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Ramal M, Corral S, Kalisz M, Lapi E, Real FX. The urothelial gene regulatory network: understanding biology to improve bladder cancer management. Oncogene 2024; 43:1-21. [PMID: 37996699 DOI: 10.1038/s41388-023-02876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
The urothelium is a stratified epithelium composed of basal cells, one or more layers of intermediate cells, and an upper layer of differentiated umbrella cells. Most bladder cancers (BLCA) are urothelial carcinomas. Loss of urothelial lineage fidelity results in altered differentiation, highlighted by the taxonomic classification into basal and luminal tumors. There is a need to better understand the urothelial transcriptional networks. To systematically identify transcription factors (TFs) relevant for urothelial identity, we defined highly expressed TFs in normal human bladder using RNA-Seq data and inferred their genomic binding using ATAC-Seq data. To focus on epithelial TFs, we analyzed RNA-Seq data from patient-derived organoids recapitulating features of basal/luminal tumors. We classified TFs as "luminal-enriched", "basal-enriched" or "common" according to expression in organoids. We validated our classification by differential gene expression analysis in Luminal Papillary vs. Basal/Squamous tumors. Genomic analyses revealed well-known TFs associated with luminal (e.g., PPARG, GATA3, FOXA1) and basal (e.g., TP63, TFAP2) phenotypes and novel candidates to play a role in urothelial differentiation or BLCA (e.g., MECOM, TBX3). We also identified TF families (e.g., KLFs, AP1, circadian clock, sex hormone receptors) for which there is suggestive evidence of their involvement in urothelial differentiation and/or BLCA. Genomic alterations in these TFs are associated with BLCA. We uncover a TF network involved in urothelial cell identity and BLCA. We identify novel candidate TFs involved in differentiation and cancer that provide opportunities for a better understanding of the underlying biology and therapeutic intervention.
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Affiliation(s)
- Maria Ramal
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Corral
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- CIBERONC, Madrid, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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2
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Kanaya T, Williams IR, Ohno H. Intestinal M cells: Tireless samplers of enteric microbiota. Traffic 2019; 21:34-44. [DOI: 10.1111/tra.12707] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Takashi Kanaya
- Department of PathologyEmory University School of Medicine Atlanta Georgia
| | - Ifor R. Williams
- Laboratory for Intestinal EcosystemRIKEN Center for Integrative Medical Sciences Yokohama Japan
| | - Hiroshi Ohno
- Department of PathologyEmory University School of Medicine Atlanta Georgia
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3
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Yoshida H, Lareau CA, Ramirez RN, Rose SA, Maier B, Wroblewska A, Desland F, Chudnovskiy A, Mortha A, Dominguez C, Tellier J, Kim E, Dwyer D, Shinton S, Nabekura T, Qi Y, Yu B, Robinette M, Kim KW, Wagers A, Rhoads A, Nutt SL, Brown BD, Mostafavi S, Buenrostro JD, Benoist C. The cis-Regulatory Atlas of the Mouse Immune System. Cell 2019; 176:897-912.e20. [PMID: 30686579 PMCID: PMC6785993 DOI: 10.1016/j.cell.2018.12.036] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/26/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023]
Abstract
A complete chart of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of differentiation and function of an organ system. We generated matched epigenome and transcriptome measurements in 86 primary cell types that span the mouse immune system and its differentiation cascades. This breadth of data enable variance components analysis that suggests that genes fall into two distinct classes, controlled by either enhancer- or promoter-driven logic, and multiple regression that connects genes to the enhancers that regulate them. Relating transcription factor (TF) expression to the genome-wide accessibility of their binding motifs classifies them as predominantly openers or closers of local chromatin accessibility, pinpointing specific cis-regulatory elements where binding of given TFs is likely functionally relevant, validated by chromatin immunoprecipitation sequencing (ChIP-seq). Overall, this cis-regulatory atlas provides a trove of information on transcriptional regulation through immune differentiation and a foundational scaffold to define key regulatory events throughout the immunological genome.
