Identification of putative transcriptomic biomarkers in irritable bowel syndrome (IBS): Differential gene expression and regulation of TPH1 and SERT by vitamin D

• Published in: PloS one Vol. 17; no. 10; p. e0275683
• Main Authors: Grozic, Aleksandra, Coker, Keaton, Dussik, Christopher M, Sabir, Marya S, Sabir, Zhela, Bradley, Arianna, Zhang, Lin, Park, Jin, Yale, Steven, Kaneko, Ichiro, Hockley, Maryam, Harris, Lucinda A, Lunsford, Tisha N, Sandrin, Todd R, Jurutka, Peter W
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 20-10-2022; Public Library of Science (PLoS)
• Subjects: Abdomen; Alfacalcidol; Analysis; Anxiety; Autoimmune diseases; Biological markers; Biology and Life Sciences; Biomarkers; Brain research; Calcifediol; Calciferol; Care and treatment; Celiac disease; Colon; Complementary DNA; Deoxyribonucleic acid; Diagnosis; Disorders; DNA; DNA chips; DNA microarrays; Dosage and administration; Enzymes; Gastrointestinal diseases; Gene expression; Gene regulation; Genes; Inflammatory bowel diseases; Intestine; Irritable bowel syndrome; Medicine and Health Sciences; Metabolism; Microbiota; Mucosa; Ontology; Pathogenesis; Pathophysiology; Patients; Physical sciences; Polymerase chain reaction; Quality of life; Research and Analysis Methods; RNA-directed DNA polymerase; Serotonin; Serotonin transporter; Serotonin uptake inhibitors; Signs and symptoms; Transcriptomes; Transcriptomics; Vitamin D; Vitamin deficiency; United States
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0275683

Irritable bowel syndrome (IBS) is one of the most common gastrointestinal disorders and affects approximately 4% of the global population. The diagnosis of IBS can be made based on symptoms using the validated Rome criteria and ruling out commonly occurring organic diseases. Although biomarkers exist for “IBS mimickers” such as celiac disease and inflammatory bowel disease (IBD), no such test exists for IBS. DNA microarrays of colonic tissue have been used to identify disease-associated variants in other gastrointestinal (GI) disorders. In this study, our objective was to identify biomarkers and unique gene expression patterns that may define the pathological state of IBS. Mucosal tissue samples were collected from the sigmoid colon of 29 participants (11 IBS and 18 healthy controls). DNA microarray analysis was used to assess gene expression profiling. Extraction and purification of RNA were then performed and used to synthesize cDNA. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) was employed to identify differentially expressed genes in patients diagnosed with IBS compared to healthy, non-IBS patient-derived cDNA. Additional testing probed vitamin D-mediated regulation of select genes associated with serotonergic metabolism. DNA microarray analyses led to the identification of 858 differentially expressed genes that may characterize the IBS pathological state. After screening a series of genes using a combination of gene ontological analysis and RT-qPCR, this spectrum of potential IBS biomarkers was narrowed to 23 genes, some of which are regulated by vitamin D. Seven putative IBS biomarkers, including genes involved in serotonin metabolism, were identified. This work further supports the hypothesis that IBS pathophysiology is evident within the human transcriptome and that vitamin D modulates differential expression of genes in IBS patients. This suggests that IBS pathophysiology may also involve vitamin D deficiency and/or an irregularity in serotonin metabolism.