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Triff K, McLean MW, Callaway E, Goldsby J, Ivanov I, Chapkin RS. Dietary fat and fiber interact to uniquely modify global histone post-translational epigenetic programming in a rat colon cancer progression model. Int J Cancer 2018; 143:1402-1415. [PMID: 29659013 DOI: 10.1002/ijc.31525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 02/21/2018] [Accepted: 03/22/2018] [Indexed: 12/15/2022]
Abstract
Dietary fermentable fiber generates short-chain fatty acids (SCFA), for example, butyrate, in the colonic lumen which serves as a chemoprotective histone deacetylase inhibitor and/or as an acetylation substrate for histone acetylases. In addition, n-3 polyunsaturated fatty acids (n-3 PUFA) in fish oil can affect the chromatin landscape by acting as ligands for tumor suppressive nuclear receptors. In an effort to gain insight into the global dimension of post-translational modification of histones (including H3K4me3 and H3K9ac) and clarify the chemoprotective impact of dietary bioactive compounds on transcriptional control in a preclinical model of colon cancer, we generated high-resolution genome-wide RNA (RNA-Seq) and "chromatin-state" (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed diets containing bioactive (i) fish oil, (ii) fermentable fiber (a rich source of SCFA), (iii) a combination of fish oil plus pectin, or (iv) control, devoid of fish oil or pectin. In general, poor correlation was observed between differentially transcribed (DE) and enriched genes (DERs) at multiple epigenetic levels. The combinatorial diet (fish oil + pectin) uniquely affected transcriptional profiles in the intestinal epithelium, for example, upregulating lipid catabolism and beta-oxidation associated genes. These genes were linked to activated ligand-dependent nuclear receptors associated with n-3 PUFA and were also correlated with the mitochondrial L-carnitine shuttle and the inhibition of lipogenesis. These findings demonstrate that the chemoprotective fish oil + pectin combination diet uniquely induces global histone state modifications linked to the expression of chemoprotective genes.
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Affiliation(s)
- Karen Triff
- Department of Nutrition and Food Science - Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX
- Department of Biology, Texas A&M University, College Station, TX
| | - Mathew W McLean
- Department of Statistics, Texas A&M University, College Station, TX
| | - Evelyn Callaway
- Department of Nutrition and Food Science - Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX
| | - Jennifer Goldsby
- Department of Nutrition and Food Science - Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX
| | - Ivan Ivanov
- Veterinary Physiology & Pharmacology, Texas A&M University, College Station, TX
| | - Robert S Chapkin
- Department of Nutrition and Food Science - Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX
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Knight JM, Ivanov I, Triff K, Chapkin RS, Dougherty ER. Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification. IEEE/ACM Trans Comput Biol Bioinform 2018; 15:484-493. [PMID: 26441451 PMCID: PMC4818202 DOI: 10.1109/tcbb.2015.2485223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Differential gene expression testing is an analysis commonly applied to RNA-Seq data. These statistical tests identify genes that are significantly different across phenotypes. We extend this testing paradigm to multivariate gene interactions from a classification perspective with the goal to detect novel gene interactions for the phenotypes of interest. This is achieved through our novel computational framework comprised of a hierarchical statistical model of the RNA-Seq processing pipeline and the corresponding optimal Bayesian classifier. Through Markov Chain Monte Carlo sampling and Monte Carlo integration, we compute quantities where no analytical formulation exists. The performance is then illustrated on an expression dataset from a dietary intervention study where we identify gene pairs that have low classification error yet were not identified as differentially expressed. Additionally, we have released the software package to perform OBC classification on RNA-Seq data under an open source license and is available at http://bit.ly/obc_package.
