Benedicte Alexandra Lie

• 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. ISSN 2045-2322. 13:17714(1), p. 1–13. doi: 10.1038/s41598-023-44693-4. Full text in Research Archive
• 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. ISSN 2079-6382. 12(7). doi: 10.3390/antibiotics12071217. Full text in Research Archive
• 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
• 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
• 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
• 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. ISSN 1664-3224. 13. doi: 10.3389/fimmu.2022.1092028. 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). 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
• Ueland, Marthe; Hajdarevic, Riad; Mella, Olav; Strand, Elin Bolle; Daysi Duarte, Sosa & 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. ISSN 2158-3188. 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.

• 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
• 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.

• 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
• 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. ISSN 2045-2322. 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.

• 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.

• 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.

• 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
• 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. ISSN 1664-3224. 12, p. 1–14. doi: 10.3389/fimmu.2021.667336. Full text in Research Archive
• Ali, Muhammad; Giannakopoulou, Eirini Chrysovalantou; Li, Yingqian; Lehander, Madeleine; Virding Culleton, Stina & 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
• 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. ISSN 1664-3224. 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.

• 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
• 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
• 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
• 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
• 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. ISSN 1664-3224. 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.

• Sandling, Johanna K.; Pucholt, Pascal; Hultin Rosenberg, Lina; 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
• Helgeland, Hanna; Gabrielsen, Ingvild Synnøve Matre; Akselsen, Helle; Meenakshi Sundaram, Arvind Yegambaram; 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. ISSN 1471-2164. 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.

• 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
• 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.

• 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. ISSN 1471-2474. 21:698, p. 1–14. doi: 10.1186/s12891-020-03720-5. Full text in Research Archive
• 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. ISSN 2296-858X. 7:162, p. 1–15. doi: 10.3389/fmed.2020.00162. Full text in Research Archive
• 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
• 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. ISSN 1664-3224. 11:194, p. 1–14. doi: 10.3389/fimmu.2020.00194. Full text in Research Archive
• Lande, Asgeir; Fluge, Øystein; Strand, Elin Bolle; Flåm, Siri Tennebø; Daysi Duarte, Sosa & 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. ISSN 2045-2322. 10:5267(1), p. 1–8. doi: 10.1038/s41598-020-62157-x. Full text in Research Archive
• 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. ISSN 2311-553X. doi: 10.3390/ncrna5040049. Full text in Research Archive
• 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. ISSN 2041-1723. 10:4955, p. 1–14. doi: 10.1038/s41467-019-12760-y. Full text in Research Archive
• 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.

• 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. ISSN 1756-1833. 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.

• 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.

• Gabrielsen, Ingvild Synnøve Matre; Helgeland, Hanna; Akselsen, Helle; Aass, Hans Christian Dalsbotten; Meenakshi Sundaram, Arvind Yegambaram & Snowhite, Isaac V. [Show all 9 contributors for this article] (2019). Transcriptomes of antigen presenting cells in human thymus. PLOS ONE. ISSN 1932-6203. 14:e0218858(7), p. 1–18. doi: 10.1371/journal.pone.0218858. Full text in Research Archive
• 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
• 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
• 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
• 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. 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)

• 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.
• 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. ISSN 2045-2322. 8. doi: 10.1038/s41598-018-27391-4. 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.
• 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.
• 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. ISSN 1932-6203. 12:e0186383(10), p. 1–9. doi: 10.1371/journal.pone.0186383.
• 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.
• 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.
• 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. ISSN 1932-6203. 12(7). doi: 10.1371/journal.pone.0179080. 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.
• 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.
• 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. ISSN 1471-2350. 17(1). doi: 10.1186/s12881-016-0285-3.
• 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. ISSN 2055-2173. 2, p. 1–4. doi: 10.1177/2055217316682976. 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.
• 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. 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.

• Dominguez Valentin, Mev; Gras Navarro, Andrea; 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.
• 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.
• 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. 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.

• 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.
• 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.
• 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. ISSN 2041-1723. 6:8442. doi: 10.1038/ncomms9442.
• 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.
• 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. ISSN 1932-6203. 10:e0133804(7). doi: 10.1371/journal.pone.0133804.
• 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. ISSN 2041-1723. 6. doi: 10.1038/ncomms8146. Full text in Research Archive
• Bossini-Castillo, Lara; de Kovel, Carolien G.F.; Källberg, Henrik; van't Slot, Ruben; 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.
• 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. 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.

