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Noh JY, Farhataziz N, Kinter MT, Yan X, Sun Y. Colonic Dysregulation of Major Metabolic Pathways in Experimental Ulcerative Colitis. Metabolites 2024; 14:194. [PMID: 38668322 PMCID: PMC11052278 DOI: 10.3390/metabo14040194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Inflammatory bowel disease (IBD) is multifactorial chronic inflammatory disease in the gastrointestinal tract, affecting patients' quality of life profoundly. The incidence of IBD has been on the rise globally for the last two decades. Because the molecular mechanisms underlying the disease remain not well understood, therapeutic development is significantly impeded. Metabolism is a crucial cellular process to generate the energy needed for an inflammatory response and tissue repair. Comprehensive understanding of the metabolic pathways in IBD would help to unravel the disease pathogenesis/progression and facilitate therapeutic discoveries. Here, we investigated four metabolic pathways altered in experimental colitis. C57BL/6J mice were treated with dextran sulfate sodium (DSS) in drinking water for 7 days to induce experimental ulcerative colitis (UC). We conducted proteomics analysis for the colon samples using LC/MS, to profile key metabolic intermediates. Our findings revealed significant alterations in four major metabolic pathways: antioxidative defense, β-oxidation, glycolysis, and TCA cycle pathways. The energy metabolism by β-oxidation, glycolysis, and TCA cycle pathways were downregulated under UC, together with reduced antioxidative defense pathways. These results reveal metabolic re-programming in intestinal cells under UC, showing dysregulation in all four major metabolic pathways. Our study underscores the importance of metabolic drivers in the pathogenesis of IBD and suggests that the modification of metabolism may serve as a novel diagnostic/therapeutic approach for IBD.
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Affiliation(s)
- Ji Yeon Noh
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (N.F.)
| | - Naser Farhataziz
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (N.F.)
| | - Michael T. Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Xin Yan
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA;
| | - Yuxiang Sun
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (N.F.)
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
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2
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Bass K, Sivaprakasam S, Dharmalingam-Nandagopal G, Thangaraju M, Ganapathy V. Colonic ketogenesis, a microbiota-regulated process, contributes to blood ketones and protects against colitis in mice. Biochem J 2024; 481:295-312. [PMID: 38372391 PMCID: PMC10903465 DOI: 10.1042/bcj20230403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
Ketogenesis is considered to occur primarily in liver to generate ketones as an alternative energy source for non-hepatic tissues when glucose availability/utilization is impaired. 3-Hydroxy-3-methylglutaryl-CoA synthase-2 (HMGCS2) mediates the rate-limiting step in this mitochondrial pathway. Publicly available databases show marked down-regulation of HMGCS2 in colonic tissues in Crohn's disease and ulcerative colitis. This led us to investigate the expression and function of this pathway in colon and its relevance to colonic inflammation in mice. Hmgcs2 is expressed in cecum and colon. As global deletion of Hmgcs2 showed significant postnatal mortality, we used a conditional knockout mouse with enzyme deletion restricted to intestinal tract. These mice had no postnatal mortality. Fasting blood ketones were lower in these mice, indicating contribution of colonic ketogenesis to circulating ketones. There was also evidence of gut barrier breakdown and increased susceptibility to experimental colitis with associated elevated levels of IL-6, IL-1β, and TNF-α in circulation. Interestingly, many of these phenomena were mostly evident in male mice. Hmgcs2 expression in colon is controlled by colonic microbiota as evidenced from decreased expression in germ-free mice and antibiotic-treated conventional mice and from increased expression in a human colonic epithelial cell line upon treatment with aqueous extracts of cecal contents. Transcriptomic analysis of colonic epithelia from control mice and Hmgcs2-null mice indicated an essential role for colonic ketogenesis in the maintenance of optimal mitochondrial function, cholesterol homeostasis, and cell-cell tight-junction organization. These findings demonstrate a sex-dependent obligatory role for ketogenesis in protection against colonic inflammation in mice.
