. & Dormoy, Anne [Show all 39 contributors for this article] (2013). HLA-NET: A REAL EXAMPLE OF 'NETWORKING IN IMMUNOGENETICS'. Tissue Antigens. ISSN 0001-2815. 81(5), p. 300–301. Full text in Research Archive

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