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Hashemi Z, Hui T, Wu A, Matouba D, Zukowski S, Nejati S, Lim C, Bruzzese J, Seabold K, Mills C, Lin C, Wrath K, Wang H, Wang H, Verzi MP, Perekatt A. Smad4 Loss in the Mouse Intestinal Epithelium Alleviates the Pathological Fibrotic Response to Injury in the Colon. bioRxiv 2024:2024.03.08.578000. [PMID: 38559102 PMCID: PMC10979917 DOI: 10.1101/2024.03.08.578000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mucosal healing is associated with better clinical outcomes in patients with inflammatory bowel diseases (IBDs). Unresolved injury and inflammation, on the other hand, increases pathological fibrosis and the predisposition to cancer. Loss of Smad4, a tumor suppressor, is known to increase colitis-associated cancer in mouse models of chronic IBD. Since common biological processes are involved in both injury repair and tumor growth, we sought to investigate the effect of Smad4 loss on the response to epithelial injury. To this end, Smad4 was knocked out specifically in the intestinal epithelium and transcriptomic and morphological changes compared between wild type mice and Smad4 knock out mice after DSS-induced injury. We find that Smad4 loss alleviates pathological fibrosis and enhances mucosal repair. The transcriptomic changes specific to epithelium indicate molecular changes that affect epithelial extracellular matrix (ECM) and promote enhanced mucosal repair. These findings suggest that the biological processes that promote wound healing alleviate the pathological fibrotic response to DSS. Therefore, these mucosal repair processes could be exploited to develop therapies that promote normal wound healing and prevent fibrosis. NEW AND NOTEWORTHY We show that transcriptomic changes due to Smad4 loss in the colonic epithelium alleviates the pathological fibrotic response to DSS in an IBD mouse model of acute inflammation. Most notably, we find that collagen deposition in the epithelial ECM, as opposed to that in the lamina propria, correlates with epithelial changes that enhance wound healing. This is the first report on a mouse model providing alleviated fibrotic response in a DSS-IBD mouse model in vivo .
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Lee S, Ali AR, Abed DA, Nguyen MU, Verzi MP, Hu L. Structural modification of C2-substituents on 1,4-bis(arylsulfonamido)benzene or naphthalene-N,N'-diacetic acid derivatives as potent inhibitors of the Keap1-Nrf2 protein-protein interaction. Eur J Med Chem 2024; 265:116104. [PMID: 38159482 PMCID: PMC10794003 DOI: 10.1016/j.ejmech.2023.116104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/02/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
The Keap1-Nrf2-ARE signaling pathway is an attractive therapeutic target for the prevention and treatment of oxidative stress-associated diseases by activating the cellular expression of cytoprotective enzymes and proteins. Small molecule inhibitors can directly disrupt the Keap1-Nrf2 protein-protein interaction (PPI), resulting in elevated levels of Nrf2 protein and subsequent stimulation of related antioxidant responses. Previously, we found that 1,4-bis(arylsulfonamido)benzene or naphthalene-N,N'-diacetic acid derivatives with an ether type C2-substituent on the benzene or naphthalene core exhibited potent inhibitory activities with IC50's in the submicromolar or nanomolar range. We here describe a more detailed structure-activity relationship study around the C2 substituents containing various polar linkers shedding new insight on their binding interactions with the Keap1 Kelch domain. The key observation from our findings is that the substituents at the C2-position of the benzene or naphthalene scaffold impact their inhibitory potencies in biochemical assays as well as activities in cell culture. The biochemical FP and TR-FRET assays revealed that the naphthalene derivatives 17b and 18 with an additional carboxylate at the C2 were the most active inhibitors against Keap1-Nrf2 PPI. In the cell-based assay, the two compounds were shown to be potent Nrf2 activators of the transcription of the Nrf2-dependent genes, such as HMOX2, GSTM3, and NQO1.
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Affiliation(s)
- Sumi Lee
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, United States
| | - Ahmed R Ali
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, United States
| | - Dhulfiqar Ali Abed
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, United States
| | - Mai-Uyen Nguyen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Life Sciences Building Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, United States
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Life Sciences Building Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, United States; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, United States
| | - Longqin Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, United States; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, United States.
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Tong K, Bandari M, Carrick JN, Zenkevich A, Kothari OA, Shamshad E, Stefanik K, Haro KS, Perekatt AO, Verzi MP. In Vitro Organoid-Based Assays Reveal SMAD4 Tumor-Suppressive Mechanisms for Serrated Colorectal Cancer Invasion. Cancers (Basel) 2023; 15:5820. [PMID: 38136364 PMCID: PMC10742020 DOI: 10.3390/cancers15245820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Colon cancer is the third most prominent cancer and second leading cause of cancer-related deaths in the United States. Up to 20% of colon cancers follow the serrated tumor pathway driven by mutations in the MAPK pathway. Loss of SMAD4 function occurs in the majority of late-stage colon cancers and is associated with aggressive cancer progression. Therefore, it is important to develop technology to accurately model and better understand the genetic mechanisms behind cancer invasion. Organoids derived from tumors found in the Smad4KO BRAFV600E/+ mouse model present multiple phenotypes characteristic of invasion both in ex vivo and in vivo systems. Smad4KO BRAFV600E/+ tumor organoids can migrate through 3D culture and infiltrate through transwell membranes. This invasive behavior can be suppressed when SMAD4 is re-expressed in the tumor organoids. RNA-Seq analysis reveals that SMAD4 expression in organoids rapidly regulates transcripts associated with extracellular matrix and secreted proteins, suggesting that the mechanisms employed by SMAD4 to inhibit invasion are associated with regulation of extracellular matrix and secretory pathways. These findings indicate new models to study SMAD4 regulation of tumor invasion and an additional layer of complexity in the tumor-suppressive function of the SMAD4/Tgfβ pathway.
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Affiliation(s)
- Kevin Tong
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack Meridian Health School of Medicine, Nutley, NJ 07110, USA
| | - Manisha Bandari
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Jillian N. Carrick
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Anastasia Zenkevich
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Om A. Kothari
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Eman Shamshad
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Katarina Stefanik
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Katherine S. Haro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Ansu O. Perekatt
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Rutgers Center for Lipid Research, New Brunswick, NJ 08901, USA
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4. bioRxiv 2023:2023.11.08.566322. [PMID: 37986803 PMCID: PMC10659318 DOI: 10.1101/2023.11.08.566322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Terminal differentiation requires a massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identified dynamic recruitment of RNA Polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II recruitment and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of- function, ChIP-seq and IP mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II recruitment at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms which drive differentiation gene expression and find pause-release of Pol II and post- transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in a renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA
- NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ 08854, USA
- Lead Contact
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Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP. TGFB1 induces fetal reprogramming and enhances intestinal regeneration. Cell Stem Cell 2023; 30:1520-1537.e8. [PMID: 37865088 PMCID: PMC10841757 DOI: 10.1016/j.stem.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/11/2023] [Revised: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
The gut epithelium has a remarkable ability to recover from damage. We employed a combination of high-throughput sequencing approaches, mouse genetics, and murine and human organoids and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. The depletion of macrophages or genetic disruption of TGFB signaling significantly impaired the regenerative response. Intestinal regeneration is characterized by the induction of a fetal-like transcriptional signature during repair. In organoid culture, TGFB1 treatment was necessary and sufficient to induce the fetal-like/regenerative state. Mesenchymal cells were also responsive to TGFB1 and enhanced the regenerative response. Mechanistically, pro-regenerative factors, YAP/TEAD and SOX9, are activated in the epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Xiaojiao Fan
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Xiaoting Xu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Prateeksha Rout
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Katherine D Walton
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ruolan Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Wenxin Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Rachel Ofer
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Alexandra Logerfo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Gaetan Barbet
- Child Health Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA
| | - Yan Wang
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nan Gao
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Ansu O Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA; Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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Joseph I, Flores J, Farrell V, Davis J, Bianchi‐Smak J, Feng Q, Goswami S, Lin X, Wei Z, Tong K, Feng Z, Verzi MP, Bonder EM, Goldenring JR, Gao N. RAB11A and RAB11B control mitotic spindle function in intestinal epithelial progenitor cells. EMBO Rep 2023; 24:e56240. [PMID: 37424454 PMCID: PMC10481667 DOI: 10.15252/embr.202256240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/05/2022] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
RAB11 small GTPases and associated recycling endosome have been localized to mitotic spindles and implicated in regulating mitosis. However, the physiological significance of such regulation has not been observed in mammalian tissues. We have used newly engineered mouse models to investigate intestinal epithelial renewal in the absence of single or double isoforms of RAB11 family members: Rab11a and Rab11b. Comparing with single knockouts, mice with compound ablation demonstrate a defective cell cycle entry and robust mitotic arrest followed by apoptosis, leading to a total penetrance of lethality within 3 days of gene ablation. Upon Rab11 deletion ex vivo, enteroids show abnormal mitotic spindle formation and cell death. Untargeted proteomic profiling of Rab11a and Rab11b immunoprecipitates has uncovered a shared interactome containing mitotic spindle microtubule regulators. Disrupting Rab11 alters kinesin motor KIF11 function and impairs bipolar spindle formation and cell division. These data demonstrate that RAB11A and RAB11B redundantly control mitotic spindle function and intestinal progenitor cell division, a mechanism that may be utilized to govern the homeostasis and renewal of other mammalian tissues.
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Affiliation(s)
- Ivor Joseph
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Juan Flores
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | | | - Justin Davis
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | | | - Qiang Feng
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | | | - Xiang Lin
- Department of Computer SciencesNew Jersey Institute of TechnologyNewarkNJUSA
| | - Zhi Wei
- Department of Computer SciencesNew Jersey Institute of TechnologyNewarkNJUSA
| | - Kevin Tong
- Department of GeneticsRutgers UniversityNew BrunswickNJUSA
| | - Zhaohui Feng
- Rutgers Cancer Institute of New JerseyNew BrunswickNJUSA
| | | | - Edward M Bonder
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - James R Goldenring
- Section of Surgical Sciences and Epithelial Biology CenterVanderbilt University Medical CenterNashvilleTNUSA
| | - Nan Gao
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
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Aita R, Chen L, Verzi MP. Evaluating Performance of IsoformSwitchAnalyzeR and mRNA Isoform Switching in Small Intestine Epithelial Differentiation. Gastro Hep Adv 2023; 2:1077-1081. [PMID: 38094226 PMCID: PMC10718563 DOI: 10.1016/j.gastha.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Affiliation(s)
- R Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Division of Environmental & Population Health Biosciences, EOHSI, New Brunswick, New Jersey
| | - L Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Division of Environmental & Population Health Biosciences, EOHSI, New Brunswick, New Jersey
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - M P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Division of Environmental & Population Health Biosciences, EOHSI, New Brunswick, New Jersey
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Vemuri K, Radi SH, Sladek FM, Verzi MP. Multiple roles and regulatory mechanisms of the transcription factor HNF4 in the intestine. Front Endocrinol (Lausanne) 2023; 14:1232569. [PMID: 37635981 PMCID: PMC10450339 DOI: 10.3389/fendo.2023.1232569] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Hepatocyte nuclear factor 4-alpha (HNF4α) drives a complex array of transcriptional programs across multiple organs. Beyond its previously documented function in the liver, HNF4α has crucial roles in the kidney, intestine, and pancreas. In the intestine, a multitude of functions have been attributed to HNF4 and its accessory transcription factors, including but not limited to, intestinal maturation, differentiation, regeneration, and stem cell renewal. Functional redundancy between HNF4α and its intestine-restricted paralog HNF4γ, and co-regulation with other transcription factors drive these functions. Dysregulated expression of HNF4 results in a wide range of disease manifestations, including the development of a chronic inflammatory state in the intestine. In this review, we focus on the multiple molecular mechanisms of HNF4 in the intestine and explore translational opportunities. We aim to introduce new perspectives in understanding intestinal genetics and the complexity of gastrointestinal disorders through the lens of HNF4 transcription factors.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Sarah H. Radi
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
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9
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Suzuki T, Kilbey A, Casa-Rodríguez N, Lawlor A, Georgakopoulou A, Hayman H, Yin Swe KL, Nordin A, Cantù C, Vantourout P, Ridgway RA, Byrne RM, Chen L, Verzi MP, Gay DM, Gil Vázquez E, Belnoue-Davis HL, Gilroy K, Køstner AH, Kersten C, Thuwajit C, Andersen DK, Wiesheu R, Jandke A, Blyth K, Roseweir AK, Leedham SJ, Dunne PD, Edwards J, Hayday A, Sansom OJ, Coffelt SB. β-Catenin Drives Butyrophilin-like Molecule Loss and γδ T-cell Exclusion in Colon Cancer. Cancer Immunol Res 2023; 11:1137-1155. [PMID: 37309673 PMCID: PMC10398359 DOI: 10.1158/2326-6066.cir-22-0644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/09/2022] [Revised: 02/20/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Intraepithelial lymphocytes (IEL) expressing γδ T-cell receptors (γδTCR) play key roles in elimination of colon cancer. However, the precise mechanisms by which progressing cancer cells evade immunosurveillance by these innate T cells are unknown. Here, we investigated how loss of the Apc tumor suppressor in gut tissue could enable nascent cancer cells to escape immunosurveillance by cytotoxic γδIELs. In contrast with healthy intestinal or colonic tissue, we found that γδIELs were largely absent from the microenvironment of both mouse and human tumors, and that butyrophilin-like (BTNL) molecules, which can critically regulate γδIEL through direct γδTCR interactions, were also downregulated in tumors. We then demonstrated that β-catenin activation through loss of Apc rapidly suppressed expression of the mRNA encoding the HNF4A and HNF4G transcription factors, preventing their binding to promoter regions of Btnl genes. Reexpression of BTNL1 and BTNL6 in cancer cells increased γδIEL survival and activation in coculture assays but failed to augment their cancer-killing ability in vitro or their recruitment to orthotopic tumors. However, inhibition of β-catenin signaling via genetic deletion of Bcl9/Bcl9L in either Apc-deficient or mutant β-catenin mouse models restored Hnf4a, Hnf4g, and Btnl gene expression and γδ T-cell infiltration into tumors. These observations highlight an immune-evasion mechanism specific to WNT-driven colon cancer cells that disrupts γδIEL immunosurveillance and furthers cancer progression.
