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Ahmadi H, Reddy S, Nguyen C, Douglawi A, Ladi‐Seyedian S, Roberts S, Ghoreifi A, Ghodoussipour S, Bhanvadia SK, Djaladat H, Schuckman A, Daneshmand S. Long‐Term Renal Function in Patients with CKD following Radical Cystectomy and Orthotopic Neobladder. BJU Int 2022; 130:200-207. [DOI: 10.1111/bju.15685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Hamed Ahmadi
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Sharath Reddy
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Charles Nguyen
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Antoin Douglawi
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Sanam Ladi‐Seyedian
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Sidney Roberts
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Alireza Ghoreifi
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Saum Ghodoussipour
- Division of Urology Department of Surgery Rutgers Cancer Institute of New Jersey Rutgers New Jersey Medical School Newark NJ USA
| | - Sumeet K. Bhanvadia
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Hooman Djaladat
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Anne Schuckman
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
| | - Siamak Daneshmand
- Department of Urology Norris Comprehensive Cancer Center University of Southern California Los Angeles CA USA
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2
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Vu H, Ernst J. Universal annotation of the human genome through integration of over a thousand epigenomic datasets. Genome Biol 2022; 23:9. [PMID: 34991667 PMCID: PMC8734071 DOI: 10.1186/s13059-021-02572-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/08/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative "stacked modeling" approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges. RESULTS Using a version of ChromHMM enhanced for large-scale applications, we apply the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, with the learned model denoted as the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we use in characterizing each state. Compared to per-cell-type annotations, the full-stack annotations directly differentiate constitutive from cell type-specific activity and is more predictive of locations of external genomic annotations. CONCLUSIONS The full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing per-cell-type annotations for studying the non-coding human genome.
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Affiliation(s)
- Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, 90095, USA
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, CA, 90095, USA
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3
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Chen B, Chen X, Wang W, Shen J, Song Z, Ji H, Zhang F, Wu J, Na J, Li S. Tissue-engineered autologous peritoneal grafts for bladder reconstruction in a porcine model. J Tissue Eng 2021; 12:2041731420986796. [PMID: 33613958 PMCID: PMC7874343 DOI: 10.1177/2041731420986796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023] Open
Abstract
Ileal neobladder construction is a common treatment for patients with bladder cancer after radical cystectomy. However, metabolic disorders caused by transposed bowel segments occur frequently. Bladder tissue engineering is a promising alternative approach. Although numerous studies have reported bladder reconstruction using acellular and cellular scaffolds, there are also disadvantages associated with these methods, such as immunogenicity of synthetic grafts and incompatible mechanical properties of the biomaterials. Here, we engineered an autologous peritoneal graft consisting of a peritoneal sheet and the seromuscular layer from the ileum. Three months after the surgery, compared with the neobladder made from the ileum, the reconstructed neobladder using our new method showed normal function and better gross morphological characteristics. Moreover, histopathological and transcriptomic analysis revealed urothelium-like cells expressing urothelial biomarkers appeared in the neobladder, while no such changes were observed in the control group. Overall, our study provides a new strategy for bladder tissue engineering and informs a variety of future research prospects.