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Affiliation(s)
- Hideyuki Yoshida
- Department of Immunology, Harvard Medical School, Boston, MA, USA; YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | | | - Samuel A Rose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara Maier
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksandra Wroblewska
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Desland
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksey Chudnovskiy
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Mortha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Julie Tellier
- The Walter and Eliza Hall Institute and Department of Medical Biology, Melbourne University, Parkville, VIC, Australia
| | - Edy Kim
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
| | - Dan Dwyer
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Tsukasa Nabekura
- Department of Microbiology and Immunology, UCSF, San Francisco, CA, USA
| | - YiLin Qi
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bingfei Yu
- Department of Biological Sciences, UCSD, La Jolla, CA, USA
| | - Michelle Robinette
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ki-Wook Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy Wagers
- Joslin Diabetes Center, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA
| | - Andrew Rhoads
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute and Department of Medical Biology, Melbourne University, Parkville, VIC, Australia
| | - Brian D Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Mostafavi
- Department of Statistics and Department Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA.
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Bykov AS, Karaulov AV, Tsomartova DA, Kartashkina NL, Goriachkina VL, Kuznetsov SL, Stonogina DA, Chereshneva YV. M CELLS ARE THE IMPORTANT POST IN THE INITIATION OF IMMUNE RESPONSE IN INTESTINE. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2018. [DOI: 10.15789/2220-7619-2018-3-263-272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Microfold cells (M cells) are specialized intestinal epithelial cells that initiate mucosal immune responses. These unique phagocytic epithelial cells are specialized for the transfer of a broad range of particulate antigens and microorganisms across the follicle-associated epithelium (FAE) into the gut-associated lymphoid tissue (GALT) by a process termed transcytosis. The molecular basis of antigen uptake by M cells has been gradually identified in the last decade. Active sampling of intestinal antigen initiates regulated immune responses that ensure intestinal homeostasis. The delivery of luminal substances across the intestinal epithelium to the immune system is a critical event in immune surveillance resulting in tolerance to dietary antigens and immunity to pathogens (e.g., bacteria, viruses, and parasites) and their toxins. Several specialized mechanisms transport luminal antigen across the gut epithelium. Discovery of M cell-specific receptors are of great interest, which could act as molecular tags for targeted delivery oral vaccine to M cells. Recent studies demonstrated that M cells utilize several receptors to recognize and transport specific luminal antigens. Vaccination through the mucosal immune system can induce effective systemic immune responses simultaneously with mucosal immunity. How this process is regulated is largely unknown. This review aims to show a new understanding of the factors that influence the development and function of M cells; to show the molecules expressed on M cells which appear to be used as immunosurveillance receptors to sample pathogenic microorganisms in the gut; to note how certain pathogens appear to exploit M cells to inject the host; and, finally, how this knowledge is used to specifically "target" antigens to M cells to attempt to improve the efficacy of mucosal vaccines. Recently, substantial progress has been made in our understanding of the factors that influence the development and function of M cells.
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Luk IY, Reehorst CM, Mariadason JM. ELF3, ELF5, EHF and SPDEF Transcription Factors in Tissue Homeostasis and Cancer. Molecules 2018; 23:molecules23092191. [PMID: 30200227 PMCID: PMC6225137 DOI: 10.3390/molecules23092191] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
The epithelium-specific ETS (ESE) transcription factors (ELF3, ELF5, EHF and SPDEF) are defined by their highly conserved ETS DNA binding domain and predominant epithelial-specific expression profile. ESE transcription factors maintain normal cell homeostasis and differentiation of a number of epithelial tissues, and their genetic alteration and deregulated expression has been linked to the progression of several epithelial cancers. Herein we review the normal function of the ESE transcription factors, the mechanisms by which they are dysregulated in cancers, and the current evidence for their role in cancer progression. Finally, we discuss potential therapeutic strategies for targeting or reactivating these factors as a novel means of cancer treatment.
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Affiliation(s)
- Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia.
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Abstract
Noroviruses are the leading cause of acute gastroenteritis around the world. An individual living in the United States is estimated to develop norovirus infection five times in his or her lifetime. Despite this, there is currently no antiviral or vaccine to combat the infection, in large part because of the historical lack of cell culture and small animal models. However, the last few years of norovirus research were marked by a number of ground-breaking advances that have overcome technical barriers and uncovered novel aspects of norovirus biology. Foremost among them was the development of two different
in vitro culture systems for human noroviruses. Underappreciated was the notion that noroviruses infect cells of the immune system as well as epithelial cells within the gastrointestinal tract and that human norovirus infection of enterocytes requires or is promoted by the presence of bile acids. Furthermore, two proteinaceous receptors are now recognized for murine norovirus, marking the first discovery of a functional receptor for any norovirus. Recent work further points to a role for certain bacteria, including those found in the gut microbiome, as potential modulators of norovirus infection in the host, emphasizing the importance of interactions with organisms from other kingdoms of life for viral pathogenesis. Lastly, we will highlight the adaptation of drop-based microfluidics to norovirus research, as this technology has the potential to reveal novel insights into virus evolution. This review aims to summarize these new findings while also including possible future directions.