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Affiliation(s)
- Toshiyasu Suzuki
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna Kilbey
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nuria Casa-Rodríguez
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Amy Lawlor
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anastasia Georgakopoulou
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Hannah Hayman
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kyi Lai Yin Swe
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Pierre Vantourout
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Ryan M. Byrne
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, United Kingdom
| | - Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - David M. Gay
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Ester Gil Vázquez
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | | | - Kathryn Gilroy
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | | | - Christian Kersten
- Department of Research, Southern Hospital Trust, Kristiansand, Norway
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | | | - Robert Wiesheu
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anett Jandke
- The Francis Crick Institute, London, United Kingdom
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonia K. Roseweir
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Simon J. Leedham
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Philip D. Dunne
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, United Kingdom
| | - Joanne Edwards
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Adrian Hayday
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Seth B. Coffelt
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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10
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Abed DA, Ali AR, Lee S, Nguyen MU, Verzi MP, Hu L. Optimization of the C2 substituents on the 1,4-bis(arylsulfonamido)naphthalene-N,N'-diacetic acid scaffold for better inhibition of Keap1-Nrf2 protein-protein interaction. Eur J Med Chem 2023; 252:115302. [PMID: 36989811 PMCID: PMC10101933 DOI: 10.1016/j.ejmech.2023.115302] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 01/27/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
Direct inhibition of the protein-protein interaction (PPI) between Kelch-like ECH-associated protein 1 (Keap1) and nuclear factor erythroid 2-related factor 2 (Nrf2) reduces the ubiquitination and subsequent degradation of Nrf2, leading to Nrf2 accumulation in the cytosol and the nuclear translocation of Nrf2. Once inside the nucleus, Nrf2 binds to and activates the expression of antioxidant response element (ARE) genes involved in redox homeostasis and detoxification. Herein, we report a series of 1,4-bis(arylsulfonamido)naphthalene-N,N'-diacetic acid analogs with varying C2 substituents to explore the structure-activity relationships at this position of the central naphthalene core. The Keap1-binding activities were first screened with a fluorescence polarization (FP) assay followed by further evaluation of the more potent compounds using a more sensitive time-resolved fluorescence energy transfer (TR-FRET) assay. It was found that compound 24a with C2-phthalimidopropyl group was the most potent in this series showing an IC50 of 2.5 nM in the TR-FRET assay with a Ki value in the subnanomolar range. Our docking study indicated that the C2-phthalimidopropyl group in compound 24a provided an extra hydrogen bonding interaction with the key residue Arg415 that may be responsible for the observed boost in binding affinity. In addition, compounds 12b, 15, and 24a were shown to activate the Nrf2 signaling pathway in NCM460D cells resulting in elevated mRNA levels of GSTM3, HMOX1 and NQO1 by 2.4-11.7 fold at 100 μM as compared to the vehicle control.
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Affiliation(s)
- Dhulfiqar Ali Abed
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Ahmed R Ali
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Sumi Lee
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Mai-Uyen Nguyen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Life Sciences Building Rutgers University, 145 Bevier Road Piscataway, NJ, 08854, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Life Sciences Building Rutgers University, 145 Bevier Road Piscataway, NJ, 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA
| | - Longqin Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
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11
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Childs CJ, Holloway EM, Sweet CW, Tsai YH, Wu A, Vallie A, Eiken MK, Capeling MM, Zwick RK, Palikuqi B, Trentesaux C, Wu JH, Pellón-Cardenas O, Zhang CJ, Glass I, Loebel C, Yu Q, Camp JG, Sexton JZ, Klein OD, Verzi MP, Spence JR. EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids. JCI Insight 2023; 8:e165566. [PMID: 36821371 PMCID: PMC10070114 DOI: 10.1172/jci.insight.165566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/19/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Epithelial organoids derived from intestinal tissue, called enteroids, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Here, we interrogated the cell signaling environment within the developing human intestine to identify niche cues that may be important for epithelial development and homeostasis. We identified an EGF family member, EPIREGULIN (EREG), which is robustly expressed in the developing human crypt. Enteroids generated from the developing human intestine grown in standard culture conditions, which contain EGF, are dominated by stem and progenitor cells and feature little differentiation and no spatial organization. Our results demonstrate that EREG can replace EGF in vitro, and EREG leads to spatially resolved enteroids that feature budded and proliferative crypt domains and a differentiated villus-like central lumen. Multiomic (transcriptome plus epigenome) profiling of native crypts, EGF-grown enteroids, and EREG-grown enteroids showed that EGF enteroids have an altered chromatin landscape that is dependent on EGF concentration, downregulate the master intestinal transcription factor CDX2, and ectopically express stomach genes, a phenomenon that is reversible. This is in contrast to EREG-grown enteroids, which remain intestine like in culture. Thus, EREG creates a homeostatic intestinal niche in vitro, enabling interrogation of stem cell function, cellular differentiation, and disease modeling.
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Affiliation(s)
- Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Caden W. Sweet
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Yu-Hwai Tsai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Angeline Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Abigail Vallie
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Meghan M. Capeling
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Rachel K. Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Brisa Palikuqi
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Coralie Trentesaux
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Joshua H. Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Oscar Pellón-Cardenas
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ian Glass
- Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
- Department of Materials Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Qianhui Yu
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - J. Gray Camp
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Jonathan Z. Sexton
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael P. Verzi
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
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12
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Chen L, Dupre A, Qiu X, Pellon-Cardenas O, Walton KD, Wang J, Perekatt AO, Hu W, Spence JR, Verzi MP. TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration. bioRxiv 2023:2023.01.13.523825. [PMID: 36711781 PMCID: PMC9882197 DOI: 10.1101/2023.01.13.523825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The adult gut epithelium has a remarkable ability to recover from damage. To achieve cellular therapies aimed at restoring and/or replacing defective gastrointestinal tissue, it is important to understand the natural mechanisms of tissue regeneration. We employed a combination of high throughput sequencing approaches, mouse genetic models, and murine and human organoid models, and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. Depletion of macrophages or genetic disruption of TGFB-signaling significantly impaired the regenerative response following irradiation. Murine intestinal regeneration is also characterized by a process where a fetal transcriptional signature is induced during repair. In organoid culture, TGFB1-treatment was necessary and sufficient to induce a transcriptomic shift to the fetal-like/regenerative state. The regenerative response was enhanced by the function of mesenchymal cells, which are also primed for regeneration by TGFB1. Mechanistically, integration of ATAC-seq, scRNA-seq, and ChIP-seq suggest that a regenerative YAP-SOX9 transcriptional circuit is activated in epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for the application of the TGFB-induced regenerative circuit in cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Katherine D. Walton
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Ansu O. Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Jason R. Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ, USA
- Member of the NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ, USA
- Lead Contact
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13
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Sailaja BS, Hassan S, Cohen E, Tmenova I, Farias-Pereira R, Verzi MP, Raskin I. Moringa isothiocyanate-1 inhibits LPS-induced inflammation in mouse myoblasts and skeletal muscle. PLoS One 2022; 17:e0279370. [PMID: 36525453 PMCID: PMC9757596 DOI: 10.1371/journal.pone.0279370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
This study aims to investigate the anti-inflammatory effects of moringa isothiocyanate-1 (MIC-1) extracted from seeds of Moringa oleifera Lam. in lipopolysaccharide (LPS)-induced inflammation models. MIC-1 decreased nitric oxide production and reduced the expression of pro-inflammatory markers (TNF-α, Ifn-α, IL-1β, IL-6) in C2C12 myoblasts. The daily oral treatment of MIC-1 (80 mg/kg) for three days significantly reduced the expression of pro-inflammatory markers in gastrocnemius muscle tissue of LPS-treated C57BL/6 male mice. Transcriptomic analysis provided further insights into the inhibitory effects of MIC-1 on the LPS-induced inflammation, which suggested that MIC-1 affects inflammation and immunity-related genes in myoblasts and skeletal muscle tissue. MIC-1 inhibited the nuclear accumulation of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) in the LPS-treated myoblasts. Our data support the hypothesis that the MIC-1's effects in the muscle cells are mediated through the inhibition of the NF-κB translocation in the nucleus, which, in turn, results in immunomodulating and anti-inflammatory responses at the gene expression levels.
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Affiliation(s)
- Badi Sri Sailaja
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sohaib Hassan
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway Township, New Jersey, United States of America
| | - Evan Cohen
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway Township, New Jersey, United States of America
| | - Irina Tmenova
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Renalison Farias-Pereira
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Michael P. Verzi
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway Township, New Jersey, United States of America
| | - Ilya Raskin
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
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14
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Aita R, Aldea D, Hassan S, Hur J, Pellon-Cardenas O, Cohen E, Chen L, Shroyer N, Christakos S, Verzi MP, Fleet JC. Genomic analysis of 1,25-dihydroxyvitamin D 3 action in mouse intestine reveals compartment and segment-specific gene regulatory effects. J Biol Chem 2022; 298:102213. [PMID: 35779631 PMCID: PMC9358460 DOI: 10.1016/j.jbc.2022.102213] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 01/01/2023] Open
Abstract
1,25-dihydroxyvitamin D (VD) regulates intestinal calcium absorption in the small intestine (SI) and also reduces risk of colonic inflammation and cancer. However, the intestine compartment-specific target genes of VD signaling are unknown. Here, we examined VD action across three functional compartments of the intestine using RNA-seq to measure VD-induced changes in gene expression and Chromatin Immunoprecipitation with next generation sequencing to measure vitamin D receptor (VDR) genomic binding. We found that VD regulated the expression of 55 shared transcripts in the SI crypt, SI villi, and in the colon, including Cyp24a1, S100g, Trpv6, and Slc30a10. Other VD-regulated transcripts were unique to the SI crypt (162 up, 210 down), villi (199 up, 63 down), or colon (102 up, 28 down), but this did not correlate with mRNA levels of the VDR. Furthermore, bioinformatic analysis identified unique VD-regulated biological functions in each compartment. VDR-binding sites were found in 70% of upregulated genes from the colon and SI villi but were less common in upregulated genes from the SI crypt and among downregulated genes, suggesting some transcript-level VD effects are likely indirect. Consistent with this, we show that VD regulated the expression of other transcription factors and their downstream targets. Finally, we demonstrate that compartment-specific VD-mediated gene expression was associated with compartment-specific VDR-binding sites (<30% of targets) and enrichment of intestinal transcription factor-binding motifs within VDR-binding peaks. Taken together, our data reveal unique spatial patterns of VD action in the intestine and suggest novel mechanisms that could account for compartment-specific functions of this hormone.