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Affiliation(s)
- Kevin Bass
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, U.S.A
| | - Sathish Sivaprakasam
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, U.S.A
| | | | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, U.S.A
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, U.S.A
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3
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Sinnett-Smith J, Torres-Marquez ME, Chang JK, Shimizu Y, Hao F, Martin MG, Rozengurt E. Statins inhibit protein kinase D (PKD) activation in intestinal cells and prevent PKD1-induced growth of murine enteroids. Am J Physiol Cell Physiol 2023; 324:C807-C820. [PMID: 36779664 PMCID: PMC10042602 DOI: 10.1152/ajpcell.00286.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 02/14/2023]
Abstract
We examined the impact of statins on protein kinase D (PKD) activation by G protein-coupled receptor (GPCR) agonists. Treatment of intestinal IEC-18 cells with cerivastatin inhibited PKD autophosphorylation at Ser916 induced by angiotensin II (ANG II) or vasopressin in a dose-dependent manner with half-maximal inhibition at 0.2 µM. Cerivastatin treatment inhibited PKD activation stimulated by these agonists for different times (5-60 min) and blunted HDAC5 phosphorylation, a substrate of PKD. Other lipophilic statins, including simvastatin, atorvastatin, and fluvastatin also prevented PKD activation in a dose-dependent manner. Using IEC-18 cell lines expressing PKD1 tagged with EGFP (enhanced green fluorescent protein), cerivastatin or simvastatin blocked GPCR-mediated PKD1-EGFP translocation to the plasma membrane and its subsequent nuclear accumulation. Similar results were obtained in IEC-18 cells expressing PKD3-EGFP. Mechanistically, statins inhibited agonist-dependent PKD activation rather than acting directly on PKD catalytic activity since exposure to cerivastatin or simvastatin did not impair PKD autophosphorylation or PKD1-EGFP membrane translocation in response to phorbol dibutyrate, which bypasses GPCRs and directly stimulates PKC and PKD. Furthermore, cerivastatin did not inhibit recombinant PKD activity determined via an in vitro kinase assay. Using enteroids generated from intestinal crypt-derived epithelial cells from PKD1 transgenic mice as a model of intestinal regeneration, we show that statins oppose PKD1-mediated increase in enteroid area, complexity (number of crypt-like buds), and DNA synthesis. Our results revealed a previously unappreciated inhibitory effect of statins on receptor-mediated PKD activation and in opposing the growth-promoting effects of PKD1 on intestinal epithelial cells.
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Affiliation(s)
- James Sinnett-Smith
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
- VA Greater Los Angeles Health Care System, Los Angeles, California, United States
| | - M Eugenia Torres-Marquez
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Jen-Kuan Chang
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Yuki Shimizu
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Fang Hao
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Martin G Martin
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Enrique Rozengurt
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
- VA Greater Los Angeles Health Care System, Los Angeles, California, United States
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4
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Holmes ZC, Villa MM, Durand HK, Jiang S, Dallow EP, Petrone BL, Silverman JD, Lin PH, David LA. Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. MICROBIOME 2022; 10:114. [PMID: 35902900 PMCID: PMC9336045 DOI: 10.1186/s40168-022-01307-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/15/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects on SCFA production in human studies, and gut microbial responses to nutritional interventions vary by individual. It is therefore possible that prebiotic therapies will require customizing to individuals. RESULTS Here, we explored prebiotic personalization by conducting a three-way crossover study of three prebiotic treatments in healthy adults. We found that within individuals, metabolic responses were correlated across the three prebiotics. Individual identity, rather than prebiotic choice, was also the major determinant of SCFA response. Across individuals, prebiotic response was inversely related to basal fecal SCFA concentration, which, in turn, was associated with habitual fiber intake. Experimental measures of gut microbial SCFA production for each participant also negatively correlated with fiber consumption, supporting a model in which individuals' gut microbiota are limited in their overall capacity to produce fecal SCFAs from fiber. CONCLUSIONS Our findings support developing personalized prebiotic regimens that focus on selecting individuals who stand to benefit, and that such individuals are likely to be deficient in fiber intake. Video Abstract.