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Hou TY, Davidson LA, Kim E, Fan YY, Fuentes NR, Triff K, Chapkin RS. Nutrient-Gene Interaction in Colon Cancer, from the Membrane to Cellular Physiology. Annu Rev Nutr 2017; 36:543-70. [PMID: 27431370 DOI: 10.1146/annurev-nutr-071715-051039] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The International Agency for Research on Cancer recently released an assessment classifying red and processed meat as "carcinogenic to humans" on the basis of the positive association between increased consumption and risk for colorectal cancer. Diet, however, can also decrease the risk for colorectal cancer and be used as a chemopreventive strategy. Bioactive dietary molecules, such as n-3 polyunsaturated fatty acids, curcumin, and fermentable fiber, have been proposed to exert chemoprotective effects, and their molecular mechanisms have been the focus of research in the dietary/chemoprevention field. Using these bioactives as examples, this review surveys the proposed mechanisms by which they exert their effects, from the nucleus to the cellular membrane. In addition, we discuss emerging technologies involving the culturing of colonic organoids to study the physiological effects of dietary bioactives. Finally, we address future challenges to the field regarding the identification of additional molecular mechanisms and other bioactive dietary molecules that can be utilized in our fight to reduce the incidence of colorectal cancer.
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Affiliation(s)
- Tim Y Hou
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843; .,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Laurie A Davidson
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843; .,Department of Nutrition and Food Science, Texas A&M University, College Station, Texas 77843.,Center for Translational Environmental Health Research, Texas A&M University, College Station, Texas 77843
| | - Eunjoo Kim
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843; .,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas 77843
| | - Yang-Yi Fan
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843; .,Department of Nutrition and Food Science, Texas A&M University, College Station, Texas 77843
| | - Natividad R Fuentes
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843; .,Faculty of Toxicology, Texas A&M University, College Station, Texas 77843
| | - Karen Triff
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843;
| | - Robert S Chapkin
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas 77843; .,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843.,Department of Nutrition and Food Science, Texas A&M University, College Station, Texas 77843.,Faculty of Toxicology, Texas A&M University, College Station, Texas 77843.,Center for Translational Environmental Health Research, Texas A&M University, College Station, Texas 77843
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Triff K, McLean MW, Konganti K, Pang J, Callaway E, Zhou B, Ivanov I, Chapkin RS. Assessment of histone tail modifications and transcriptional profiling during colon cancer progression reveals a global decrease in H3K4me3 activity. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1392-1402. [PMID: 28315775 DOI: 10.1016/j.bbadis.2017.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/08/2017] [Accepted: 03/14/2017] [Indexed: 01/07/2023]
Abstract
During colon cancer, epigenetic alterations contribute to the dysregulation of major cellular functions and signaling pathways. Modifications in chromatin signatures such as H3K4me3 and H3K9ac, which are associated with transcriptionally active genes, can lead to genomic instability and perturb the expression of gene sets associated with oncogenic processes. In order to further elucidate early pre-tumorigenic epigenetic molecular events driving CRC, we integrated diverse, genome-wide, epigenetic inputs (by high throughput sequencing of RNA, H3K4me3, and H3K9ac) and compared differentially expressed transcripts (DE) and enriched regions (DER) in an in-vivo rat colon cancer progression model. Carcinogen (AOM) effects were detected genome-wide at the RNA (116 DE genes), K9ac (49 DERs including 24 genes) and K4me3 (7678 DERs including 3792 genes) level. RNA-seq differential expression and pathway analysis indicated that interferon-associated innate immune responses were impacted by AOM exposure. Despite extensive associations between K4me3 DERs and colon tumorigenesis (1210 genes were linked to colorectal carcinoma) including FOXO3, GNAI2, H2AFX, MSH2, NR3C1, PDCD4 and VEGFA, these changes were not reflected at the RNA gene expression level during early cancer progression. Collectively, our results indicate that carcinogen-induced changes in gene K4me3 DERs are harbingers of future transcriptional events, which drive malignant transformation of the colon.
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Affiliation(s)
- Karen Triff
- Department of Nutrition and Food Science and Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Mathew W McLean
- Department of Statistics in Texas A&M University, College Station, 77843, TX, USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
| | - Jiahui Pang
- Department of Nutrition and Food Science and Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX 77843, USA
| | - Evelyn Callaway
- Department of Nutrition and Food Science and Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX 77843, USA
| | - Beiyan Zhou
- Veterinary Physiology & Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Ivan Ivanov
- Department of Nutrition and Food Science and Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX 77843, USA; Department of Statistics in Texas A&M University, College Station, 77843, TX, USA; Veterinary Physiology & Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Robert S Chapkin
- Department of Nutrition and Food Science and Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX 77843, USA.