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Affiliation(s)
- Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Dennis Aldea
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Sohaib Hassan
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Joseph Hur
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Evan Cohen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA
| | - Noah Shroyer
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas, USA
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA.
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Institute of Food, Nutrition, and Health, EOHSI, Rutgers University, New Jersey, USA.
| | - James C Fleet
- Department of Nutritional Science, University of Texas, Austin, Texas, USA.
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15
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Das S, Feng Q, Balasubramanian I, Lin X, Liu H, Pellón-Cardenas O, Yu S, Zhang X, Liu Y, Wei Z, Bonder EM, Verzi MP, Hsu W, Zhang L, Wang TC, Gao N. Colonic healing requires Wnt produced by epithelium as well as Tagln+ and Acta2+ stromal cells. Development 2022; 149:273689. [PMID: 34910127 PMCID: PMC8881740 DOI: 10.1242/dev.199587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023]
Abstract
Although Wnt signaling is clearly important for the intestinal epithelial homeostasis, the relevance of various sources of Wnt ligands themselves remains incompletely understood. Blocking the release of Wnt in distinct stromal cell types suggests obligatory functions of several stromal cell sources and yields different observations. The physiological contribution of epithelial Wnt to tissue homeostasis remains unclear. We show here that blocking epithelial Wnts affects colonic Reg4+ epithelial cell differentiation and impairs colonic epithelial regeneration after injury in mice. Single-cell RNA analysis of intestinal stroma showed that the majority of Wnt-producing cells were contained in transgelin (Tagln+) and smooth muscle actin α2 (Acta2+) expressing populations. We genetically attenuated Wnt production from these stromal cells using Tagln-Cre and Acta2-CreER drivers, and found that blockage of Wnt release from either epithelium or Tagln+ and Acta2+ stromal cells impaired colonic epithelial healing after chemical-induced injury. Aggregated blockage of Wnt release from both epithelium and Tagln+ or Acta2+ stromal cells drastically diminished epithelial repair, increasing morbidity and mortality. These results from two uncharacterized stromal populations suggested that colonic recovery from colitis-like injury depends on multiple Wnt-producing sources.
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Affiliation(s)
- Soumyashree Das
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Qiang Feng
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | | | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Haoran Liu
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | | | - Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Xiao Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Edward M. Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Wei Hsu
- Department of Biomedical Genetics, Center for Oral Biology, James P Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY 04642, USA
| | - Lanjing Zhang
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA,Department of Pathology, University Medical Center of Princeton, Plainsboro, NJ 08536, USA
| | - Timothy C. Wang
- Department of Medicine, Division of Digestive and Liver Diseases, Irving Cancer Research Center, Columbia University, New York, NY 10027, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA,Author for correspondence ()
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16
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Gu W, Wang H, Huang X, Kraiczy J, Singh PNP, Ng C, Dagdeviren S, Houghton S, Pellon-Cardenas O, Lan Y, Nie Y, Zhang J, Banerjee KK, Onufer EJ, Warner BW, Spence J, Scherl E, Rafii S, Lee RT, Verzi MP, Redmond D, Longman R, Helin K, Shivdasani RA, Zhou Q. SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling. Cell Stem Cell 2022; 29:101-115.e10. [PMID: 34582804 PMCID: PMC8741647 DOI: 10.1016/j.stem.2021.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 01/09/2023]
Abstract
Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.
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Affiliation(s)
- Wei Gu
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Hua Wang
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA
| | - Xiaofeng Huang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Judith Kraiczy
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Pratik N. P. Singh
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Charles Ng
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Sezin Dagdeviren
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Sean Houghton
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ying Lan
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Yaohui Nie
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jiaoyue Zhang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Emily J. Onufer
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Jason Spence
- Department of Internal Medicine, University of Michigan, 1500 E Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Shahin Rafii
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Richard T. Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - David Redmond
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200 Denmark,The Novo Nordisk Foundation for Stem Cell Biology (Danstem), University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ramesh A. Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Qiao Zhou
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA,Lead Contact ()
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17
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Kwon M, Rubio G, Nolan N, Auteri P, Volmar JA, Adem A, Javidian P, Zhou Z, Verzi MP, Pine SR, Libutti SK. FILIP1L Loss Is a Driver of Aggressive Mucinous Colorectal Adenocarcinoma and Mediates Cytokinesis Defects through PFDN1. Cancer Res 2021; 81:5523-5539. [PMID: 34417201 DOI: 10.1158/0008-5472.can-21-0897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/25/2021] [Accepted: 08/17/2021] [Indexed: 12/24/2022]
Abstract
Aneuploid mucinous colorectal adenocarcinoma (MAC) is an aggressive subtype of colorectal cancer with poor prognosis. The tumorigenic mechanisms in aneuploid MAC are currently unknown. Here we show that downregulation of Filamin A-interacting protein 1-like (FILIP1L) is a driver of MAC. Loss of FILIP1L increased xenograft growth, and, in colon-specific knockout mice, induced colonic epithelial hyperplasia and mucin secretion. The molecular chaperone prefoldin 1 (PFDN1) was identified as a novel binding partner of FILIP1L at the centrosomes throughout mitosis. FILIP1L was required for proper centrosomal localization of PFDN1 and regulated proteasome-dependent degradation of PFDN1. Importantly, increased PFDN1, caused by downregulation of FILIP1L, drove multinucleation and cytokinesis defects in vitro and in vivo, which were confirmed by time-lapse imaging and 3D cultures of normal epithelial cells. Overall, these findings suggest that downregulation of FILIP1L and subsequent upregulation of PFDN1 is a driver of the unique neoplastic characteristics in aggressive aneuploid MAC. SIGNIFICANCE: This study identifies FILIP1L as a tumor suppressor in mucinous colon cancer and demonstrates that FILIP1L loss results in aberrant stabilization of a centrosome-associated chaperone protein to drive aneuploidy and disease progression.
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Affiliation(s)
- Mijung Kwon
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Genesaret Rubio
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Nicholas Nolan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Peter Auteri
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Jean Arly Volmar
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Asha Adem
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Parisa Javidian
- Department of Pathology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| | - Zhongren Zhou
- Department of Pathology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Sharon R Pine
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Pharmacology and Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| | - Steven K Libutti
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.
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18
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Criss ZK, Bhasin N, Di Rienzi SC, Rajan A, Deans-Fielder K, Swaminathan G, Kamyabi N, Zeng XL, Doddapaneni H, Menon VK, Chakravarti D, Estrella C, Yu X, Patil K, Petrosino JF, Fleet JC, Verzi MP, Christakos S, Helmrath MA, Arimura S, DePinho RA, Britton RA, Maresso AW, Grande-Allen KJ, Blutt SE, Crawford SE, Estes MK, Ramani S, Shroyer NF. Drivers of transcriptional variance in human intestinal epithelial organoids. Physiol Genomics 2021; 53:486-508. [PMID: 34612061 DOI: 10.1152/physiolgenomics.00061.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 01/01/2023] Open
Abstract
Human intestinal epithelial organoids (enteroids and colonoids) are tissue cultures used for understanding the physiology of the human intestinal epithelium. Here, we explored the effect on the transcriptome of common variations in culture methods, including extracellular matrix substrate, format, tissue segment, differentiation status, and patient heterogeneity. RNA-sequencing datasets from 276 experiments performed on 37 human enteroid and colonoid lines from 29 patients were aggregated from several groups in the Texas Medical Center. DESeq2 and gene set enrichment analysis (GSEA) were used to identify differentially expressed genes and enriched pathways. PERMANOVA, Pearson's correlation, and dendrogram analysis of the data originally indicated three tiers of influence of culture methods on transcriptomic variation: substrate (collagen vs. Matrigel) and format (3-D, transwell, and monolayer) had the largest effect; segment of origin (duodenum, jejunum, ileum, colon) and differentiation status had a moderate effect; and patient heterogeneity and specific experimental manipulations (e.g., pathogen infection) had the smallest effect. GSEA identified hundreds of pathways that varied between culture methods, such as IL1 cytokine signaling enriched in transwell versus monolayer cultures and E2F target genes enriched in collagen versus Matrigel cultures. The transcriptional influence of the format was furthermore validated in a synchronized experiment performed with various format-substrate combinations. Surprisingly, large differences in organoid transcriptome were driven by variations in culture methods such as format, whereas experimental manipulations such as infection had modest effects. These results show that common variations in culture conditions can have large effects on intestinal organoids and should be accounted for when designing experiments and comparing results between laboratories. Our data constitute the largest RNA-seq dataset interrogating human intestinal epithelial organoids.
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Affiliation(s)
- Zachary K Criss
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Nobel Bhasin
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Kali Deans-Fielder
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | | | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Clarissa Estrella
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiaomin Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - James C Fleet
- Department of Nutrition Sciences, The University of Texas, Austin, Texas
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey
| | - Michael A Helmrath
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sumimasa Arimura
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Noah F Shroyer
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
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19
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Tong K, Kothari OA, Haro KS, Panda A, Bandari MM, Carrick JN, Hur JJ, Zhang L, Chan CS, Xing J, Gatza ML, Ganesan S, Verzi MP. SMAD4 is critical in suppression of BRAF-V600E serrated tumorigenesis. Oncogene 2021; 40:6034-6048. [PMID: 34453124 PMCID: PMC8559887 DOI: 10.1038/s41388-021-01997-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/04/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023]
Abstract
BRAF-driven colorectal cancer is among the poorest prognosis subtypes of colon cancer. Previous studies suggest that BRAF-mutant serrated cancers frequently exhibit Microsatellite Instability (MSI) and elevated levels of WNT signaling. The loss of tumor-suppressor Smad4 in oncogenic BRAF-V600E mouse models promotes rapid serrated tumor development and progression, and SMAD4 mutations co-occur in human patient tumors with BRAF-V600E mutations. This study assesses the role of SMAD4 in early-stage serrated tumorigenesis. SMAD4 loss promotes microsatellite stable (MSS) serrated tumors in an oncogenic BRAF-V600E context, providing a model for MSS serrated cancers. Inactivation of Msh2 in these mice accelerated tumor formation, and whole-exome sequencing of both MSS and MSI serrated tumors derived from these mouse models revealed that all serrated tumors developed oncogenic WNT mutations, predominantly in the WNT-effector gene Ctnnb1 (β-catenin). Mouse models mimicking the oncogenic β-catenin mutation show that the combination of three oncogenic mutations (Ctnnb1, Braf, and Smad4) are critical to drive rapid serrated dysplasia formation. Re-analysis of human tumor data reveals BRAF-V600E mutations co-occur with oncogenic mutations in both WNT and SMAD4/TGFβ pathways. These findings identify SMAD4 as a critical factor in early-stage serrated cancers and helps broaden the knowledge of this rare but aggressive subset of colorectal cancer.
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Affiliation(s)
- Kevin Tong
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Om A. Kothari
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Katherine S. Haro
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Manisha M. Bandari
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Jillian N. Carrick
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Joseph J. Hur
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Lanjing Zhang
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA,Department of Pathology, Penn Medicine Princeton Medical Center, Plainsboro, NJ, USA
| | - Chang S. Chan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Michael L. Gatza
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA,Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA,Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA,Corresponding Author: Michael P. Verzi,
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20
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Chen L, Luo S, Dupre A, Vasoya RP, Parthasarathy A, Aita R, Malhotra R, Hur J, Toke NH, Chiles E, Yang M, Cao W, Flores J, Ellison CE, Gao N, Sahota A, Su X, Bonder EM, Verzi MP. The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac. Nat Commun 2021; 12:2886. [PMID: 34001900 PMCID: PMC8129143 DOI: 10.1038/s41467-021-22761-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
The brush border is comprised of microvilli surface protrusions on the apical surface of epithelia. This specialized structure greatly increases absorptive surface area and plays crucial roles in human health. However, transcriptional regulatory networks controlling brush border genes are not fully understood. Here, we identify that hepatocyte nuclear factor 4 (HNF4) transcription factor is a conserved and important regulator of brush border gene program in multiple organs, such as intestine, kidney and yolk sac. Compromised brush border gene signatures and impaired transport were observed in these tissues upon HNF4 loss. By ChIP-seq, we find HNF4 binds and activates brush border genes in the intestine and kidney. H3K4me3 HiChIP-seq identifies that HNF4 loss results in impaired chromatin looping between enhancers and promoters at gene loci of brush border genes, and instead enhanced chromatin looping at gene loci of stress fiber genes in the intestine. This study provides comprehensive transcriptional regulatory mechanisms and a functional demonstration of a critical role for HNF4 in brush border gene regulation across multiple murine epithelial tissues.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA.