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Affiliation(s)
- Zachary C. Holmes
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
| | - Max M. Villa
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Center for Genomic and Computational Biology, Duke University, 3 Genome Court, Durham, NC 27705 USA
| | - Heather K. Durand
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Center for Genomic and Computational Biology, Duke University, 3 Genome Court, Durham, NC 27705 USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Center for Genomic and Computational Biology, Duke University, 3 Genome Court, Durham, NC 27705 USA
| | - Eric P. Dallow
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Center for Genomic and Computational Biology, Duke University, 3 Genome Court, Durham, NC 27705 USA
| | - Brianna L. Petrone
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Medical Scientist Training Program, Duke University, 3 Genome Court, Durham, NC 27705 USA
| | - Justin D. Silverman
- College of Information Science and Technology, Penn State University, Westgate Bldg, University Park, PA 16802 USA
- Department of Medicine, Penn State University, Hershey, Westgate Bldg, University Park, PA 16802 USA
- Institute for Computational and Data Science, Penn State University, Westgate Bldg, University Park, PA 16802 USA
| | - Pao-Hwa Lin
- Duke Molecular Physiology Institute, Duke University, Stedman Nutrition Ctr, 3475 Erwin Rd, Durham, NC 27705 USA
- Department of Medicine, Duke University Medical Center, Stedman Nutrition Ctr, 3475 Erwin Rd, Durham, NC 27705 USA
| | - Lawrence A. David
- Department of Molecular Genetics and Microbiology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Center for Genomic and Computational Biology, Duke University, 3 Genome Court, Durham, NC 27705 USA
- Program in Computational Biology and Bioinformatics, Duke University, 3 Genome Court, Durham, NC 27705 USA
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Söderman J, Berglind L, Almer S. Inverse and Concordant Mucosal Pathway Gene Expressions in Inflamed and Non-Inflamed Ulcerative Colitis Patients: Potential Relevance to Aetiology and Pathogenesis. Int J Mol Sci 2022; 23:ijms23136944. [PMID: 35805947 PMCID: PMC9266769 DOI: 10.3390/ijms23136944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/05/2023] Open
Abstract
Ulcerative colitis (UC) arises from a complex interplay between host and environmental factors, but with a largely unsolved pathophysiology. The pathophysiology was outlined by RNA-sequencing of mucosal biopsies from non-inflamed and inflamed colon of UC patients (14 and 17, respectively), and from 27 patients without intestinal inflammation. Genes differentially expressed (DE), or present in enriched gene sets, were investigated using statistical text analysis of functional protein information. Compared with controls, inflamed and non-inflamed UC mucosa displayed 9360 and 52 DE genes, respectively. Seventy-three non-pseudogenes were DE relative to both gender and inflammation. Mitochondrial processes were downregulated in inflamed and upregulated in non-inflamed UC mucosa, whereas angiogenesis and endoplasmic reticulum (ER) stress were upregulated in both tissue states. Immune responses were upregulated in inflamed mucosa, whereas the non-inflamed UC mucosa presented both up- and downregulated gene sets. DE and enriched genes overlapped with genes present in inflammatory bowel disease genome-wide associated loci (p = 1.43 × 10−18), especially regarding immune responses, respiratory chain, angiogenesis, ER stress, and steroid hormone metabolism. Apart from confirming established pathophysiological mechanisms of immune cells, our study provides evidence for involvement of less described pathways (e.g., respiratory chain, ER stress, fatty-acid oxidation, steroid hormone metabolism and angiogenesis).
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Affiliation(s)
- Jan Söderman
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden;
- Correspondence:
| | - Linda Berglind
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden;
| | - Sven Almer
- Department of Medicine, Solna, Karolinska Institutet, 171 77 Stockholm, Sweden;
- IBD Unit, Division of Gastroenterology, Karolinska University Hospital, 171 76 Stockholm, Sweden
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6
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Ornelas A, Dowdell AS, Lee JS, Colgan SP. Microbial Metabolite Regulation of Epithelial Cell-Cell Interactions and Barrier Function. Cells 2022; 11:cells11060944. [PMID: 35326394 PMCID: PMC8946845 DOI: 10.3390/cells11060944] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Epithelial cells that line tissues such as the intestine serve as the primary barrier to the outside world. Epithelia provide selective permeability in the presence of a large constellation of microbes, termed the microbiota. Recent studies have revealed that the symbiotic relationship between the healthy host and the microbiota includes the regulation of cell–cell interactions at the level of epithelial tight junctions. The most recent findings have identified multiple microbial-derived metabolites that influence intracellular signaling pathways which elicit activities at the epithelial apical junction complex. Here, we review recent findings that place microbiota-derived metabolites as primary regulators of epithelial cell–cell interactions and ultimately mucosal permeability in health and disease.