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Affiliation(s)
- Biao Chen
- School of Clinical Medicine, Tsinghua University, Beijing, China.,Department of Urology, The First Hospital of Tsinghua University, Beijing, China
| | - Xia Chen
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Wenjia Wang
- Department of Urology, The First Hospital of Tsinghua University, Beijing, China
| | - Jun Shen
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhiqiang Song
- Department of Urology, The First Hospital of Tsinghua University, Beijing, China
| | - Haoyu Ji
- School of Clinical Medicine, Tsinghua University, Beijing, China.,Department of Urology, The First Hospital of Tsinghua University, Beijing, China
| | - Fangyuan Zhang
- School of Clinical Medicine, Tsinghua University, Beijing, China.,Department of Urology, The First Hospital of Tsinghua University, Beijing, China
| | - Jianchen Wu
- Department of Urology, The First Hospital of Tsinghua University, Beijing, China
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Shengwen Li
- School of Clinical Medicine, Tsinghua University, Beijing, China.,Department of Urology, The First Hospital of Tsinghua University, Beijing, China
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4
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Abstract
There is emerging evidence that the immune biology associated with lung and other solid tumors, as well as patient immune genetic traits, contributes to individual survival. At this time, dramatic advances in immunologic approaches to the study and management of human cancers are taking place, including lung and head and neck squamous cell carcinoma. However, major obstacles for therapies are the profound immune alterations in blood and in the tumor microenvironment that arise in tandem with the cancer. Although there is a significant current effort underway across the cancer research community to probe the tumor environment to uncover the dynamics of the immune response, little similar work is being done to understand the dynamics of immune alterations in peripheral blood, despite evidence showing the prognostic relevance of the neutrophil/lymphocyte ratio for these cancers. A prominent feature of cancer-associated inflammation is the generation of myeloid-derived suppressor cells, which arise centrally in bone marrow myelopoiesis and peripherally in response to tumor factors. Two classes of myeloid-derived suppressor cells are recognized: granulocytic and monocytic. To date, such immune factors have not been integrated into molecular classification or prognostication. Here, we advocate for a more complete characterization of patient immune profiles, using DNA from archival peripheral blood after application of methylation profiling (immunomethylomics). At the heart of this technology are cell libraries of differentially methylated regions that provide the "fingerprints" of immune cell subtypes. Going forward, opportunities exist to explore aberrant immune profiles in the context of cancer-associated inflammation, potentially adding significantly to prognostic and mechanistic information for solid tumors.
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5
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Liu M, Thomas SL, DeWitt AK, Zhou W, Madaj ZB, Ohtani H, Baylin SB, Liang G, Jones PA. Dual Inhibition of DNA and Histone Methyltransferases Increases Viral Mimicry in Ovarian Cancer Cells. Cancer Res 2018; 78:5754-5766. [PMID: 30185548 DOI: 10.1158/0008-5472.can-17-3953] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/28/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
Ovarian cancer ranks as the most deadly gynecologic cancer, and there is an urgent need to develop more effective therapies. Previous studies have shown that G9A, a histone methyltransferase that catalyzes mono- and dimethylation of histone H3 lysine9, is highly expressed in ovarian cancer tumors, and its overexpression is associated with poor prognosis. Here we report that pharmacologic inhibition of G9A in ovarian cancer cell lines with high levels of G9A expression induces synergistic antitumor effects when combined with the DNA methylation inhibitor (DNMTi) 5-aza-2'-deoxycytidine (5-aza-CdR). These antitumor effects included upregulation of endogenous retroviruses (ERV), activation of the viral defense response, and induction of cell death, which have been termed "viral mimicry" effects induced by DNMTi. G9Ai treatment further reduced H3K9me2 levels within the long terminal repeat regions of ERV, resulting in further increases of ERV expression and enhancing "viral mimicry" effects. In contrast, G9Ai and 5-aza-CdR were not synergistic in cell lines with low basal G9A levels. Taken together, our results suggest that the synergistic effects of combination treatment with DNMTi and G9Ai may serve as a novel therapeutic strategy for patients with ovarian cancer with high levels of G9A expression.Significance: Dual inhibition of DNA methylation and histone H3 lysine 9 dimethylation by 5-aza-CdR and G9Ai results in synergistic upregulation of ERV and induces an antiviral response, serving as a basis for exploring this novel combination treatment in patients with ovarian cancer. Cancer Res; 78(20); 5754-66. ©2018 AACR.
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Affiliation(s)
- Minmin Liu
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | | | - Wanding Zhou
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | | | - Stephen B Baylin
- Van Andel Research Institute, Grand Rapids, Michigan.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan.
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6
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Fiziev P, Ernst J. ChromTime: modeling spatio-temporal dynamics of chromatin marks. Genome Biol 2018; 19:109. [PMID: 30097049 PMCID: PMC6085762 DOI: 10.1186/s13059-018-1485-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/17/2018] [Indexed: 11/17/2022] Open
Abstract
To model spatial changes of chromatin mark peaks over time we develop and apply ChromTime, a computational method that predicts peaks to be either expanding, contracting, or holding steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provide information about gene expression changes beyond localized signal density changes. ChromTime detects asymmetric expansions and contractions, which for some marks associate with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.