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
| | - Shirley Luo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Roshan P Vasoya
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Aditya Parthasarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Raj Malhotra
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Joseph Hur
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Natalie H Toke
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Eric Chiles
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Min Yang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Amrik Sahota
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Xiaoyang Su
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA.
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ, USA.
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21
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Suzuki K, Masuike Y, Mizuno R, Sachdeva UM, Chatterji P, Andres SF, Sun W, Klein-Szanto AJ, Besharati S, Remotti HE, Verzi MP, Rustgi AK. LIN28B induces a differentiation program through CDX2 in colon cancer. JCI Insight 2021; 6:140382. [PMID: 33755595 PMCID: PMC8262288 DOI: 10.1172/jci.insight.140382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/18/2021] [Indexed: 12/03/2022] Open
Abstract
Most colorectal cancers (CRCs) are moderately differentiated or well differentiated, a status that is preserved even in metastatic tumors. However, the molecular mechanisms underlying CRC differentiation remain to be elucidated. Herein, we unravel a potentially novel posttranscriptional regulatory mechanism via a LIN28B/CDX2 signaling axis that plays a critical role in mediating CRC differentiation. Owing to a large number of mRNA targets, the mRNA-binding protein LIN28B has diverse functions in development, metabolism, tissue regeneration, and tumorigenesis. Our RNA-binding protein IP (RIP) assay revealed that LIN28B directly binds CDX2 mRNA, which is a pivotal homeobox transcription factor in normal intestinal epithelial cell identity and differentiation. Furthermore, LIN28B overexpression resulted in enhanced CDX2 expression to promote differentiation in subcutaneous xenograft tumors generated from CRC cells and metastatic tumor colonization through mesenchymal-epithelial transition in CRC liver metastasis mouse models. A ChIP sequence for CDX2 identified α-methylacyl-CoA racemase (AMACR) as a potentially novel transcriptional target of CDX2 in the context of LIN28B overexpression. We also found that AMACR enhanced intestinal alkaline phosphatase activity, which is known as a key component of intestinal differentiation, through the upregulation of butyric acid. Overall, we demonstrated that LIN28B promotes CRC differentiation through the CDX2/AMACR axis.
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Affiliation(s)
- Kensuke Suzuki
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Disease, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Yasunori Masuike
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Disease, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Rei Mizuno
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Uma M Sachdeva
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Priya Chatterji
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | - Sarah F Andres
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Wenping Sun
- Institute for Biomedical informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andres J Klein-Szanto
- Histopathology Facility and Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Sepideh Besharati
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Helen E Remotti
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Disease, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
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22
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Yu S, Balasubramanian I, Laubitz D, Tong K, Bandyopadhyay S, Lin X, Flores J, Singh R, Liu Y, Macazana C, Zhao Y, Béguet-Crespel F, Patil K, Midura-Kiela MT, Wang D, Yap GS, Ferraris RP, Wei Z, Bonder EM, Häggblom MM, Zhang L, Douard V, Verzi MP, Cadwell K, Kiela PR, Gao N. Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine. Immunity 2021; 53:398-416.e8. [PMID: 32814028 DOI: 10.1016/j.immuni.2020.07.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 03/26/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Paneth cells are the primary source of C-type lysozyme, a β-1,4-N-acetylmuramoylhydrolase that enzymatically processes bacterial cell walls. Paneth cells are normally present in human cecum and ascending colon, but are rarely found in descending colon and rectum; Paneth cell metaplasia in this region and aberrant lysozyme production are hallmarks of inflammatory bowel disease (IBD) pathology. Here, we examined the impact of aberrant lysozyme production in colonic inflammation. Targeted disruption of Paneth cell lysozyme (Lyz1) protected mice from experimental colitis. Lyz1-deficiency diminished intestinal immune responses to bacterial molecular patterns and resulted in the expansion of lysozyme-sensitive mucolytic bacteria, including Ruminococcus gnavus, a Crohn's disease-associated pathobiont. Ectopic lysozyme production in colonic epithelium suppressed lysozyme-sensitive bacteria and exacerbated colitis. Transfer of R. gnavus into Lyz1-/- hosts elicited a type 2 immune response, causing epithelial reprograming and enhanced anti-colitogenic capacity. In contrast, in lysozyme-intact hosts, processed R. gnavus drove pro-inflammatory responses. Thus, Paneth cell lysozyme balances intestinal anti- and pro-inflammatory responses, with implications for IBD.
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Affiliation(s)
- Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | | | - Daniel Laubitz
- Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Kevin Tong
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | | | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Rajbir Singh
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Carlos Macazana
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Yanlin Zhao
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Fabienne Béguet-Crespel
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Karuna Patil
- Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | | | - Daniel Wang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - George S Yap
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ronaldo P Ferraris
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA; Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA
| | - Veronique Douard
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Ken Cadwell
- Department of Microbiology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Pawel R Kiela
- Department of Pediatrics, University of Arizona, Tucson, AZ, USA; Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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23
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Chen L, Cao W, Aita R, Aldea D, Flores J, Gao N, Bonder EM, Ellison CE, Verzi MP. Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4. Cell Rep 2021; 34:108679. [PMID: 33503426 PMCID: PMC7899294 DOI: 10.1016/j.celrep.2020.108679] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
Cells in renewing tissues exhibit dramatic transcriptional changes as they differentiate. The contribution of chromatin looping to tissue renewal is incompletely understood. Enhancer-promoter interactions could be relatively stable as cells transition from progenitor to differentiated states; alternatively, chromatin looping could be as dynamic as the gene expression from their loci. The intestinal epithelium is the most rapidly renewing mammalian tissue. Proliferative cells in crypts of Lieberkühn sustain a stream of differentiated cells that are continually shed into the lumen. We apply chromosome conformation capture combined with chromatin immunoprecipitation (HiChIP) and sequencing to measure enhancer-promoter interactions in progenitor and differentiated cells of the intestinal epithelium. Despite dynamic gene regulation across the differentiation axis, we find that enhancer-promoter interactions are relatively stable. Functionally, we find HNF4 transcription factors are required for chromatin looping at target genes. Depletion of HNF4 disrupts local chromatin looping, histone modifications, and target gene expression. This study provides insights into transcriptional regulatory mechanisms governing homeostasis in renewing tissues. Chen et al. provide a survey of enhancer-promoter 3D looping in the intestinal epithelium by HiChIP, in vivo. They find that enhancer-promoter interactions are highly dependent upon the key intestinal transcription factor HNF4. Their findings provide insights into transcriptional regulatory mechanisms governing homeostasis in renewing tissues.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Dennis Aldea
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA.
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24
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Li S, De La Cruz J, Hutchens S, Mukhopadhyay S, Criss ZK, Aita R, Pellon-Cardenas O, Hur J, Soteropoulos P, Husain S, Dhawan P, Verlinden L, Carmeliet G, Fleet JC, Shroyer NF, Verzi MP, Christakos S. Analysis of 1,25-Dihydroxyvitamin D 3 Genomic Action Reveals Calcium-Regulating and Calcium-Independent Effects in Mouse Intestine and Human Enteroids. Mol Cell Biol 2020; 41:e00372-20. [PMID: 33139494 PMCID: PMC7849401 DOI: 10.1128/mcb.00372-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/24/2020] [Indexed: 01/27/2023] Open
Abstract
Although vitamin D is critical for the function of the intestine, most studies have focused on the duodenum. We show that transgenic expression of the vitamin D receptor (VDR) only in the distal intestine of VDR null mice (KO/TG mice) results in the normalization of serum calcium and rescue of rickets. Although it had been suggested that calcium transport in the distal intestine involves a paracellular process, we found that the 1,25-dihydroxyvitamin D3 [1,25(OH)2D3]-activated genes in the proximal intestine associated with active calcium transport (Trpv6, S100g, and Atp2b1) are also induced by 1,25(OH)2D3 in the distal intestine of KO/TG mice. In addition, Slc30a10, encoding a manganese efflux transporter, was one of the genes most induced by 1,25(OH)2D3 in both proximal and distal intestine. Both villus and crypt were found to express Vdr and VDR target genes. RNA sequence (RNA-seq) analysis of human enteroids indicated that the effects of 1,25(OH)2D3 observed in mice are conserved in humans. Using Slc30a10-/- mice, a loss of cortical bone and a marked decrease in S100g and Trpv6 in the intestine was observed. Our findings suggest an interrelationship between vitamin D and intestinal Mn efflux and indicate the importance of distal intestinal segments to vitamin D action.
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Affiliation(s)
- Shanshan Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Jessica De La Cruz
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Steven Hutchens
- Division of Pharmacology and Toxicology, College of Pharmacy, Institute for Cellular and Molecular Biology and Institute for Neuroscience, The University of Texas at Austin, Austin, Texas, USA
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology and Toxicology, College of Pharmacy, Institute for Cellular and Molecular Biology and Institute for Neuroscience, The University of Texas at Austin, Austin, Texas, USA
| | - Zachary K Criss
- Integrative Molecular and Biomedical Sciences Graduate Program, Division of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Rohit Aita
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, USA
| | | | - Joseph Hur
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, USA
| | - Patricia Soteropoulos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
- Genomics Center, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Seema Husain
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
- Genomics Center, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Puneet Dhawan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
- Genomics Center, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Lieve Verlinden
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, Leuven, Belgium
| | - Geert Carmeliet
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, Leuven, Belgium
| | - James C Fleet
- Department of Nutrition Science, Purdue University, West Lafayette, Indiana, USA
| | - Noah F Shroyer
- Integrative Molecular and Biomedical Sciences Graduate Program, Division of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, USA
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
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25
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Zhang X, Bandyopadhyay S, Araujo LP, Tong K, Flores J, Laubitz D, Zhao Y, Yap G, Wang J, Zou Q, Ferraris R, Zhang L, Hu W, Bonder EM, Kiela PR, Coffey R, Verzi MP, Ivanov II, Gao N. Elevating EGFR-MAPK program by a nonconventional Cdc42 enhances intestinal epithelial survival and regeneration. JCI Insight 2020; 5:135923. [PMID: 32686657 PMCID: PMC7455142 DOI: 10.1172/jci.insight.135923] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
The regulatory mechanisms enabling the intestinal epithelium to maintain a high degree of regenerative capacity during mucosal injury remain unclear. Ex vivo survival and clonogenicity of intestinal stem cells (ISCs) strictly required growth response mediated by cell division control 42 (Cdc42) and Cdc42-deficient enteroids to undergo rapid apoptosis. Mechanistically, Cdc42 engaging with EGFR was required for EGF-stimulated, receptor-mediated endocytosis and sufficient to promote MAPK signaling. Proteomics and kinase analysis revealed that a physiologically, but nonconventionally, spliced Cdc42 variant 2 (V2) exhibited stronger MAPK-activating capability. Human CDC42-V2 is transcriptionally elevated in some colon tumor tissues. Accordingly, mice engineered to overexpress Cdc42-V2 in intestinal epithelium showed elevated MAPK signaling, enhanced regeneration, and reduced mucosal damage in response to irradiation. Overproducing Cdc42-V2 specifically in mouse ISCs enhanced intestinal regeneration following injury. Thus, the intrinsic Cdc42-MAPK program is required for intestinal epithelial regeneration, and elevating this signaling cascade is capable of initiating protection from genotoxic injury.