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Affiliation(s)
- Alfredo Ornelas
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19th Ave, Mailstop B146, Aurora, CO 80045, USA; (A.O.); (A.S.D.); (J.S.L.)
| | - Alexander S. Dowdell
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19th Ave, Mailstop B146, Aurora, CO 80045, USA; (A.O.); (A.S.D.); (J.S.L.)
| | - J. Scott Lee
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19th Ave, Mailstop B146, Aurora, CO 80045, USA; (A.O.); (A.S.D.); (J.S.L.)
| | - Sean P. Colgan
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19th Ave, Mailstop B146, Aurora, CO 80045, USA; (A.O.); (A.S.D.); (J.S.L.)
- Rocky Mountain Regional Veterans Affairs Medical Center, 1700 N. Wheeling St., Aurora, CO 80045, USA
- Correspondence:
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Bai L, Scott MKD, Steinberg E, Kalesinskas L, Habtezion A, Shah NH, Khatri P. Computational drug repositioning of atorvastatin for ulcerative colitis. J Am Med Inform Assoc 2021; 28:2325-2335. [PMID: 34529084 PMCID: PMC8510297 DOI: 10.1093/jamia/ocab165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/22/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Ulcerative colitis (UC) is a chronic inflammatory disorder with limited effective therapeutic options for long-term treatment and disease maintenance. We hypothesized that a multi-cohort analysis of independent cohorts representing real-world heterogeneity of UC would identify a robust transcriptomic signature to improve identification of FDA-approved drugs that can be repurposed to treat patients with UC. MATERIALS AND METHODS We performed a multi-cohort analysis of 272 colon biopsy transcriptome samples across 11 publicly available datasets to identify a robust UC disease gene signature. We compared the gene signature to in vitro transcriptomic profiles induced by 781 FDA-approved drugs to identify potential drug targets. We used a retrospective cohort study design modeled after a target trial to evaluate the protective effect of predicted drugs on colectomy risk in patients with UC from the Stanford Research Repository (STARR) database and Optum Clinformatics DataMart. RESULTS Atorvastatin treatment had the highest inverse-correlation with the UC gene signature among non-oncolytic FDA-approved therapies. In both STARR (n = 827) and Optum (n = 7821), atorvastatin intake was significantly associated with a decreased risk of colectomy, a marker of treatment-refractory disease, compared to patients prescribed a comparator drug (STARR: HR = 0.47, P = .03; Optum: HR = 0.66, P = .03), irrespective of age and length of atorvastatin treatment. DISCUSSION & CONCLUSION These findings suggest that atorvastatin may serve as a novel therapeutic option for ameliorating disease in patients with UC. Importantly, we provide a systematic framework for integrating publicly available heterogeneous molecular data with clinical data at a large scale to repurpose existing FDA-approved drugs for a wide range of human diseases.
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Affiliation(s)
- Lawrence Bai
- Immunology Program, Stanford University School of Medicine, Stanford, California, USA.,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA.,Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
| | - Ethan Steinberg
- Computer Science Program, Department of Computer Science, Stanford University, Stanford, California, USA
| | - Laurynas Kalesinskas
- Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, USA
| | - Aida Habtezion
- Immunology Program, Stanford University School of Medicine, Stanford, California, USA.,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Nigam H Shah
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
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McIntosh AT, Wei R, Ahn J, Aouizerat BE, Kassaye SG, Augenbraun MH, Price JC, French AL, Gange SJ, Anastos KM, Goldman R. A genomic variant of ALPK2 is associated with increased liver fibrosis risk in HIV/HCV coinfected women. PLoS One 2021; 16:e0247277. [PMID: 33705408 PMCID: PMC7951908 DOI: 10.1371/journal.pone.0247277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/03/2021] [Indexed: 01/21/2023] Open
Abstract
HIV coinfection is associated with more rapid liver fibrosis progression in hepatitis C (HCV) infection. Recently, much work has been done to improve outcomes of liver disease and to identify targets for pharmacological intervention in coinfected patients. In this study, we analyzed clinical data of 1,858 participants from the Women's Interagency HIV Study (WIHS) to characterize risk factors associated with changes in the APRI and FIB-4 surrogate measurements for advanced fibrosis. We assessed 887 non-synonymous single nucleotide variants (nsSNV) in a subset of 661 coinfected participants for genetic associations with changes in liver fibrosis risk. The variants utilized produced amino acid substitutions that either altered an N-linked glycosylation (NxS/T) sequon or mapped to a gene related to glycosylation processes. Seven variants were associated with an increased likelihood of liver fibrosis. The most common variant, ALPK2 rs3809973, was associated with liver fibrosis in HIV/HCV coinfected patients; individuals homozygous for the rare C allele displayed elevated APRI (0.61, 95% CI, 0.334 to 0.875) and FIB-4 (0.74, 95% CI, 0.336 to 1.144) relative to those coinfected women without the variant. Although warranting replication, ALPK2 rs3809973 may show utility to detect individuals at increased risk for liver disease progression.
