• Analysis of methylation data with imputation with blocks (MethylBlocks) 

      Meng, Wei; Ray, Mithlesh Kumar; Fenton, Christopher Graham; Anderssen, Endre; Paulssen, Ruth H (Conference object; Konferansebidrag, 2022)
      <p><i>Background -</i> Analysis of methylation data is dependent on two inputs. The total number of reads at any given cytosine site (coverage), and how many of those cytosines are methylated (methylation). Both the large number of sites and low coverage can cause problems in the analysis of methylation data. Likewise finding DMR is computationally and statistically challenging. Here we present a ...
    • Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis 

      Meng, Wei; Johnsen, Kay-Martin; Fenton, Christopher Graham; Florholmen, Jon; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-05-18)
      Due to the lack of clinical, immunologic, genetic, and laboratory markers to predict remission in ulcerative colitis (UC) without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and ...
    • Anti-dsDNA Antibodies Promote Initiation, and Acquired Loss of Renal Dnase1 Promotes Progression of Lupus Nephritis in Autoimmune (NZBxNZW)F1 mice 

      Fenton, Kristin Andreassen; Fismen, Silje; Hedberg, Annica; Seredkina, Natalya; Fenton, Christopher Graham; Mortensen, Elin; Rekvik, Ole Petter (Journal article; Tidsskriftartikkel; Peer reviewed, 2009)
    • Changes in the human transcriptome upon vitamin D supplementation 

      Pasing, Yvonne; Fenton, Christopher Graham; Jorde, Rolf; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-03-19)
      Vitamin D is hydroxylated in the liver and kidneys to its active form, which can bind to the vitamin D receptor (VDR). The VDR is present in a wide variety of different cells types and tissues and acts as a transcription factor. Although activation of the VDR is estimated to regulate expression of up to 5% of the human genome, our study is the first analysing gene expression after supplementation ...
    • Clinical phenotype associations with various types of anti-dsDNA antibodies in patients with recent onset of rheumatic symptoms. Results from a multicentre observational study 

      Compagno, Michele; Rekvig, Ole Petter; Bengtsson, Anders; Sturfeld, Gunnar; Heegaard, Niels H. H.; Jönsen, Andreas; Jacobsen, Rasmus S.; Eilertsen, Gro Østli; Fenton, Christopher Graham; Truedsson, Lennart; Nossent, Johannes C; Jacobsen, Søren (Journal article; Tidsskriftartikkel, 2014)
    • Differences in gene expression between first and third trimester human placenta : a microarray study. 

      Sitras, Vasilis; Fenton, Christopher Graham; Paulssen, Ruth H; Vårtun, Åse; Acharya, Ganesh (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      The human placenta is a rapidly developing organ that undergoes structural and functional changes throughout the pregnancy. Our objectives were to investigate the differences in global gene expression profile, the expression of imprinted genes and the effect of smoking in first and third trimester normal human placentas. Placental samples were collected from 21 women with uncomplicated pregnancies ...
    • DNA hypo-methylation facilitates anti-inflammatory responses in severe ulcerative colitis 

      Taman, Hagar; Fenton, Christopher Graham; Anderssen, Endre; Florholmen, Jon; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-04-01)
      Severe ulcerative colitis (UC) is a potentially life-threatening disease with a potential colorectal cancer (CRC) risk. The aim of this study was to explore the relationship between transcriptomic and genome-wide DNA methylation profiles in a well-stratified, treatment-naïve severe UC patient population in order to define specific epigenetic changes that could be responsible for the grade of disease ...
    • Endogenous IL-1 receptor antagonist restricts healthy and malignant myeloproliferation 