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Affiliation(s)
- Xiao Zhang
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Leandro Pires Araujo
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Kevin Tong
- Department of Genetics, Division of Life Sciences, School of Arts and Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Juan Flores
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Daniel Laubitz
- Department of Pediatrics, University of Arizona, Tucson, Arizona, USA
| | - Yanlin Zhao
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - George Yap
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Jingren Wang
- Department of Mechanical and Aerospace Engineering, School of Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Qingze Zou
- Department of Mechanical and Aerospace Engineering, School of Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Lanjing Zhang
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
- Department of Pathology, University Medical Center of Princeton, Plainsboro, New Jersey, USA
| | - Wenwei Hu
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Edward M Bonder
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Pawel R Kiela
- Department of Pediatrics, University of Arizona, Tucson, Arizona, USA
| | - Robert Coffey
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael P Verzi
- Department of Genetics, Division of Life Sciences, School of Arts and Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ivaylo I Ivanov
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Nan Gao
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
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26
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Abstract
To fulfill the lifelong need to supply diverse epithelial cells, intestinal stem cells (ISCs) rely on executing accurate transcriptional programs. This review addresses the mechanisms that control those programs. Genes that define cell behaviors and identities are regulated principally through thousands of dispersed enhancers, each individually <1 kb long and positioned from a few to hundreds of kilobases away from transcription start sites, upstream or downstream from coding genes or within introns. Wnt, Notch, and other epithelial control signals feed into these cis-regulatory DNA elements, which are also common loci of polymorphisms and mutations that confer disease risk. Cell-specific gene activity requires promoters to interact with the correct combination of signal-responsive enhancers. We review the current state of knowledge in ISCs regarding active enhancers, the nucleosome modifications that may enable appropriate and hinder inappropriate enhancer-promoter contacts, and the roles of lineage-restricted transcription factors.
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Affiliation(s)
- Michael P. Verzi
- 1Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey,2Cancer Institute of New Jersey and Human Genetics Institute of New Jersey, Piscataway, New Jersey
| | - Ramesh A. Shivdasani
- 3Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts,4Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,5Harvard Stem Cell Institute, Cambridge, Massachusetts
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27
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Chen L, Vasoya RP, Toke NH, Parthasarathy A, Luo S, Chiles E, Flores J, Gao N, Bonder EM, Su X, Verzi MP. HNF4 Regulates Fatty Acid Oxidation and Is Required for Renewal of Intestinal Stem Cells in Mice. Gastroenterology 2020; 158:985-999.e9. [PMID: 31759926 PMCID: PMC7062567 DOI: 10.1053/j.gastro.2019.11.031] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/22/2019] [Accepted: 11/15/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Functions of intestinal stem cells (ISCs) are regulated by diet and metabolic pathways. Hepatocyte nuclear factor 4 (HNF4) family are transcription factors that bind fatty acids. We investigated how HNF4 transcription factors regulate metabolism and their functions in ISCs in mice. METHODS We performed studies with Villin-CreERT2;Lgr5-EGFP-IRES-CreERT2;Hnf4αf/f;Hnf4γCrispr/Crispr mice, hereafter referred to Hnf4αγDKO. Mice were given tamoxifen to induce Cre recombinase. Mice transgenic with only Cre alleles (Villin-CreERT2, Lgr5-EGFP-IRES-CreERT2, Hnf4α+/+, and Hnf4γ+/+) or mice given vehicle were used as controls. Crypt and villus cells were isolated, incubated with fluorescently labeled fatty acids or glucose analog, and analyzed by confocal microscopy. Fatty acid oxidation activity and tricarboxylic acid (TCA) cycle metabolites were measured in cells collected from the proximal half of the small intestine of Hnf4αγDKO and control mice. We performed chromatin immunoprecipitation and gene expression profiling analyses to identify genes regulated by HNF4 factors. We established organoids from duodenal crypts, incubated them with labeled palmitate or acetate, and measured production of TCA cycle metabolites or fatty acids. Acetate, a precursor of acetyl coenzyme A (CoA) (a product of fatty acid β-oxidation [FAO]), or dichloroacetate, a compound that promotes pyruvate oxidation and generation of mitochondrial acetyl-CoA, were used for metabolic intervention. RESULTS Crypt cells rapidly absorbed labeled fatty acids, and messenger RNA levels of Lgr5+ stem cell markers (Lgr5, Olfm4, Smoc2, Msi1, and Ascl2) were down-regulated in organoids incubated with etomoxir, an inhibitor of FAO, indicating that FAO was required for renewal of ISCs. HNF4A and HNF4G were expressed in ISCs and throughout the intestinal epithelium. Single knockout of either HNF4A or HNF4G did not affect maintenance of ISCs, but double-knockout of HNF4A and HNF4G resulted in ISC loss; stem cells failed to renew. FAO supports ISC renewal, and HNF4 transcription factors directly activate FAO genes, including Acsl5 and Acsf2 (encode regulators of acyl-CoA synthesis), Slc27a2 (encodes a fatty acid transporter), Fabp2 (encodes fatty acid binding protein), and Hadh (encodes hydroxyacyl-CoA dehydrogenase). In the intestinal epithelium of Hnf4αγDKO mice, expression levels of FAO genes, FAO activity, and metabolites of TCA cycle were all significantly decreased, but fatty acid synthesis transcripts were increased, compared with control mice. The contribution of labeled palmitate or acetate to the TCA cycle was reduced in organoids derived from Hnf4αγDKO mice, compared with control mice. Incubation of organoids derived from double-knockout mice with acetate or dichloroacetate restored stem cells. CONCLUSIONS In mice, the transcription factors HNF4A and HNF4G regulate the expression of genes required for FAO and are required for renewal of ISCs.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Roshan P. Vasoya
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalie H. Toke
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Aditya Parthasarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Shirley Luo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Eric Chiles
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Edward M. Bonder
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Xiaoyang Su
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA,Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA,Rutgers Center for Lipid Research, New Brunswick, NJ 08901, USA,Correspondence: (M.P.V.)
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28
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Christakos S, Li S, De La Cruz J, Shroyer NF, Criss ZK, Verzi MP, Fleet JC. Vitamin D and the intestine: Review and update. J Steroid Biochem Mol Biol 2020; 196:105501. [PMID: 31655181 PMCID: PMC6954280 DOI: 10.1016/j.jsbmb.2019.105501] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/04/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022]
Abstract
The central role of vitamin D in calcium homeostasis is to increase calcium absorption from the intestine. This article describes the early work that served as the foundation for the initial model of vitamin D mediated calcium absorption. In addition, other research related to the role of vitamin D in the intestine, including those which have challenged the traditional model and the crucial role of specific calcium transport proteins, are reviewed. More recent work identifying novel targets of 1,25(OH)2D3 action in the intestine and highlighting the importance of 1,25(OH)2D3 action across the proximal/distal and crypt/villus axes in the intestine is summarized.
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Affiliation(s)
- Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ 07103, USA.
| | - Shanshan Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ 07103, USA
| | - Jessica De La Cruz
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ 07103, USA
| | - Noah F Shroyer
- Integrative Molecular and Biomedical Sciences Graduate Program, Division of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zachary K Criss
- Integrative Molecular and Biomedical Sciences Graduate Program, Division of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, New Brunswick, NJ 08854, USA
| | - James C Fleet
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
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29
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Vazquez BN, Thackray JK, Simonet NG, Chahar S, Kane-Goldsmith N, Newkirk SJ, Lee S, Xing J, Verzi MP, An W, Vaquero A, Tischfield JA, Serrano L. SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina. Nucleic Acids Res 2019; 47:7870-7885. [PMID: 31226208 PMCID: PMC6735864 DOI: 10.1093/nar/gkz519] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Long interspersed elements-1 (LINE-1, L1) are retrotransposons that hold the capacity of self-propagation in the genome with potential mutagenic outcomes. How somatic cells restrict L1 activity and how this process becomes dysfunctional during aging and in cancer cells is poorly understood. L1s are enriched at lamin-associated domains, heterochromatic regions of the nuclear periphery. Whether this association is necessary for their repression has been elusive. Here we show that the sirtuin family member SIRT7 participates in the epigenetic transcriptional repression of L1 genome-wide in both mouse and human cells. SIRT7 depletion leads to increased L1 expression and retrotransposition. Mechanistically, we identify a novel interplay between SIRT7 and Lamin A/C in L1 repression. Our results demonstrate that SIRT7-mediated H3K18 deacetylation regulates L1 expression and promotes L1 association with elements of the nuclear lamina. The failure of such activity might contribute to the observed genome instability and compromised viability in SIRT7 knockout mice. Overall, our results reveal a novel function of SIRT7 on chromatin organization by mediating the anchoring of L1 to the nuclear envelope, and a new functional link of the nuclear lamina with transcriptional repression.
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Affiliation(s)
- Berta N Vazquez
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.,Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona 08916, Spain
| | - Joshua K Thackray
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Nicolas G Simonet
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Spain
| | - Sanjay Chahar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.,Montpellier Institute of Molecular Genetics (IGMM), CNRS and the University of Montpellier, 34090, France
| | - Noriko Kane-Goldsmith
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Simon J Newkirk
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, South Dakota State University, Brookings, SD 57007, USA
| | - Suman Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, South Dakota State University, Brookings, SD 57007, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, South Dakota State University, Brookings, SD 57007, USA
| | - Alejandro Vaquero
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona 08916, Spain.,Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Spain
| | - Jay A Tischfield
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lourdes Serrano
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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30
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Chen L, Toke NH, Luo S, Vasoya RP, Aita R, Parthasarathy A, Tsai YH, Spence JR, Verzi MP. HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine. Development 2019; 146:dev.179432. [PMID: 31345929 DOI: 10.1242/dev.179432] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022]
Abstract
As embryos mature, cells undergo remarkable transitions that are accompanied by shifts in transcription factor regulatory networks. Mechanisms driving developmental transitions are incompletely understood. The embryonic intestine transitions from a rapidly proliferating tube with pseudostratified epithelium prior to murine embryonic day (E) 14.5 to an exquisitely folded columnar epithelium in fetal stages. We sought to identify factors driving mouse fetal intestinal maturation by mining chromatin accessibility data for transcription factor motifs. ATAC-seq accessible regions shift during tissue maturation, with CDX2 transcription factor motifs abundant at chromatin-accessible regions of the embryo. Hepatocyte nuclear factor 4 (HNF4) transcription factor motifs are the most abundant in the fetal stages (>E16.5). Genetic inactivation of Hnf4a and its paralog Hnf4g revealed that HNF4 factors are redundantly required for fetal maturation. CDX2 binds to and activates Hnf4 gene loci to elevate HNF4 expression at fetal stages. HNF4 and CDX2 transcription factors then occupy shared genomic regulatory sites to promote chromatin accessibility and gene expression in the maturing intestine. Thus, HNF4 paralogs are key components of an intestinal transcription factor network shift during the embryonic to fetal transition.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Natalie H Toke
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Shirley Luo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Roshan P Vasoya
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Aditya Parthasarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA.,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
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31
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D'Agostino L, Nie Y, Goswami S, Tong K, Yu S, Bandyopadhyay S, Flores J, Zhang X, Balasubramanian I, Joseph I, Sakamori R, Farrell V, Li Q, Yang CS, Gao B, Ferraris RP, Yehia G, Bonder EM, Goldenring JR, Verzi MP, Zhang L, Ip YT, Gao N. Recycling Endosomes in Mature Epithelia Restrain Tumorigenic Signaling. Cancer Res 2019; 79:4099-4112. [PMID: 31239271 DOI: 10.1158/0008-5472.can-18-4075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/11/2019] [Accepted: 06/11/2019] [Indexed: 11/16/2022]
Abstract
The effects of polarized membrane trafficking in mature epithelial tissue on cell growth and cancer progression have not been fully explored in vivo. A majority of colorectal cancers have reduced and mislocalized Rab11, a small GTPase dedicated to trafficking of recycling endosomes. Patients with low Rab11 protein expression have poor survival rates. Using genetic models across species, we show that intact recycling endosome function restrains aberrant epithelial growth elicited by APC or RAS mutations. Loss of Rab11 protein led to epithelial dysplasia in early animal development and synergized with oncogenic pathways to accelerate tumor progression initiated by carcinogen, genetic mutation, or aging. Transcriptomic analysis uncovered an immediate expansion of the intestinal stem cell pool along with cell-autonomous Yki/Yap activation following disruption of Rab11a-mediated recycling endosomes. Intestinal tumors lacking Rab11a traffic exhibited marked elevation of nuclear Yap, upd3/IL6-Stat3, and amphiregulin-MAPK signaling, whereas suppression of Yki/Yap or upd3/IL6 reduced gut epithelial dysplasia and hyperplasia. Examination of Rab11a function in enteroids or cultured cell lines suggested that this endosome unit is required for suppression of the Yap pathway by Hippo kinases. Thus, recycling endosomes in mature epithelia constitute key tumor suppressors, loss of which accelerates carcinogenesis. SIGNIFICANCE: Recycling endosome traffic in mature epithelia constitutes a novel tumor suppressing mechanism.