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Affiliation(s)
- Alec T. McIntosh
- Department of Oncology, Georgetown University, Washington, DC, United States of America
| | - Renhuizi Wei
- Department of Oncology, Georgetown University, Washington, DC, United States of America
| | - Jaeil Ahn
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, Washington, DC, United States of America
| | - Brad E. Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, New York, United States of America
| | - Seble G. Kassaye
- Department of Infectious Diseases, Georgetown University Medical Center, Washington, DC, United States of America
| | - Michael H. Augenbraun
- Division of Infectious Diseases, Department of Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York, United States of America
| | - Jennifer C. Price
- Division of Liver Diseases, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Audrey L. French
- Division of Infectious Disease, Department of Internal Medicine, Stroger Hospital of Cook County, Chicago, Illinois, United States of America
| | - Stephen J. Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kathryn M. Anastos
- Departments of Medicine and Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Radoslav Goldman
- Department of Oncology, Georgetown University, Washington, DC, United States of America,Department of Biochemistry and Molecular & Cell Biology, Georgetown University Medical Center, Washington, DC, United States of America,Clinical Translational Glycoscience Research Center, Georgetown University Medical Center, Washington, DC, United States of America,* E-mail:
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9
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Banfi D, Moro E, Bosi A, Bistoletti M, Cerantola S, Crema F, Maggi F, Giron MC, Giaroni C, Baj A. Impact of Microbial Metabolites on Microbiota-Gut-Brain Axis in Inflammatory Bowel Disease. Int J Mol Sci 2021; 22:1623. [PMID: 33562721 PMCID: PMC7915037 DOI: 10.3390/ijms22041623] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
The complex bidirectional communication system existing between the gastrointestinal tract and the brain initially termed the "gut-brain axis" and renamed the "microbiota-gut-brain axis", considering the pivotal role of gut microbiota in sustaining local and systemic homeostasis, has a fundamental role in the pathogenesis of Inflammatory Bowel Disease (IBD). The integration of signals deriving from the host neuronal, immune, and endocrine systems with signals deriving from the microbiota may influence the development of the local inflammatory injury and impacts also more distal brain regions, underlying the psychophysiological vulnerability of IBD patients. Mood disorders and increased response to stress are frequently associated with IBD and may affect the disease recurrence and severity, thus requiring an appropriate therapeutic approach in addition to conventional anti-inflammatory treatments. This review highlights the more recent evidence suggesting that alterations of the microbiota-gut-brain bidirectional communication axis may concur to IBD pathogenesis and sustain the development of both local and CNS symptoms. The participation of the main microbial-derived metabolites, also defined as "postbiotics", such as bile acids, short-chain fatty acids, and tryptophan metabolites in the development of IBD-associated gut and brain dysfunction will be discussed. The last section covers a critical evaluation of the main clinical evidence pointing to the microbiome-based therapeutic approaches for the treatment of IBD-related gastrointestinal and neuropsychiatric symptoms.
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Affiliation(s)
- Davide Banfi
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Elisabetta Moro
- Department of Internal Medicine and Therapeutics, Section of Pharmacology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (E.M.); (F.C.)
| | - Annalisa Bosi
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Michela Bistoletti
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Silvia Cerantola
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti 2, 35131 Padova, Italy; (S.C.); (M.C.G.)
| | - Francesca Crema
- Department of Internal Medicine and Therapeutics, Section of Pharmacology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (E.M.); (F.C.)