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Ying W, Tseng A, Chang RCA, Morin A, Brehm T, Triff K, Nair V, Zhuang G, Song H, Kanameni S, Wang H, Golding MC, Bazer FW, Chapkin RS, Safe S, Zhou B. MicroRNA-223 is a crucial mediator of PPARγ-regulated alternative macrophage activation. J Clin Invest 2015; 125:4149-59. [PMID: 26436647 DOI: 10.1172/jci81656] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 08/27/2015] [Indexed: 12/27/2022] Open
Abstract
Polarized activation of adipose tissue macrophages (ATMs) is crucial for maintaining adipose tissue function and mediating obesity-associated cardiovascular risk and metabolic abnormalities; however, the regulatory network of this key process is not well defined. Here, we identified a PPARγ/microRNA-223 (miR-223) regulatory axis that controls macrophage polarization by targeting distinct downstream genes to shift the cellular response to various stimuli. In BM-derived macrophages, PPARγ directly enhanced miR-223 expression upon exposure to Th2 stimuli. ChIP analysis, followed by enhancer reporter assays, revealed that this effect was mediated by PPARγ binding 3 PPARγ regulatory elements (PPREs) upstream of the pre-miR-223 coding region. Moreover, deletion of miR-223 impaired PPARγ-dependent macrophage alternative activation in cells cultured ex vivo and in mice fed a high-fat diet. We identified Rasa1 and Nfat5 as genuine miR-223 targets that are critical for PPARγ-dependent macrophage alternative activation, whereas the proinflammatory regulator Pknox1, which we reported previously, mediated miR-223-regulated macrophage classical activation. In summary, this study provides evidence to support the crucial role of a PPARγ/miR-223 regulatory axis in controlling macrophage polarization via distinct downstream target genes.
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Triff K, Knight J, Ivanov I, Zhou B, Chapkin R. Epigenetic Mechanisms by Which Chemoprotective Natural Compounds Promote RXR/FXR Signaling and Reduce Colon Cancer Progression. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.394.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Karen Triff
- Program in Integrative Nutrition & Complex Diseases Texas A&M UniversityCollege StationTexasUnited States
| | - Jason Knight
- Program in Integrative Nutrition & Complex Diseases Texas A&M UniversityCollege StationTexasUnited States
| | - Ivan Ivanov
- Veterinary Physiology & Pharmacology Texas A&M UniversityCollege StationTexasUnited States
| | - Beiyan Zhou
- Veterinary Physiology & Pharmacology Texas A&M UniversityCollege StationTexasUnited States
| | - Robert Chapkin
- Program in Integrative Nutrition & Complex Diseases Texas A&M UniversityCollege StationTexasUnited States
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Triff K, Konganti K, Gaddis S, Zhou B, Ivanov I, Chapkin RS. Genome-wide analysis of the rat colon reveals proximal-distal differences in histone modifications and proto-oncogene expression. Physiol Genomics 2013; 45:1229-43. [PMID: 24151245 DOI: 10.1152/physiolgenomics.00136.2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the colonic longitudinal axis, contributes to the differential incidence of site-specific pathology. To test this hypothesis, we assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. Crypts were isolated from the proximal and distal colonic regions from rats maintained on a semipurified diet, and mRNA gene expression profiles were generated by RNA-Seq. The remaining isolated crypts were formaldehyde-cross-linked and chromatin immunoprecipitated with antibodies against H3K4me3, H3K9me3, and RNA polymerase II. Globally, RNA-Seq results indicate that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. Gene ontology analysis indicates that crypt location significantly affected both chromatin and transcriptional regulation of genes involved in enterocyte movement, lipid metabolism, lymphatic development, and immune cell trafficking. Gene function analysis indicates that the PI3-kinase signaling pathway was regulated in a site-specific manner, e.g., proto-oncogenes, JUN, FOS, and ATF, were upregulated in the distal colon. Middle and long noncoding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon.
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Affiliation(s)
- Karen Triff
- Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, Texas
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