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Affiliation(s)
- Luca D'Agostino
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Yingchao Nie
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Sayantani Goswami
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Kevin Tong
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | | | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Xiao Zhang
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | | | - Ivor Joseph
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Ryotaro Sakamori
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Victoria Farrell
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Qi Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Chung S Yang
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey
| | - Bin Gao
- Department of Internal Medicine, Taixing Chinese Medicine Hospital, Taixing, Jiangsu, China
| | - Ronaldo P Ferraris
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Ghassan Yehia
- Rutgers Genome Editing Core Facility, Rutgers University, New Brunswick, New Jersey
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - James R Goldenring
- Department of Surgery, Cell and Developmental Biology, and Epithelial Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, New Jersey.,Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Pathology, Princeton Medical Center, Plainsboro, New Jersey
| | - Y Tony Ip
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts.
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, New Jersey. .,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
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32
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Chen L, Toke NH, Luo S, Vasoya RP, Fullem RL, Parthasarathy A, Perekatt AO, Verzi MP. A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity. Nat Genet 2019; 51:777-785. [PMID: 30988513 PMCID: PMC6650150 DOI: 10.1038/s41588-019-0384-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 02/28/2019] [Indexed: 12/30/2022]
Abstract
BMP/SMAD signaling is a crucial regulator of intestinal differentiation1–4. However, the molecular underpinnings of the BMP pathway in this context are unknown. Here, we characterize the mechanism by which BMP/SMAD signaling drives enterocyte differentiation. We establish that the transcription factor HNF4A acts redundantly with an intestine-restricted HNF4 paralog, HNF4G, to activate enhancer chromatin and upregulate the majority of transcripts enriched in the differentiated epithelium; cells fail to differentiate upon double knockout of both HNF4 paralogs. Furthermore, we show that SMAD4 and HNF4 function via a reinforcing feed-forward loop, activating each other’s expression and co-binding to regulatory elements of differentiation genes. This feed-forward regulatory module promotes and stabilizes enterocyte cell identity; disruption of the HNF4-SMAD4 module results in loss of enterocyte fate in favor of progenitor and secretory cell lineages. This intersection of signaling and transcriptional control provides a framework to understand regenerative tissue homeostasis, particularly in tissues with inherent cellular plasticity5.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Natalie H Toke
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Shirley Luo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Roshan P Vasoya
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Robert L Fullem
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Aditya Parthasarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Ansu O Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA. .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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33
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Tong K, Pellón-Cárdenas O, Sirihorachai VR, Warder BN, Kothari OA, Perekatt AO, Fokas EE, Fullem RL, Zhou A, Thackray JK, Tran H, Zhang L, Xing J, Verzi MP. Degree of Tissue Differentiation Dictates Susceptibility to BRAF-Driven Colorectal Cancer. Cell Rep 2019; 21:3833-3845. [PMID: 29281831 DOI: 10.1016/j.celrep.2017.11.104] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/09/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
Oncogenic mutations in BRAF are believed to initiate serrated colorectal cancers; however, the mechanisms of BRAF-driven colon cancer are unclear. We find that oncogenic BRAF paradoxically suppresses stem cell renewal and instead promotes differentiation. Correspondingly, tumor formation is inefficient in BRAF-driven mouse models of colon cancer. By reducing levels of differentiation via genetic manipulation of either of two distinct differentiation-promoting factors (Smad4 or Cdx2), stem cell activity is restored in BRAFV600E intestines, and the oncogenic capacity of BRAFV600E is amplified. In human patients, we observe that reduced levels of differentiation in normal tissue is associated with increased susceptibility to serrated colon tumors. Together, these findings help resolve the conditions necessary for BRAF-driven colon cancer initiation. Additionally, our results predict that genetic and/or environmental factors that reduce tissue differentiation will increase susceptibility to serrated colon cancer. These findings offer an opportunity to identify susceptible individuals by assessing their tissue-differentiation status.
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Affiliation(s)
- Kevin Tong
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Oscar Pellón-Cárdenas
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Veerin R Sirihorachai
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Bailey N Warder
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Om A Kothari
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Ansu O Perekatt
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Emily E Fokas
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Robert L Fullem
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Anbo Zhou
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Joshua K Thackray
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Hiep Tran
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Lanjing Zhang
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Pathology, University Medical Center of Princeton, Plainsboro, NJ 08536, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA.
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34
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Kumar N, Tsai YH, Chen L, Zhou A, Banerjee KK, Saxena M, Huang S, Toke NH, Xing J, Shivdasani RA, Spence JR, Verzi MP. The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Development 2019; 146:dev172189. [PMID: 30745430 PMCID: PMC6432663 DOI: 10.1242/dev.172189] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 09/25/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
Lineage-restricted transcription factors, such as the intestine-specifying factor CDX2, often have dual requirements across developmental time. Embryonic loss of CDX2 triggers homeotic transformation of intestinal fate, whereas adult-onset loss compromises crucial physiological functions but preserves intestinal identity. It is unclear how such diverse requirements are executed across the developmental continuum. Using primary and engineered human tissues, mouse genetics, and a multi-omics approach, we demonstrate that divergent CDX2 loss-of-function phenotypes in embryonic versus adult intestines correspond to divergent CDX2 chromatin-binding profiles in embryonic versus adult stages. CDX2 binds and activates distinct target genes in developing versus adult mouse and human intestinal cells. We find that temporal shifts in chromatin accessibility correspond to these context-specific CDX2 activities. Thus, CDX2 is not sufficient to activate a mature intestinal program; rather, CDX2 responds to its environment, targeting stage-specific genes to contribute to either intestinal patterning or mature intestinal function. This study provides insights into the mechanisms through which lineage-specific regulatory factors achieve divergent functions over developmental time.
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Affiliation(s)
- Namit Kumar
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lei Chen
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Anbo Zhou
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Kushal K Banerjee
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Madhurima Saxena
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Sha Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natalie H Toke
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jason R Spence
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
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35
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Guo Y, Wu R, Gaspar JM, Sargsyan D, Su ZY, Zhang C, Gao L, Cheng D, Li W, Wang C, Yin R, Fang M, Verzi MP, Hart RP, Kong AN. DNA methylome and transcriptome alterations and cancer prevention by curcumin in colitis-accelerated colon cancer in mice. Carcinogenesis 2019; 39:669-680. [PMID: 29547900 DOI: 10.1093/carcin/bgy043] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/12/2018] [Indexed: 12/17/2022] Open
Abstract
Inflammation is highly associated with colon carcinogenesis. Epigenetic mechanisms could play an important role in the initiation and progression of colon cancer. Curcumin, a dietary phytochemical, shows promising effects in suppressing colitis-associated colon cancer in azoxymethane-dextran sulfate sodium (AOM-DSS) mice. However, the potential epigenetic mechanisms of curcumin in colon cancer remain unknown. In this study, the anticancer effect of curcumin in suppressing colon cancer in an 18-week AOM-DSS colon cancer mouse model was confirmed. We identified lists of differentially expressed and differentially methylated genes in pairwise comparisons and several pathways involved in the potential anticancer effect of curcumin. These pathways include LPS/IL-1-mediated inhibition of RXR function, Nrf2-mediated oxidative stress response, production of NO and ROS in macrophages and IL-6 signaling. Among these genes, Tnf stood out with decreased DNA CpG methylation of Tnf in the AOM-DSS group and reversal of the AOM-DSS induced Tnf demethylation by curcumin. These observations in Tnf methylation correlated with increased and decreased Tnf expression in RNA-seq. The functional role of DNA methylation of Tnf was further confirmed by in vitro luciferase transcriptional activity assay. In addition, the DNA methylation level in a group of inflammatory genes was decreased in the AOM+DSS group but restored by curcumin and was validated by pyrosequencing. This study shows for the first time epigenomic changes in DNA CpG methylation in the inflammatory response from colitis-associated colon cancer and the reversal of their CpG methylation changes by curcumin. Future clinical epigenetic studies with curcumin in inflammation-associated colon cancer would be warranted.
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Affiliation(s)
- Yue Guo
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - John M Gaspar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zheng-Yuan Su
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City, Taiwan
| | - Chengyue Zhang
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Linbo Gao
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - David Cheng
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Wenji Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Chao Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Mingzhu Fang
- Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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36
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Ma X, Das NK, Castillo C, Gourani A, Perekatt AO, Verzi MP, Shah YM. SMAD family member 3 (SMAD3) and SMAD4 repress HIF2α-dependent iron-regulatory genes. J Biol Chem 2019; 294:3974-3986. [PMID: 30659096 DOI: 10.1074/jbc.ra118.005549] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/09/2019] [Indexed: 01/11/2023] Open
Abstract
Hypoxia-inducible factor 2α (HIF2α) directly regulates a battery of genes essential for intestinal iron absorption. Interestingly, iron deficiency and overload disorders do not result in increased intestinal expression of glycolytic or angiogenic HIF2α target genes. Similarly, inflammatory and tumor foci can induce a distinct subset of HIF2α target genes in vivo These observations indicate that different stimuli activate distinct subsets of HIF2α target genes via mechanisms that remain unclear. Here, we conducted a high-throughput siRNA-based screen to identify genes that regulate HIF2α's transcriptional activity on the promoter of the iron transporter gene divalent metal transporter-1 (DMT1). SMAD family member 3 (SMAD3) and SMAD4 were identified as potential transcriptional repressors. Further analysis revealed that SMAD4 signaling selectively represses iron-absorptive gene promoters but not the inflammatory or glycolytic HIF2α or HIF1α target genes. Moreover, the highly homologous SMAD2 did not alter HIF2α transcriptional activity. During iron deficiency, SMAD3 and SMAD4 expression was significantly decreased via proteasomal degradation, allowing for derepression of iron target genes. Several iron-regulatory genes contain a SMAD-binding element (SBE) in their proximal promoters; however, mutation of the putative SBE on the DMT1 promoter did not alter the repressive function of SMAD3 or SMAD4. Importantly, the transcription factor forkhead box protein A1 (FOXA1) was critical in SMAD4-induced DMT1 repression, and DNA binding of SMAD4 was essential for the repression of HIF2α activity, suggesting an indirect repressive mechanism through DNA binding. These results provide mechanistic clues to how HIF signaling can be regulated by different cellular cues.
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Affiliation(s)
- Xiaoya Ma
- From the Departments of Molecular & Integrative Physiology and
| | - Nupur K Das
- From the Departments of Molecular & Integrative Physiology and
| | | | - Ayla Gourani
- From the Departments of Molecular & Integrative Physiology and
| | - Ansu O Perekatt
- the Department of Genetics, Human Genetics Institute, and Rutgers Cancer Institute, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Michael P Verzi
- the Department of Genetics, Human Genetics Institute, and Rutgers Cancer Institute, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - Yatrik M Shah
- From the Departments of Molecular & Integrative Physiology and .,Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor Michigan 48109 and
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37
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Banerjee KK, Saxena M, Kumar N, Chen L, Cavazza A, Toke NH, O'Neill NK, Madha S, Jadhav U, Verzi MP, Shivdasani RA. Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development. Genes Dev 2018; 32:1430-1442. [PMID: 30366903 PMCID: PMC6217732 DOI: 10.1101/gad.318832.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined. Banerjee et al. show that the midgut endoderm is primed for heterologous cell fates and that transcription factors act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined (commitment). We investigated the chromatin basis for these developmental milestones in mouse endoderm, a tissue with recognizable rostro–caudal patterning and transcription factor (TF)-dependent interim plasticity. Foregut-specific enhancers are as accessible and active in early midgut as in foregut endoderm, and intestinal enhancers and identity are established only after ectopic cis-regulatory elements are decommissioned. Depletion of the intestinal TF CDX2 before this cis element transition stabilizes foregut enhancers, reinforces ectopic transcriptional programs, and hence imposes foregut identities on the midgut. Later in development, as the window of chromatin plasticity elapses, CDX2 depletion weakens intestinal, without strengthening foregut, enhancers. Thus, midgut endoderm is primed for heterologous cell fates, and TFs act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. Similar principles likely govern other fate commitments.