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Affiliation(s)
- Petko Fiziev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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7
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Abstract
Noncoding DNA regions have central roles in human biology, evolution, and disease. ChromHMM helps to annotate the noncoding genome using epigenomic information across one or multiple cell types. It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type. ChromHMM learns chromatin-state signatures using a multivariate hidden Markov model (HMM) that explicitly models the combinatorial presence or absence of each mark. ChromHMM uses these signatures to generate a genome-wide annotation for each cell type by calculating the most probable state for each genomic segment. ChromHMM provides an automated enrichment analysis of the resulting annotations to facilitate the functional interpretations of each chromatin state. ChromHMM is distinguished by its modeling emphasis on combinations of marks, its tight integration with downstream functional enrichment analyses, its speed, and its ease of use. Chromatin states are learned, annotations are produced, and enrichments are computed within 1 d.
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8
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Barnicle A, Seoighe C, Greally JM, Golden A, Egan LJ. Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis. Epigenetics 2017; 12:591-606. [PMID: 28557546 DOI: 10.1080/15592294.2017.1334023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate <0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes PRAC1 and PRAC2. Four genes showed inverse correlation between methylation and gene expression; ROR1, GXYLT2, FOXA2, and, notably, RARB, a gene previously identified as a tumor suppressor in colorectal adenocarcinoma as well as breast, lung and prostate cancer. We highlight targeted and specific patterns of DNA methylation and gene expression in epithelial cells from inflamed colon, while challenging the importance of epithelial cells in the pathogenesis of chronic inflammation.
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Affiliation(s)
- Alan Barnicle
- a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland.,b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland
| | - Cathal Seoighe
- b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland
| | - John M Greally
- c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA
| | - Aaron Golden
- b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland.,c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA.,d Department of Mathematical Sciences , Yeshiva University , 2495 Amsterdam Avenue, New York , NY , USA
| | - Laurence J Egan
- a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland
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9
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Sadler T, Bhasin JM, Xu Y, Barnholz-Sloan J, Chen Y, Ting AH, Stylianou E. Genome-wide analysis of DNA methylation and gene expression defines molecular characteristics of Crohn's disease-associated fibrosis. Clin Epigenetics 2016; 8:30. [PMID: 26973718 PMCID: PMC4789277 DOI: 10.1186/s13148-016-0193-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/29/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Fibrosis of the intestine is a common and poorly understood complication of Crohn's disease (CD) characterized by excessive deposition of extracellular matrix and accompanied by narrowing and obstruction of the gut lumen. Defining the molecular characteristics of this fibrotic disorder is a vital step in the development of specific prediction, prevention, and treatment strategies. Previous epigenetic studies indicate that alterations in DNA methylation could explain the mechanism by which mesenchymal cells adopt the requisite pro-fibrotic phenotype that promotes fibrosis progression. However, to date, genome-wide analysis of the DNA methylome of any type of human fibrosis is lacking. We employed an unbiased approach using deep sequencing to define the DNA methylome and transcriptome of purified fibrotic human intestinal fibroblasts (HIF) from the colons of patients with fibrostenotic CD. RESULTS When compared with normal fibroblasts, we found that the majority of differential DNA methylation was within introns and intergenic regions and not associated with CpG islands. Only a low percentage occurred in the promoters and exons of genes. Integration of the DNA methylome and transcriptome identified regions in three genes that inversely correlated with gene expression: wingless-type mouse mammary tumor virus integration site family, member 2B (WNT2B) and two eicosanoid synthesis pathway enzymes (prostacyclin synthase and prostaglandin D2 synthase). These findings were independently validated by RT-PCR and bisulfite sequencing. Network analysis of the data also identified candidate molecular interactions relevant to fibrosis pathology. CONCLUSIONS Our definition of a genome-wide fibrosis-specific DNA methylome provides new gene networks and epigenetic states by which to understand mechanisms of pathological gene expression that lead to fibrosis. Our data also provide a basis for development of new fibrosis-specific therapies, as genes dysregulated in fibrotic Crohn's disease, following functional validation, can serve as new therapeutic targets.