      Villatoro, Alicia; Cuminetti, Vincent; Bernal, Aurora; Torroja, Carlos; Cossío, Itziar; Benguría, Alberto; Ferré, Marc; Konieczny, Joanna; Vázquez, Enrique; Rubio, Andrea; Utnes, Peter Andree; You, Xiaona; Fenton, Christopher Graham; Paulssen, Ruth H; Zhang, Jing; Sánchez-Cabo, Fatima; Dopazo, Ana; Vik, Anders; Anderssen, Endre; Hidalgo, Andres; Arranz, Lorena (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-01-03)
      Here we explored the role of interleukin-1β (IL-1β) repressor cytokine, IL-1 receptor antagonist (IL-1rn), in both healthy and abnormal hematopoiesis. Low IL-1RN is frequent in acute myeloid leukemia (AML) patients and represents a prognostic marker of reduced survival. Treatments with IL-1RN and the IL-1β monoclonal antibody canakinumab reduce the expansion of leukemic cells, including CD34+ ...
    • Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida 

      Hansen, Geir Åsmund; Ahmad, Rafi; Hjerde, erik; Fenton, Christopher Graham; Willassen, Nils Peder; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio ...
    • Fibrosis Mediators in the Colonic Mucosa of Acute and Healed Ulcerative Colitis 

      Gundersen, Mona Dixon; Goll, Rasmus; Fenton, Christopher Graham; Anderssen, Endre; Sørbye, Sveinung Wergeland; Florholmen, Jon; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-10-03)
      <i>OBJECTIVES</i>: A healed intestinal mucosa is the aim of therapy in acute ulcerative colitis (UC). Disruption of mucosal wound healing may lead to severe complications including intestinal fibrosis. This study examined mucosal gene expression in the healing process of acute UC with a special focus on known mediators of fibrosis.<p> <p><i>METHODS</i>: Endoscopic biopsies from patients with ...
    • Genome-Wide DNA Methylation in Treatment-Naïve Ulcerative Colitis 

      Taman, Hagar; Fenton, Christopher Graham; Hensel, Inga Viktoria; Anderssen, Endre; Florholmen, Jon; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-22)
      <p><i>Background and Aims</i>: The aim of this study was to investigate the genome-wide DNA methylation status in treatment-naïve ulcerative colitis [UC], and to explore the relationship between DNA methylation patterns and gene expression levels in tissue biopsies from a well-stratified treatment-naïve UC patient group.</p> <p><i>Methods</i>; Mucosal biopsies from treatment-naïve patients [n = ...
    • ICAM1 expression is induced by proinflammatory cytokines and associated with TLS formation in aggressive breast cancer subtypes 

      Figenschau, Stine; Knutsen, Erik; Urbarova, Ilona; Fenton, Christopher Graham; Elston, Bryan; Perander, Maria; Mortensen, Elin Synnøve; Fenton, Kristin Andreassen (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-06)
      Intratumoral formation of tertiary lymphoid structures (TLS) within the tumor microenvironment is considered to be a consequence of antigen challenge during anti-tumor responses. Intracellular adhesion molecule 1 (ICAM1) has been implicated in a variety of immune and inflammatory responses, in addition to associate with triple negative breast cancer (TNBC). In this study, we detected TLS in the ...
    • Identifying anti-TNF response biomarkers in ulcerative colitis using a diffusion-based signalling model 

      Singh, Amrinder; Anderssen, Endre; Fenton, Christopher Graham; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-08-18)
      <p><i>Motivation:</i> Resistance to anti-TNF therapy in subgroups of ulcerative colitis (UC) patients is a major challenge and incurs significant treatment costs. Identification of patients at risk of nonresponse to anti-TNF is of major clinical importance. To date, no quantitative computational framework exists to develop a complex biomarker for the prognosis of UC treatment. Modelling patient-wise ...
    • Identifying predictive signalling networks for Vedolizumab response in ulcerative colitis. 