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Affiliation(s)
- Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Namit Kumar
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Lei Chen
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Alessia Cavazza
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Natalie H Toke
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Nicholas K O'Neill
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shariq Madha
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Unmesh Jadhav
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA.,Cancer Institute of New Jersey, Piscataway, New Jersey 08854, USA.,Human Genetics Institute of New Jersey, Piscataway, New Jersey 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02139, USA
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38
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Srivillibhuthur M, Warder BN, Toke NH, Shah PP, Feng Q, Gao N, Bonder EM, Verzi MP. TFAM is required for maturation of the fetal and adult intestinal epithelium. Dev Biol 2018; 439:92-101. [PMID: 29684311 PMCID: PMC5978755 DOI: 10.1016/j.ydbio.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 11/01/2017] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022]
Abstract
During development, the embryo transitions from a metabolism favoring glycolysis to a metabolism favoring mitochondrial respiration. How metabolic shifts regulate developmental processes, or how developmental processes regulate metabolic shifts, remains unclear. To test the requirement of mitochondrial function in developing endoderm-derived tissues, we genetically inactivated the mitochondrial transcription factor, Tfam, using the Shh-Cre driver. Tfam mutants did not survive postnatally, exhibiting defects in lung development. In the developing intestine, TFAM-loss was tolerated until late fetal development, during which the process of villus elongation was compromised. While progenitor cell populations appeared unperturbed, markers of enterocyte maturation were diminished and villi were blunted. Loss of TFAM was also tested in the adult intestinal epithelium, where enterocyte maturation was similarly dependent upon the mitochondrial transcription factor. While progenitor cells in the transit amplifying zone of the adult intestine remained proliferative, intestinal stem cell renewal was dependent upon TFAM, as indicated by molecular profiling and intestinal organoid formation assays. Taken together, these studies point to critical roles for the mitochondrial regulator TFAM for multiple aspects of intestinal development and maturation, and highlight the importance of mitochondrial regulators in tissue development and homeostasis.
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Affiliation(s)
- Manasa Srivillibhuthur
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA 19140, USA
| | - Bailey N Warder
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Natalie H Toke
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Pooja P Shah
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Qiang Feng
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Michael P Verzi
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA.
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39
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Perekatt AO, Shah PP, Cheung S, Jariwala N, Wu A, Gandhi V, Kumar N, Feng Q, Patel N, Chen L, Joshi S, Zhou A, Taketo MM, Xing J, White E, Gao N, Gatza ML, Verzi MP. SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium. Cancer Res 2018; 78:4878-4890. [PMID: 29986996 DOI: 10.1158/0008-5472.can-18-0043] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/26/2018] [Accepted: 07/02/2018] [Indexed: 12/22/2022]
Abstract
The cell of origin of colon cancer is typically thought to be the resident somatic stem cells, which are immortal and escape the continual cellular turnover characteristic of the intestinal epithelium. However, recent studies have identified certain conditions in which differentiated cells can acquire stem-like properties and give rise to tumors. Defining the origins of tumors will inform cancer prevention efforts as well as cancer therapies, as cancers with distinct origins often respond differently to treatments. We report here a new condition in which tumors arise from the differentiated intestinal epithelium. Inactivation of the differentiation-promoting transcription factor SMAD4 in the intestinal epithelium was surprisingly well tolerated in the short term. However, after several months, adenomas developed with characteristics of activated WNT signaling. Simultaneous loss of SMAD4 and activation of the WNT pathway led to dedifferentiation and rapid adenoma formation in differentiated tissue. Transcriptional profiling revealed acquisition of stem cell characteristics, and colabeling indicated that cells expressing differentiated enterocyte markers entered the cell cycle and reexpressed stem cell genes upon simultaneous loss of SMAD4 and activation of the WNT pathway. These results indicate that SMAD4 functions to maintain differentiated enterocytes in the presence of oncogenic WNT signaling, thus preventing dedifferentiation and tumor formation in the differentiated intestinal epithelium.Significance: This work identifies a mechanism through which differentiated cells prevent tumor formation by suppressing oncogenic plasticity. Cancer Res; 78(17); 4878-90. ©2018 AACR.
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Affiliation(s)
- Ansu O Perekatt
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Pooja P Shah
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Shannon Cheung
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Nidhi Jariwala
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Alex Wu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Vishal Gandhi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Namit Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Qiang Feng
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, New Jersey
| | - Neeket Patel
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Shilpy Joshi
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Anbo Zhou
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - M Mark Taketo
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Sakyo Kyoto, Japan
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Nan Gao
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Biological Sciences, Rutgers University, Newark, New Jersey, New Jersey
| | - Michael L Gatza
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey. .,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
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40
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Yu S, Tong K, Zhao Y, Balasubramanian I, Yap GS, Ferraris RP, Bonder EM, Verzi MP, Gao N. Paneth Cell Multipotency Induced by Notch Activation following Injury. Cell Stem Cell 2018; 23:46-59.e5. [PMID: 29887318 PMCID: PMC6035085 DOI: 10.1016/j.stem.2018.05.002] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [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: 05/21/2017] [Revised: 01/08/2018] [Accepted: 05/04/2018] [Indexed: 02/08/2023]
Abstract
Paneth cells are post-mitotic intestinal epithelial cells supporting the stem cell niche and mucosal immunity. Paneth cell pathologies are observed in various gastrointestinal diseases, but their plasticity and response to genomic and environmental challenges remain unclear. Using a knockin allele engineered at the mouse Lyz1 locus, we performed detailed Paneth cell-lineage tracing. Irradiation induced a subset of Paneth cells to proliferate and differentiate into villus epithelial cells. RNA sequencing (RNA-seq) revealed that Paneth cells sorted from irradiated mice acquired a stem cell-like transcriptome; when cultured in vitro, these individual Paneth cells formed organoids. Irradiation activated Notch signaling, and forced expression of Notch intracellular domain (NICD) in Paneth cells, but not Wnt/β-catenin pathway activation, induced their dedifferentiation. This study documents Paneth cell plasticity, particularly their ability to participate in epithelial replenishment following stem cell loss, adding to a growing body of knowledge detailing the molecular pathways controlling injury-induced regeneration.
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Affiliation(s)
- Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Kevin Tong
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Yanlin Zhao
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ 07101, USA
| | | | - George S Yap
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ 07101, USA
| | - Ronaldo P Ferraris
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ 07101, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.
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41
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Guo Y, Su ZY, Zhang C, Gaspar JM, Wang R, Hart RP, Verzi MP, Kong ANT. Mechanisms of colitis-accelerated colon carcinogenesis and its prevention with the combination of aspirin and curcumin: Transcriptomic analysis using RNA-seq. Biochem Pharmacol 2017; 135:22-34. [PMID: 28267439 DOI: 10.1016/j.bcp.2017.02.021] [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] [Received: 11/27/2016] [Accepted: 02/28/2017] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) remains the leading cause of cancer-related death in the world. Aspirin (ASA) and curcumin (CUR) are widely investigated chemopreventive candidates for CRC. However, the precise mechanisms of their action and their combinatorial effects have not been evaluated. The purpose of the present study was to determine the effect of ASA, CUR, and their combination in azoxymethane/dextran sulfate sodium (AOM/DSS)-induced colitis-accelerated colorectal cancer (CAC). We also aimed to characterize the differential gene expression profiles in AOM/DSS-induced tumors as well as in tumors modulated by ASA and CUR using RNA-seq. Diets supplemented with 0.02% ASA, 2% CUR or 0.01% ASA+1% CUR were given to mice from 1week prior to the AOM injection until the experiment was terminated 22weeks after AOM initiation. Our results showed that CUR had a superior inhibitory effect in colon tumorigenesis compared to that of ASA. The combination of ASA and CUR at a lower dose exhibited similar efficacy to that of a higher dose of CUR at 2%. RNA isolated from colonic tissue from the control group and from tumor samples from the experimental groups was subjected to RNA-seq. Transcriptomic analysis suggested that the low-dose combination of ASA and CUR modulated larger gene sets than the single treatment. These differentially expressed genes were situated in several canonical pathways important in the inflammatory network and liver metastasis in CAC. We identified a small subset of genes as potential molecular targets involved in the preventive action of the combination of ASA and CUR. Taken together, the current results provide the first evidence in support of the chemopreventive effect of a low-dose combination of ASA and CUR in CAC. Moreover, the transcriptional profile obtained in our study may provide a framework for identifying the mechanisms underlying the carcinogenesis process from normal colonic tissue to tumor development as well as the cancer inhibitory effects and potential molecular targets of ASA and CUR.
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Affiliation(s)
- Yue Guo
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zheng-Yuan Su
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
| | - Chengyue Zhang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John M Gaspar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rui Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Shanghai Roche Pharmaceuticals Ltd, Shanghai 10020, China
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ah-Ng Tony Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, Jung G, Shao PP, Childers EP, Liu S, Kulesa A, Garcia BA, Becker ML, Hwang NS, Madabhushi A, Verzi MP, Moghe PV. Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Sci Rep 2017; 7:39406. [PMID: 28051095 PMCID: PMC5209743 DOI: 10.1038/srep39406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
While distinct stem cell phenotypes follow global changes in chromatin marks, single-cell chromatin technologies are unable to resolve or predict stem cell fates. We propose the first such use of optical high content nanoscopy of histone epigenetic marks (epi-marks) in stem cells to classify emergent cell states. By combining nanoscopy with epi-mark textural image informatics, we developed a novel approach, termed EDICTS (Epi-mark Descriptor Imaging of Cell Transitional States), to discern chromatin organizational changes, demarcate lineage gradations across a range of stem cell types and robustly track lineage restriction kinetics. We demonstrate the utility of EDICTS by predicting the lineage progression of stem cells cultured on biomaterial substrates with graded nanotopographies and mechanical stiffness, thus parsing the role of specific biophysical cues as sensitive epigenetic drivers. We also demonstrate the unique power of EDICTS to resolve cellular states based on epi-marks that cannot be detected via mass spectrometry based methods for quantifying the abundance of histone post-translational modifications. Overall, EDICTS represents a powerful new methodology to predict single cell lineage decisions by integrating high content super-resolution nanoscopy and imaging informatics of the nuclear organization of epi-marks.
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Affiliation(s)
- Joseph J Kim
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Neal K Bennett
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Mitchel S Devita
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Sanjay Chahar
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Satish Viswanath
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Eunjee A Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Giyoung Jung
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea.,Division of Heath Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul P Shao
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Erin P Childers
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
| | - Shichong Liu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anthony Kulesa
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew L Becker
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
| | - Nathaniel S Hwang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Prabhas V Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey, USA
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43
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Kumar N, Srivillibhuthur M, Joshi S, Walton KD, Zhou A, Faller WJ, Perekatt AO, Sansom OJ, Gumucio DL, Xing J, Bonder EM, Gao N, White E, Verzi MP. A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis. Development 2016; 143:3711-3722. [PMID: 27802136 PMCID: PMC5087649 DOI: 10.1242/dev.137992] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 03/23/2016] [Accepted: 08/25/2016] [Indexed: 12/28/2022]
Abstract
During late gestation, villi extend into the intestinal lumen to dramatically increase the surface area of the intestinal epithelium, preparing the gut for the neonatal diet. Incomplete development of the intestine is the most common gastrointestinal complication in neonates, but the causes are unclear. We provide evidence in mice that Yin Yang 1 (Yy1) is crucial for intestinal villus development. YY1 loss in the developing endoderm had no apparent consequences until late gestation, after which the intestine differentiated poorly and exhibited severely stunted villi. Transcriptome analysis revealed that YY1 is required for mitochondrial gene expression, and ultrastructural analysis confirmed compromised mitochondrial integrity in the mutant intestine. We found increased oxidative phosphorylation gene expression at the onset of villus elongation, suggesting that aerobic respiration might function as a regulator of villus growth. Mitochondrial inhibitors blocked villus growth in a fashion similar to Yy1 loss, thus further linking oxidative phosphorylation with late-gestation intestinal development. Interestingly, we find that necrotizing enterocolitis patients also exhibit decreased expression of oxidative phosphorylation genes. Our study highlights the still unappreciated role of metabolic regulation during organogenesis, and suggests that it might contribute to neonatal gastrointestinal disorders.