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Affiliation(s)
- Tammy Sadler
- Department of Pathobiology, Cleveland Clinic Lerner Research Institute, 9500 Euclid Avenue/NC-22, Cleveland, OH 44195 USA
| | - Jeffrey M Bhasin
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue/NC-22, Cleveland, OH 44195 USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Jill Barnholz-Sloan
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH USA
| | - Yanwen Chen
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH USA
| | - Angela H Ting
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue/NC-22, Cleveland, OH 44195 USA
| | - Eleni Stylianou
- Department of Pathobiology, Cleveland Clinic Lerner Research Institute, 9500 Euclid Avenue/NC-22, Cleveland, OH 44195 USA.,Department of Gastroenterology and Hepatology, Digestive Diseases Institute, Cleveland Clinic, Cleveland, OH USA
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10
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Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ. Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells. Physiol Genomics 2016; 48:257-73. [PMID: 26812987 DOI: 10.1152/physiolgenomics.00046.2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 01/13/2016] [Indexed: 12/24/2022] Open
Abstract
Region and cell-type specific differences in the molecular make up of colon epithelial cells have been reported. Those differences may underlie the region-specific characteristics of common colon epithelial diseases such as colorectal cancer and inflammatory bowel disease. DNA methylation is a cell-type specific epigenetic mark, essential for transcriptional regulation, silencing of repetitive DNA and genomic imprinting. Little is known about any region-specific variations in methylation patterns in human colon epithelial cells. Using purified epithelial cells and whole biopsies (n= 19) from human subjects, we generated epigenome-wide DNA methylation data (using the HELP-tagging assay), comparing the methylation signatures of the proximal and distal colon. We identified a total of 125 differentially methylated sites (DMS) mapping to transcription start sites of protein-coding genes, most notably several members of the homeobox (HOX) family of genes. Patterns of differential methylation were validated with MassArray EpiTYPER. We also examined DNA methylation in whole biopsies, applying a computational technique to deconvolve variation in methylation within cell types and variation in cell-type composition across biopsies. Including inferred epithelial proportions as a covariate in differential methylation analysis applied to the whole biopsies resulted in greater overlap with the results obtained from purified epithelial cells compared with when the covariate was not included. Results obtained from both approaches highlight region-specific methylation patterns of HOX genes in colonic epithelium. Regional variation in methylation patterns has implications for the study of diseases that exhibit regional expression patterns in the human colon, such as inflammatory bowel disease and colorectal cancer.
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Affiliation(s)
- Alan Barnicle
- Clinical Pharmacology, School of Medicine, National University of Ireland, Galway, Ireland; School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland; and
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland; and
| | - Aaron Golden
- Center of Epigenomics and Department of Genetics (Division of Computational Genetics), Albert Einstein College of Medicine, Bronx, New York
| | - John M Greally
- Center of Epigenomics and Department of Genetics (Division of Computational Genetics), Albert Einstein College of Medicine, Bronx, New York
| | - Laurence J Egan
- Clinical Pharmacology, School of Medicine, National University of Ireland, Galway, Ireland;
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11
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Hah N, Sherman MH, Yu RT, Downes M, Evans RM. Targeting Transcriptional and Epigenetic Reprogramming in Stromal Cells in Fibrosis and Cancer. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:249-55. [PMID: 26801159 DOI: 10.1101/sqb.2015.80.027185] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The basis of many human diseases arises from both genetic and epigenetic regulation. Recent advances in the understanding of the mechanisms underlying transcriptional and epigenetic regulation and their prevalence as contributors to a diverse range of human diseases have led us to focus on transcription and epigenetic changes in a variety of human disease conditions. Specifically, our recent studies in liver fibrosis and pancreatic cancer have demonstrated that the epigenetic regulation in hepatic stellate cells (HSCs) and pancreatic stellate cells (PSCs) significantly contributes to the progress in such diseases and presents great therapeutic potential. We show that the vitamin D receptor (VDR) acts as a master genomic suppressor in both HSC and PSC activation. The studies also have demonstrated that the VDR ligand reduces fibrosis and inflammation in a murine liver fibrosis and pancreatitis model. Although our current studies focus on characterizing the roles of VDR and regulatory regions within gene promoters and regulatory enhancers, we have expanded our effort to epigenetic mechanisms as major determinants of gene activation and repression in order to develop potential therapeutics to modulate stroma-associated pathologies including inflammation, fibrosis, and cancer.
