1. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response
- Author
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Haberman, Yael, Karns, Rebekah, Dexheimer, Phillip J, Schirmer, Melanie, Somekh, Judith, Jurickova, Ingrid, Braun, Tzipi, Novak, Elizabeth, Bauman, Laura, Collins, Margaret H, Mo, Angela, Rosen, Michael J, Bonkowski, Erin, Gotman, Nathan, Marquis, Alison, Nistel, Mason, Rufo, Paul A, Baker, Susan S, Sauer, Cary G, Markowitz, James, Pfefferkorn, Marian D, Rosh, Joel R, Boyle, Brendan M, Mack, David R, Baldassano, Robert N, Shah, Sapana, Leleiko, Neal S, Heyman, Melvin B, Grifiths, Anne M, Patel, Ashish S, Noe, Joshua D, Aronow, Bruce J, Kugathasan, Subra, Walters, Thomas D, Gibson, Greg, Thomas, Sonia Davis, Mollen, Kevin, Shen-Orr, Shai, Huttenhower, Curtis, Xavier, Ramnik J, Hyams, Jeffrey S, and Denson, Lee A
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Immunology ,Nutrition ,Inflammatory Bowel Disease ,Clinical Research ,Autoimmune Disease ,Digestive Diseases ,Genetics ,Biotechnology ,4.1 Discovery and preclinical testing of markers and technologies ,Aetiology ,2.1 Biological and endogenous factors ,Detection ,screening and diagnosis ,Oral and gastrointestinal ,Good Health and Well Being ,Adolescent ,Adult ,Anti-Inflammatory Agents ,Non-Steroidal ,Child ,Colitis ,Ulcerative ,Feces ,Female ,Gene Expression Profiling ,Genes ,Mitochondrial ,Glucocorticoids ,Humans ,Integrins ,Intestinal Mucosa ,Male ,Mesalamine ,Microbiota ,Mitochondria ,Mitochondrial Diseases ,Precision Medicine ,Prospective Studies ,Rectum ,Remission Induction ,Sequence Analysis ,RNA ,Severity of Illness Index ,Transcriptome ,Treatment Outcome ,Tumor Necrosis Factor-alpha - Abstract
Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota profiles, in 206 pediatric UC patients receiving standardised therapy. We validate our key findings in adult and paediatric UC cohorts of 408 participants. We observe a marked suppression of mitochondrial genes and function across cohorts in active UC, and that increasing disease severity is notable for enrichment of adenoma/adenocarcinoma and innate immune genes. A subset of severity genes improves prediction of corticosteroid-induced remission in the discovery cohort; this gene signature is also associated with response to anti-TNFα and anti-α4β7 integrin in adults. The severity and therapeutic response gene signatures were in turn associated with shifts in microbes previously implicated in mucosal homeostasis. Our data provide insights into UC pathogenesis, and may prioritise future therapies for nonresponders to current approaches.
- Published
- 2019