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Affiliation(s)
- Namit Kumar
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Manasa Srivillibhuthur
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Shilpy Joshi
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Katherine D Walton
- Cell and Developmental Biology Department, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anbo Zhou
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | | | - Ansu O Perekatt
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Deborah L Gumucio
- Cell and Developmental Biology Department, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jinchuan Xing
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Michael P Verzi
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
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Affiliation(s)
- Pauline K Lund
- Department of Cell Biology and Physiology and Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, and Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey
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45
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Tsai YH, Hill DR, Kumar N, Huang S, Chin AM, Dye BR, Nagy MS, Verzi MP, Spence JR. LGR4 and LGR5 Function Redundantly During Human Endoderm Differentiation. Cell Mol Gastroenterol Hepatol 2016; 2:648-662.e8. [PMID: 28078320 PMCID: PMC5042889 DOI: 10.1016/j.jcmgh.2016.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/11/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS The Lgr family of transmembrane proteins (Lgr4, 5, 6) act as functional receptors for R-spondin proteins (Rspo 1, 2, 3, 4), and potentiate Wnt signaling in different contexts. Lgr5 is arguably the best characterized of the Lgr family members in a number of adult and embryonic contexts in mice. However, the function of LGR family members in early embryonic development is unclear, and has not been explored during human development or tissue differentiation in detail. METHODS We interrogated the function and expression of LGR family members using human pluripotent stem cell-derived tissues including definitive endoderm, mid/hindgut, and intestinal organoids. We performed embryonic lineage tracing in Lgr5-GFP-IRES-CreERT2 mice. RESULTS We show that LGR5 is part of the human definitive endoderm (DE) gene signature, and LGR5 transcripts are induced robustly when human pluripotent stem cells are differentiated into DE. Our results show that LGR4 and 5 are functionally required for efficient human endoderm induction. Consistent with data in human DE, we observe Lgr5 reporter (eGFP) activity in the embryonic day 8.5 mouse endoderm, and show the ability to lineage trace these cells into the adult intestine. However, gene expression data also suggest that there are human-mouse species-specific differences at later time points of embryonic development. CONCLUSIONS Our results show that LGR5 is induced during DE differentiation, LGR receptors are functionally required for DE induction, and that they function to potentiate WNT signaling during this process.
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Key Words
- CDX2, caudal type homeobox2
- ChIPseq, chromatin immunoprecipitation sequencing
- Ct, cycle threshold
- DE, definitive endoderm
- E, embryonic day
- Endoderm
- GFP, green fluorescent protein
- Intestine
- LGR5
- Organoid
- Pluripotent Stem Cells
- Rspo, R-spondin protein
- WNT
- creER, cre recombinase protein fused to estrogen receptor
- hESC, human embryonic stem cell
- mRNA, messenger RNA
- qRT-PCR, quantitative reverse-transcription polymerase chain reaction
- shRNA, short hairpin RNA
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Affiliation(s)
- Yu-Hwai Tsai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - David R. Hill
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Namit Kumar
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Sha Huang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alana M. Chin
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Briana R. Dye
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Melinda S. Nagy
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michael P. Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan,Correspondence Address correspondence to: Jason R. Spence, PhD, Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109. fax: (734) 763-4686.Division of GastroenterologyDepartment of Internal MedicineUniversity of Michigan Medical SchoolAnn ArborMichigan 48109
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46
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Hu J, Verzi MP, Robinson AS, Tang PLF, Hua LL, Xu SM, Kwok PY, Black BL. Endothelin signaling activates Mef2c expression in the neural crest through a MEF2C-dependent positive-feedback transcriptional pathway. Development 2015; 142:2775-80. [PMID: 26160899 DOI: 10.1242/dev.126391] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 06/30/2015] [Indexed: 11/20/2022]
Abstract
Endothelin signaling is essential for neural crest development, and dysregulated Endothelin signaling is associated with several neural crest-related disorders, including Waardenburg and other syndromes. However, despite the crucial roles of this pathway in neural crest development and disease, the transcriptional effectors directly activated by Endothelin signaling during neural crest development remain incompletely elucidated. Here, we establish that the MADS box transcription factor MEF2C is an immediate downstream transcriptional target and effector of Endothelin signaling in the neural crest. We show that Endothelin signaling activates Mef2c expression in the neural crest through a conserved enhancer in the Mef2c locus and that CRISPR-mediated deletion of this Mef2c neural crest enhancer from the mouse genome abolishes Endothelin induction of Mef2c expression. Moreover, we demonstrate that Endothelin signaling activates neural crest expression of Mef2c by de-repressing MEF2C activity through a Calmodulin-CamKII-histone deacetylase signaling cascade. Thus, these findings identify a MEF2C-dependent, positive-feedback mechanism for Endothelin induction and establish MEF2C as an immediate transcriptional effector and target of Endothelin signaling in the neural crest.
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Affiliation(s)
- Jianxin Hu
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Michael P Verzi
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Ashley S Robinson
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Paul Ling-Fung Tang
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Lisa L Hua
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Shan-Mei Xu
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA Department of Dermatology, University of California, San Francisco, CA 94143, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
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Das S, Yu S, Sakamori R, Vedula P, Feng Q, Flores J, Hoffman A, Fu J, Stypulkowski E, Rodriguez A, Dobrowolski R, Harada A, Hsu W, Bonder EM, Verzi MP, Gao N. Rab8a vesicles regulate Wnt ligand delivery and Paneth cell maturation at the intestinal stem cell niche. J Cell Sci 2015. [DOI: 10.1242/jcs.175828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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48
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Das S, Yu S, Sakamori R, Vedula P, Feng Q, Flores J, Hoffman A, Fu J, Stypulkowski E, Rodriguez A, Dobrowolski R, Harada A, Hsu W, Bonder EM, Verzi MP, Gao N. Rab8a vesicles regulate Wnt ligand delivery and Paneth cell maturation at the intestinal stem cell niche. Development 2015; 142:2147-62. [PMID: 26015543 PMCID: PMC4483769 DOI: 10.1242/dev.121046] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/16/2015] [Indexed: 12/11/2022]
Abstract
Communication between stem and niche supporting cells maintains the homeostasis of adult tissues. Wnt signaling is a crucial regulator of the stem cell niche, but the mechanism that governs Wnt ligand delivery in this compartment has not been fully investigated. We identified that Wnt secretion is partly dependent on Rab8a-mediated anterograde transport of Gpr177 (wntless), a Wnt-specific transmembrane transporter. Gpr177 binds to Rab8a, depletion of which compromises Gpr177 traffic, thereby weakening the secretion of multiple Wnts. Analyses of generic Wnt/β-catenin targets in Rab8a knockout mouse intestinal crypts indicate reduced signaling activities; maturation of Paneth cells – a Wnt-dependent cell type – is severely affected. Rab8a knockout crypts show an expansion of Lgr5+ and Hopx+ cells in vivo. However, in vitro, the knockout enteroids exhibit significantly weakened growth that can be partly restored by exogenous Wnts or Gsk3β inhibitors. Immunogold labeling and surface protein isolation identified decreased plasma membrane localization of Gpr177 in Rab8a knockout Paneth cells and fibroblasts. Upon stimulation by exogenous Wnts, Rab8a-deficient cells show ligand-induced Lrp6 phosphorylation and transcriptional reporter activation. Rab8a thus controls Wnt delivery in producing cells and is crucial for Paneth cell maturation. Our data highlight the profound tissue plasticity that occurs in response to stress induced by depletion of a stem cell niche signal. Summary: In maturing mouse Paneth cells, Wnt secretion is partly dependent on a Rab8a-mediated anterograde transport of Gpr177. Rab8a is required for Paneth cell maturation.
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Affiliation(s)
- Soumyashree Das
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Ryotaro Sakamori
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Pavan Vedula
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Qiang Feng
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Andrew Hoffman
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Jiang Fu
- Department of Biomedical Genetics, Center for Oral Biology, James P. Wilmot Cancer Center, Stem Cell and Regenerative Medicine Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ewa Stypulkowski
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Alexis Rodriguez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Radek Dobrowolski
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Akihiro Harada
- Department of Cell Biology, Graduate School of Medicine, Osaka University 2-2, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wei Hsu
- Department of Biomedical Genetics, Center for Oral Biology, James P. Wilmot Cancer Center, Stem Cell and Regenerative Medicine Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
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49
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San Roman AK, Aronson BE, Krasinski SD, Shivdasani RA, Verzi MP. Transcription factors GATA4 and HNF4A control distinct aspects of intestinal homeostasis in conjunction with transcription factor CDX2. J Biol Chem 2014; 290:1850-60. [PMID: 25488664 DOI: 10.1074/jbc.m114.620211] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [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: 11/06/2022] Open
Abstract
Distinct groups of transcription factors (TFs) assemble at tissue-specific cis-regulatory sites, implying that different TF combinations may control different genes and cellular functions. Within such combinations, TFs that specify or maintain a lineage and are therefore considered master regulators may play a key role. Gene enhancers often attract these tissue-restricted TFs, as well as TFs that are expressed more broadly. However, the contributions of the individual TFs to combinatorial regulatory activity have not been examined critically in many cases in vivo. We address this question using a genetic approach in mice to inactivate the intestine-specifying and intestine-restricted factor CDX2 alone or in combination with its more broadly expressed partner factors, GATA4 and HNF4A. Compared with single mutants, each combination produced significantly greater defects and rapid lethality through distinct anomalies. Intestines lacking Gata4 and Cdx2 were deficient in crypt cell replication, whereas combined loss of Hnf4a and Cdx2 specifically impaired viability and maturation of villus enterocytes. Integrated analysis of TF binding and of transcripts affected in Hnf4a;Cdx2 compound-mutant intestines indicated that this TF pair controls genes required to construct the apical brush border and absorb nutrients, including dietary lipids. This study thus defines combinatorial TF activities, their specific requirements during tissue homeostasis, and modules of transcriptional targets in intestinal epithelial cells in vivo.
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Affiliation(s)
- Adrianna K San Roman
- From the Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, the Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115
| | - Boaz E Aronson
- the Division of Pediatric Gastroenterology and Nutrition, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, Emma Children's Hospital, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Stephen D Krasinski
- the Division of Pediatric Gastroenterology and Nutrition, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Ramesh A Shivdasani
- From the Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, the Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, and
| | - Michael P Verzi
- From the Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, the Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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50
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Sakamori R, Yu S, Zhang X, Hoffman A, Sun J, Das S, Vedula P, Li G, Fu J, Walker F, Yang CS, Yi Z, Hsu W, Yu DH, Shen L, Rodriguez AJ, Taketo MM, Bonder EM, Verzi MP, Gao N. CDC42 inhibition suppresses progression of incipient intestinal tumors. Cancer Res 2014; 74:5480-92. [PMID: 25113996 DOI: 10.1158/0008-5472.can-14-0267] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mutations in the APC or β-catenin genes are well-established initiators of colorectal cancer, yet modifiers that facilitate the survival and progression of nascent tumor cells are not well defined. Using genetic and pharmacologic approaches in mouse colorectal cancer and human colorectal cancer xenograft models, we show that incipient intestinal tumor cells activate CDC42, an APC-interacting small GTPase, as a crucial step in malignant progression. In the mouse, Cdc42 ablation attenuated the tumorigenicity of mutant intestinal cells carrying single APC or β-catenin mutations. Similarly, human colorectal cancer with relatively higher levels of CDC42 activity was particularly sensitive to CDC42 blockade. Mechanistic studies suggested that Cdc42 may be activated at different levels, including at the level of transcriptional activation of the stem cell-enriched Rho family exchange factor Arhgef4. Our results indicate that early-stage mutant intestinal epithelial cells must recruit the pleiotropic functions of Cdc42 for malignant progression, suggesting its relevance as a biomarker and therapeutic target for selective colorectal cancer intervention.
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Affiliation(s)
- Ryotaro Sakamori
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Xiao Zhang
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Andrew Hoffman
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey
| | - Jiaxin Sun
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Soumyashree Das
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Pavan Vedula
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Guangxun Li
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey
| | - Jiang Fu
- Department of Biomedical Genetics, Center for Oral Biology, James P. Wilmot Cancer Center, University of Rochester Medical Center, Rochester, New York
| | | | - Chung S Yang
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey. Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Zheng Yi
- Division of Experimental Hematology and Cancer Biology, Children's Hospital Research Foundation, Cincinnati, Ohio
| | - Wei Hsu
- Department of Biomedical Genetics, Center for Oral Biology, James P. Wilmot Cancer Center, University of Rochester Medical Center, Rochester, New York
| | - Da-Hai Yu
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Lanlan Shen
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alexis J Rodriguez
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Makoto M Taketo
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey. Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, New Jersey. Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.
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