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Maria Cecilia Giron
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti 2, 35131 Padova, Italy; (S.C.); (M.C.G.)
| | - Cristina Giaroni
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
- Centre of Neuroscience, University of Insubria, 21100 Varese, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
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10
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Han Y, Wang X, Cheng X, Zhao M, Zhao T, Guo L, Liu D, Wu K, Fan M, Shi M, Zhu L. Close Homolog of L1 Deficiency Exacerbated Intestinal Epithelial Barrier Function in Mouse Model of Dextran Sulfate Sodium-Induced Colitis. Front Physiol 2020; 11:584508. [PMID: 33240104 PMCID: PMC7677258 DOI: 10.3389/fphys.2020.584508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/12/2020] [Indexed: 12/02/2022] Open
Abstract
The cell adhesion molecule CHL1, which belongs to the immunoglobulin superfamily, functions in a variety of physiological and pathological processes, including neural development, tissue injury, and repair. We previously found that the loss of CHL1 exacerbated the dextran sulfate sodium (DSS)-induced colitis in mice. In the present study, we further addressed the role of CHL1 in mouse model of DSS-induced colitis and its’ potential mechanism. Colon tissues were collected from CHL1+/+, CHL1+/−, and CHL1−/− mice after DSS induction to investigate the effects of CHL1 on the development of colitis. The data showed that CHL1 was expressed in intestine tissue, and expression of CHL1 was increased by DSS-induced inflammation. CHL1 deficiency induced more pronounced colitis features, exacerbated inflammation, and damage to colonic tissues in DSS-induced mice. Moreover, colonic tissues of CHL1−/− mice showed a marked increase in neutrophil and macrophage infiltration, be accompanied by more severe damage to intestinal epithelial cells and higher fluorescein isothiocyanate (FITC) leakage. Our results revealed deficiency of CHL1 exacerbated DSS-induced colitis, and this pathogenesis was potentially mediated by disruption of intestinal barrier integrity, indicating that CHL1 may be an attractive therapeutic target for inflammatory bowel diseases (IBDs) in mice.
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Affiliation(s)
- Ying Han
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China.,Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Xiaomeng Wang
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Xiang Cheng
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Ming Zhao
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Tong Zhao
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Liang Guo
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Dan Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Kuiwu Wu
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Ming Fan
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China.,Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China
| | - Ming Shi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Lingling Zhu
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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11
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Al-Mustanjid M, Mahmud SMH, Royel MRI, Rahman MH, Islam T, Rahman MR, Moni MA. Detection of molecular signatures and pathways shared in inflammatory bowel disease and colorectal cancer: A bioinformatics and systems biology approach. Genomics 2020; 112:3416-3426. [PMID: 32535071 DOI: 10.1016/j.ygeno.2020.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/03/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
Abstract
Emerging evidence indicates IBD is a risk factor for the increasing incidence of colorectal cancer (CRC) development. We used a system biology approach to identify common molecular signatures and pathways that interact between IBD and CRC and the indispensable pathological mechanisms. First, we identified 177 common differentially expressed genes (DEGs) between IBD and CRC. Gene set enrichment, protein-protein, DEGs-transcription factors, DEGs-microRNAs, protein-drug interaction, gene-disease association, Gene Ontology, pathway enrichment analyses were conducted to these common genes. The inclusion of common DEGs with bimolecular networks disclosed hub proteins (LYN, PLCB1, NPSR1, WNT5A, CDC25B, CD44, RIPK2, ASAP1), transcription factors (SCD, SLC7A5, IKZF3, SLC16A1, SLC7A11) and miRNAs (mir-335-5p, mir-26b-5p, mir-124-3p, mir-16-5p, mir-192-5p, mir-548c-3p, mir-29b-3p, mir-155-5p, mir-21-5p, mir-15a-5p). Analysis of the interaction between protein and drug discovered ASAP1 interacts with cysteine sulfonic acid and double oxidized cysteine drug compounds. Gene-disease association analysis retrieved ASAP1 also associated with pulmonary and bladder neoplasm diseases.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka 1207, Bangladesh
| | - S M Hasan Mahmud
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Md Rejaul Islam Royel
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka 1207, Bangladesh
| | - Md Habibur Rahman
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Tania Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali, University, Enayetpur, Sirajganj 6751, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia.