      Singh, A.; Fenton, Christopher Graham; Anderssen, Endre; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-05-11)
      Background - In ulcerative colitis (UC), the molecular mechanisms that drive disease development and patient response to therapy are not well understood. A significant proportion of patients with UC fail to respond adequately to biologic therapy. Therefore, there is an unmet need for biomarkers that can predict patients’ responsiveness to the available UC therapies as well as ascertain the most ...
    • Kidney tertiary lymphoid structures in Lupus Nephritis develop into large interconnected networks and resemble lymph nodes in gene signature 

      Dorraji, Seyed Esmaeil; Kanapathippillai, Premasany; Hovd, Aud-Malin Karlsson; Stenersrød, Mikael Ryan; Horvei, Kjersti Daae; Ursvik, anita; Figenschau, Stine; Thiyagarajan, Dhivya Borra; Fenton, Christopher Graham; Pedersen, Hege Lynum; Fenton, Kristin Andreassen (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-08-16)
      Immune aggregates organized as tertiary lymphoid structures (TLS) are observed within the kidneys of patients with systemic lupus erythematosus and lupus nephritis (LN). Renal TLS was characterized in lupus-prone New Zealand black × New Zealand white F1 mice analyzing cell composition and vessel formation. RNA sequencing was performed on transcriptomes isolated from lymph nodes, macrodissected TLS ...
    • Methylation-regulated long non-coding RNA expression in ulcerative colitis 

      Fenton, Christopher Graham; Ray, Mithlesh Kumar; Meng, Wei; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-06-22)
      Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics ...
    • MicroRNA Signatures in Tumor Tissue Related to Angiogenesis in Non-Small Cell Lung Cancer 

      Dønnem, Tom; Fenton, Christopher Graham; Lønvik, Kenneth; Berg, Thomas; Eklo, Katrine; Andersen, Sigve; Stenvold, Helge; Al-Shibli, Khalid Ibrahim; Al-Saad, Samer; Bremnes, Roy M.; Busund, Lill-Tove (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      Angiogenesis is regarded as a hallmark in cancer development, and anti-angiogenic treatment is presently used in non-small cell lung cancer (NSCLC) patients. MicroRNAs (miRs) are small non-coding, endogenous, single stranded RNAs that regulate gene expression. In this study we aimed to identify significantly altered miRs related to angiogenesis in NSCLC. From a large cohort of 335 NSCLC patients, ...
    • Mucosal gene transcription of ulcerative colitis in endoscopic remission 

      Arkteg, Christian Børde; Goll, Rasmus; Gundersen, Mona Dixon; Anderssen, Endre; Fenton, Christopher Graham; Florholmen, Jon (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-01-09)
      <i>Aim/Objective</i>: Ulcerative colitis (UC) is a chronic inflammatory bowel disease. In UC, a wide range of criteria are used for disease remission, with few studies investigating the differences between disease remission and normal control groups. This paper compares known inflammatory and healing mediators in the mucosa of UC in clinical remission and normal controls, in order to better describe ...
    • Novel long non-coding RNAs of relevance for ulcerative colitis pathogenesis 

      Ray, Mithlesh Kumar; Fenton, Christopher Graham; Paulssen, Ruth H (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-02-06)
      Background and aims: The study aimed to identify yet unknown and uncharacterized long non-coding RNAs (lncRNAs) in treatment-naïve ulcerative colitis (UC), and to define their possible roles in UC pathogenesis. For that purpose, accurate quantification methods for lncRNA transcript detection, multiple and “stringent” strategies were applied. New insights in the regulation of functional genes and ...
    • Novel long-coding RNAs of relevance for ulcerative colitis pathogenesis 

      Ray, Mithlesh Kumar; Fenton, Christopher Graham; Paulssen, Ruth H (Conference object; Konferansebidrag, 2022)
      <p>Introduction - LncRNAs have become a growing field of research. They are involved in diverse biological processes including expression regulation, and chromatin modification. Many lncRNAs have been characterized as involved in the occurrence and development of various human diseases, including cancer. A growing body of evidence implies a role for lncRNAs in UC by modulating the intestinal barrier, ...