• 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. ISSN 1932-6203. 10:e 0123057(4). doi: 10.1371/journal.pone.0123057. 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.
• 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
• Mæhlen, Marthe Thoresen; Olsen, Inge Christoffer; Kulle Andreassen, Bettina; 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.
• 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. ISSN 2328-9503. 1(5), p. 329–339. doi: 10.1002/acn3.51.
• 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.
• 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. ISSN 1471-2407. 14. doi: 10.1186/1471-2407-14-845.
• 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. ISSN 1932-6203. 9:e0114486(12). doi: 10.1371/journal.pone.0114486.
• 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.
• 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. ISSN 1471-2377. 14(1). doi: 10.1186/s12883-014-0196-x. Full text in Research Archive
• 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.
• Næss, Sigrid; Björnsson, Einar; Anmarkrud, Jarl Andreas; Al Mamari, Said; 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.
• 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.
• 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.
• 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.
• 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. ISSN 1932-6203. 8(7:e68295). doi: 10.1371/journal.pone.0068295.
• 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.
• Namløs Nordang, Gry Beate; 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.
• 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.
• 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.
• Mæhlen, Marthe Thoresen; Provan, Sella Aarrestad; de Rooy, Diederik P.C.; van der Helm-van Mil, Annette H.M.; Krabben, Annemarie & Saxne, Tore [Show all 14 contributors for this article] (2013). Associations between APOE Genotypes and Disease Susceptibility, Joint Damage and Lipid Levels in Patients with Rheumatoid Arthritis. PLOS ONE. ISSN 1932-6203. 8(4). doi: 10.1371/journal.pone.0060970.
• Omair, Ahmad; Holden, Marit; Lie, Benedicte Alexandra; Reikerås, Olav & Brox, Jens Ivar (2013). Treatment outcome of chronic low back pain and radiographic lumbar disc degeneration are associated with inflammatory and matrix degrading gene variants: a prospective genetic association study. BMC Musculoskeletal Disorders. ISSN 1471-2474. 14(105). doi: 10.1186/1471-2474-14-105. Show summary

  Background: Inflammatory and matrix degrading gene variants have been reported to be associated with disc degeneration. Some of these variants also modulate peripheral pain. This study examines the association of these genetic variants with radiographic lumbar disc degeneration and changes in pain and disability at long-term after surgical and cognitive behavioural management. Methods: 93 unrelated patients with chronic low back pain (CLBP) for duration of >1 year and lumbar disc degeneration were treated with lumbar fusion or cognitive intervention and exercises. Standardised questionnaires included the Oswestry Disability Index (ODI) and Visual Analog Score (VAS) for CLBP, were filled in by patients both at baseline and at 9 years follow-up. Degenerative changes at baseline Magnetic Resonance Imaging and Computed Tomography scans, were graded as moderate and severe (N=79). Yield and quality of blood and saliva DNA was assessed by nano drop spectrophotometry. Eight SNPs in 5 inflammatory and matrix degrading genes were successfully genotyped. Single marker and haplotype association with severity of degeneration, number of discs involved, changes in ODI and VAS CLBP, was done using Haploview, linear regression and R-package Haplostats. Results: Association analysis of individual SNPs revealed association of IL18RAP polymorphism rs1420100 with severe degeneration (p = 0.05) and more than one degenerated disc (p = 0.02). From the same gene two SNPs, rs917997 and rs1420106, were found to be in strong linkage disequilibrium (LD) and were associated with post treatment improvement in disability (p = 0.02). Haplotype association analysis of 5 SNPs spanning across IL18RAP, IL18R1 and IL1A genes revealed significant associations with improvement in disability (p=0.02) and reduction in pain (p=0.04). An association was found between MMP3 polymorphism rs72520913 and improvement in pain (p = 0.03) and with severe degeneration (p = 0.006). Conclusions: The findings of the current study suggest a role of variation at inflammatory and matrix degrading genes with severity of lumbar disc degeneration, pain and disability.

• 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.
• 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. ISSN 1932-6203. 8(3). doi: 10.1371/journal.pone.0058352.
• Gregersen, Peter K.; Kosoy, Roman; Lee, Annette T.; Lamb, Janine; Sussman, Jon & McKee, David [Show all 29 contributors for this article] (2012). Risk for Myasthenia Gravis Maps to a 151Pro!Ala Change in TNIP1 and to Human Leukocyte Antigen-B*08. Annals of Neurology. ISSN 0364-5134. 72(6), p. 927–935. doi: 10.1002/ana.23691.

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• Vigeland, Maria Dehli & Lie, Benedicte Alexandra (2023). Kvinner er i unødvendig mye smerte, mener forsker. [Newspaper]. Morgenbladet.
• 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.
• 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.
• 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.
• 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.
• 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.
• Zaiss, Dietmar; Bekker, Cornelis; Grne, Andrea; Lie, Benedicte Alexandra & Sijts, Alice (2012). Proteasome immunosubunits protect against the development of CD8 T-cell-mediated autoimmune diseases. Molecular Immunology. ISSN 0161-5890. 51(1), p. 30–31. doi: 10.1016/j.molimm.2012.02.084.
• Viken, Marte K; Flåm, Siri Tennebø; Sollid, Ludvig Magne; Skrivarhaug, Torild; Dahl-Jørgensen, Knut & Lie, Benedicte Alexandra (2012). STUDY OF THE HLA-DRB1 AND-DQB1 GENES IN PATIENTS WITH COEXISTING TYPE 1 DIABETES AND CELIAC DISEASE. Tissue Antigens. ISSN 0001-2815. 79(6), p. 584–584.

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