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12
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Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol 2019; 10:277. [PMID: 30915065 PMCID: PMC6421268 DOI: 10.3389/fimmu.2019.00277] [Citation(s) in RCA: 1729] [Impact Index Per Article: 345.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
Ulcerative colitis (UC) and Crohn's disease (CD), collectively known as Inflammatory Bowel Diseases (IBD), are caused by a complex interplay between genetic, immunologic, microbial and environmental factors. Dysbiosis of the gut microbiome is increasingly considered to be causatively related to IBD and is strongly affected by components of a Western life style. Bacteria that ferment fibers and produce short chain fatty acids (SCFAs) are typically reduced in mucosa and feces of patients with IBD, as compared to healthy individuals. SCFAs, such as acetate, propionate and butyrate, are important metabolites in maintaining intestinal homeostasis. Several studies have indeed shown that fecal SCFAs levels are reduced in active IBD. SCFAs are an important fuel for intestinal epithelial cells and are known to strengthen the gut barrier function. Recent findings, however, show that SCFAs, and in particular butyrate, also have important immunomodulatory functions. Absorption of SCFAs is facilitated by substrate transporters like MCT1 and SMCT1 to promote cellular metabolism. Moreover, SCFAs may signal through cell surface G-protein coupled receptors (GPCRs), like GPR41, GPR43, and GPR109A, to activate signaling cascades that control immune functions. Transgenic mouse models support the key role of these GPCRs in controlling intestinal inflammation. Here, we present an overview of microbial SCFAs production and their effects on the intestinal mucosa with specific emphasis on their relevance for IBD. Moreover, we discuss the therapeutic potential of SCFAs for IBD, either applied directly or by stimulating SCFAs-producing bacteria through pre- or probiotic approaches.
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Affiliation(s)
- Daniela Parada Venegas
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marjorie K De la Fuente
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Glauben Landskron
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - María Julieta González
- Program of Cell and Molecular Biology, Faculty of Medicine, Institute of Biomedical Sciences, Universidad de Chile, Santiago, Chile
| | - Rodrigo Quera
- Inflammatory Bowel Diseases Program, Department of Gastroenterology, Clínica Las Condes, Santiago, Chile
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Marcela A Hermoso
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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13
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Baker KT, Salk JJ, Brentnall TA, Risques RA. Precancer in ulcerative colitis: the role of the field effect and its clinical implications. Carcinogenesis 2018; 39:11-20. [PMID: 29087436 PMCID: PMC6248676 DOI: 10.1093/carcin/bgx117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/22/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022] Open
Abstract
Cumulative evidence indicates that a significant proportion of cancer evolution may occur before the development of histological abnormalities. While recent improvements in DNA sequencing technology have begun to reveal the presence of these early preneoplastic clones, the concept of 'premalignant field' was already introduced by Slaughter more than half a century ago. Also referred to as 'field effect', 'field defect' or 'field cancerization', these terms describe the phenomenon by which molecular alterations develop in normal-appearing tissue and expand to form premalignant patches with the potential to progress to dysplasia and cancer. Field effects have been well-characterized in ulcerative colitis, an inflammatory bowel disease that increases the risk of colorectal cancer. The study of the molecular alterations that define these fields is informative of mechanisms of tumor initiation and progression and has provided potential targets for early cancer detection. Herein, we summarize the current knowledge about the molecular alterations that comprise the field effect in ulcerative colitis and the clinical utility of these fields for cancer screening and prevention.