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Affiliation(s)
- Nasun Hah
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Mara H Sherman
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Ruth T Yu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Michael Downes
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Ronald M Evans
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037 Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037
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12
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Evangelista M, Baroudi ME, Rizzo M, Tuccoli A, Poliseno L, Pellegrini M, Rainaldi G. Alkaline Phosphatase-Positive Immortal Mouse Embryo Fibroblasts Are Cells in a Transitional Reprogramming State Induced to Face Environmental Stresses. GENETICS & EPIGENETICS 2016; 7:33-41. [PMID: 26740745 PMCID: PMC4694620 DOI: 10.4137/geg.s27696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/25/2015] [Accepted: 05/27/2015] [Indexed: 12/31/2022]
Abstract
In this study, we report that immortal mouse embryonic fibroblasts (I-MEFs) have a baseline level of cells positive for alkaline phosphatase (AP+) staining. Environmental stresses, including long-lasting growth in the absence of expansion and treatment with drugs, enhance the frequency of AP+ I-MEFs. By adapting fast red AP staining to the sorting procedure, we separated AP+ and AP− I-MEFs and demonstrated that the differentially expressed genes are consistent with a reprogrammed phenotype. In particular, we found that sestrin 1 is upregulated in AP+ I-MEFs. We focused on this gene and demonstrated that increased sestrin 1 expression is accompanied by the growth of I-MEFs in the absence of expansion and occurs before the formation of AP+ I-MEFs. Together with sestrin 1 upregulation, we found that AP+ I-MEFs accumulated in the G1 phase of the cell cycle, suggesting that the two events are causally related. Accordingly, we found that silencing sestrin 1 expression reduced the frequency and G1 accumulation of AP+ I-MEFs. Taken together, our data suggested that I-MEFs stressed by environmental changes acquire the AP+ phenotype and achieve a quiescent state characterized by a new transcriptional network.
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Affiliation(s)
| | | | - Milena Rizzo
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.; Tuscan Tumor Institute (ITT), Firenze, Italy
| | - Andrea Tuccoli
- Oncogenomics Unit, Core Research Laboratory (CRL), Tuscan Tumor Institute (ITT), Pisa, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.; Oncogenomics Unit, Core Research Laboratory (CRL), Tuscan Tumor Institute (ITT), Pisa, Italy
| | - Marco Pellegrini
- Laboratory of Integrative Systems Medicine (LISM), CNR, Pisa, Italy
| | - Giuseppe Rainaldi
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.; Tuscan Tumor Institute (ITT), Firenze, Italy
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13
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Roznovăţ IA, Ruskin HJ. Theoretical cross-comparative analysis on dynamics of small intestine and colon crypts during cancer initiation. IET Syst Biol 2015; 9:259-67. [PMID: 26577160 DOI: 10.1049/iet-syb.2015.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetics is emerging as a fundamentally important area of biological and medical research that has implications for our understanding of human diseases including cancer, autoimmune and neuropsychiatric disorders. In the context of recent efforts on personalised medicine, a novel research direction is concerned with identification of intra-individual epigenetic variation linked to disease predisposition and development, i.e. epigenome-wide association studies. A computational model has been developed to describe the dynamics and structure of human intestinal crypts and to perform a comparative analysis on aberrant DNA methylation level induced in these during cancer initiation. The crypt framework, AgentCrypt, is an agent-based model of crypt dynamics, which handles intra- and inter-dependencies. In addition, the AgentCrypt model is used to investigate the effect of a set of potential inhibitors with respect to methylation modification in intestinal tissue during initiation of disease. Methylation level decrease over a relatively short period of 90 days is marked for the colon compared to the small intestine, although similar alterations are induced in both tissues. In addition, inhibitor effect is notable for abnormal crypt groups, with largest average methylation differences observed ≈0.75% lower in the colon and ≈0.79% lower in the small intestine with inhibitor present.
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Affiliation(s)
- Irina A Roznovăţ
- Current address: European Institute for Systems Biology and Medicine (EISBM), CNRS-ENS-UCBL, Campus Charles Mérieux, Université de Lyon, 50 Avenue Tony Garnier, 69366 Lyon cedex 07, France.
| | - Heather J Ruskin
- Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM), School of Computing, Dublin City University, Dublin, Ireland
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