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Affiliation(s)
- Kathryn T Baker
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Jesse J Salk
- Division of Hematology and Oncology, Department of Medicine, University of
Washington, Seattle, WA, USA
- TwinStrand Biosciences Seattle, WA, USA
| | - Teresa A Brentnall
- Division of Gasteroenterology, Department of Medicine, University of
Washington, Seattle, WA, USA
| | - Rosa Ana Risques
- To whom correspondence should be addressed. Tel: +206-616-4976; Fax:
+206-543-1140;
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14
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Palmieri O, Creanza TM, Bossa F, Latiano T, Corritore G, Palumbo O, Martino G, Biscaglia G, Scimeca D, Carella M, Ancona N, Andriulli A, Latiano A. Functional Implications of MicroRNAs in Crohn's Disease Revealed by Integrating MicroRNA and Messenger RNA Expression Profiling. Int J Mol Sci 2017; 18:E1580. [PMID: 28726756 PMCID: PMC5536068 DOI: 10.3390/ijms18071580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 07/12/2017] [Accepted: 07/16/2017] [Indexed: 12/11/2022] Open
Abstract
Crohn's disease (CD) is a debilitating inflammatory bowel disease (IBD) that emerges due to the influence of genetic and environmental factors. microRNAs (miRNAs) have been identified in the tissue and sera of IBD patients and may play an important role in the induction of IBD. Our study aimed to identify differentially expressed miRNAs and miRNAs with the ability to alter transcriptome activity by comparing inflamed tissue samples with their non-inflamed counterparts. We studied changes in miRNA-mRNA interactions associated with CD by examining their differential co-expression relative to normal mucosa from the same patients. Correlation changes between the two conditions were incorporated into scores of predefined gene sets to identify biological processes with altered miRNA-mediated control. Our study identified 28 miRNAs differentially expressed (p-values < 0.01), of which 14 are up-regulated. Notably, our differential co-expression analysis highlights microRNAs (i.e., miR-4284, miR-3194 and miR-21) that have known functional interactions with key mechanisms implicated in IBD. Most of these miRNAs cannot be detected by differential expression analysis that do not take into account miRNA-mRNA interactions. The identification of differential miRNA-mRNA co-expression patterns will facilitate the investigation of the miRNA-mediated molecular mechanisms underlying CD pathogenesis and could suggest novel drug targets for validation.
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Affiliation(s)
- Orazio Palmieri
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Teresa Maria Creanza
- Institute of Intelligent Systems for Automation, National Research Council, CNR-ISSIA, 70126 Bari, Italy.
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, 10124 Turin, Italy.
| | - Fabrizio Bossa
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Tiziana Latiano
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Giuseppe Corritore
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Orazio Palumbo
- IRCCS 'Casa Sollievo della Sofferenza', Division of Medical Genetics, 71013 San Giovanni Rotondo, Italy.
| | - Giuseppina Martino
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Giuseppe Biscaglia
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Daniela Scimeca
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Massimo Carella
- IRCCS 'Casa Sollievo della Sofferenza', Division of Medical Genetics, 71013 San Giovanni Rotondo, Italy.
| | - Nicola Ancona
- Institute of Intelligent Systems for Automation, National Research Council, CNR-ISSIA, 70126 Bari, Italy.
| | - Angelo Andriulli
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
| | - Anna Latiano
- IRCCS 'Casa Sollievo della Sofferenza', Division of Gastroenterology, 71013 San Giovanni Rotondo, Italy.
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15
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Klaus B, Reisenauer S. An end to end workflow for differential gene expression using Affymetrix microarrays. F1000Res 2016; 5:1384. [PMID: 30101006 PMCID: PMC6063319 DOI: 10.12688/f1000research.8967.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 09/27/2023] Open
Abstract
In this article, we walk through an end-to-end Affymetrix microarray differential expression workflow using Bioconductor packages. This workflow is directly applicable to current "Gene" type arrays, e.g. the HuGene or MoGene arrays but can easily adapted to similar platforms. The data re-analyzed is a typical clinical microarray data set that compares inflammed and non-inflammed colon tissue in two disease subtypes. We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis. As experimental designs can be complex, a self contained introduction to linear models is also part of the workflow.
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16
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Klaus B, Reisenauer S. An end to end workflow for differential gene expression using Affymetrix microarrays. F1000Res 2016; 5:1384. [PMID: 30101006 PMCID: PMC6063319 DOI: 10.12688/f1000research.8967.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2018] [Indexed: 01/12/2023] Open
Abstract
In this article, we walk through an end-to-end Affymetrix microarray differential expression workflow using Bioconductor packages. This workflow is directly applicable to current "Gene'' type arrays, e.g.the HuGene or MoGene arrays, but can easily be adapted to similar platforms. The data analyzed here is a typical clinical microarray data set that compares inflamed and non-inflamed colon tissue in two disease subtypes. For each disease, the differential gene expression between inflamed- and non-inflamed colon tissue was analyzed. We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis.
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