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Affiliation(s)
- Eric Bartnicki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Juliana Bragazzi Cunha
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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Ohno H. Intestinal M cells. J Biochem 2015; 159:151-60. [PMID: 26634447 DOI: 10.1093/jb/mvv121] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 11/27/2015] [Indexed: 11/13/2022] Open
Abstract
We have an enormous number of commensal bacteria in our intestine, moreover, the foods that we ingest and the water we drink is sometimes contaminated with pathogenic microorganisms. The intestinal epithelium is always exposed to such microbes, friend or foe, so to contain them our gut is equipped with specialized gut-associated lymphoid tissue (GALT), literally the largest peripheral lymphoid tissue in the body. GALT is the intestinal immune inductive site composed of lymphoid follicles such as Peyer's patches. M cells are a subset of intestinal epithelial cells (IECs) residing in the region of the epithelium covering GALT lymphoid follicles. Although the vast majority of IEC function to absorb nutrients from the intestine, M cells are highly specialized to take up intestinal microbial antigens and deliver them to GALT for efficient mucosal as well as systemic immune responses. I will discuss recent advances in our understanding of the molecular mechanisms of M-cell differentiation and functions.
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Affiliation(s)
- Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Sakhon OS, Ross B, Gusti V, Pham AJ, Vu K, Lo DD. M cell-derived vesicles suggest a unique pathway for trans-epithelial antigen delivery. Tissue Barriers 2015; 3:e1004975. [PMID: 25838974 DOI: 10.1080/21688370.2015.1004975] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/26/2014] [Indexed: 12/30/2022] Open
Abstract
M cells are a subset of mucosal epithelial cells with specialized capability to transport antigens across the mucosal barrier, but there is limited information on antigen transfer in the subepithelial zone due to the challenges in tracking microparticles and antigens that are transcytosed by this unique cell. Using transgenic reporter mice expressing dsRed in the cytoplasm of M cells and EGFP in myeloid cells, we observed that the M cell basolateral pocket hosts a close interaction between B lymphocytes and dendritic cells. Interestingly, we identified a population of previously undescribed M cell-derived vesicles (MCM) that are constitutively shed into the subepithelial space and readily taken up by CX3CR1(+)CD11b(+) CD11c(+) dendritic cells. These MCM are characterized by their cytoplasmic dsRed confirming their origin from the M cell cytoplasm. MCM showed preferential colocalization in dendritic cells with transcytosed bacteria but not transcytosed polystyrene beads, indicating a selective sorting of cargo fate in the subepithelial zone. The size and number of MCM were found to be upregulated by bacterial transcytosis and soluble toll-like receptor 2 (TLR2) agonist, further pointing to dynamic regulation of this mechanism. These results suggest that MCM provide a unique function by delivering to dendritic cells, various materials such as M cell-derived proteins, effector proteins, toxins, and particles found in the M cell cytoplasm during infection or surveillance.
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Affiliation(s)
- Olivia S Sakhon
- Division of Biomedical Sciences; School of Medicine ; University of California , Riverside; Riverside, CA USA
| | - Brittany Ross
- Division of Biomedical Sciences; School of Medicine ; University of California , Riverside; Riverside, CA USA
| | - Veronica Gusti
- Division of Biomedical Sciences; School of Medicine ; University of California , Riverside; Riverside, CA USA
| | - An Joseph Pham
- Division of Biomedical Sciences; School of Medicine ; University of California , Riverside; Riverside, CA USA
| | - Kathy Vu
- Division of Biomedical Sciences; School of Medicine ; University of California , Riverside; Riverside, CA USA
| | - David D Lo
- Division of Biomedical Sciences; School of Medicine ; University of California , Riverside; Riverside, CA USA
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Kanaya T, Ohno H. The Mechanisms of M-cell Differentiation. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2014; 33:91-7. [PMID: 25032083 PMCID: PMC4098651 DOI: 10.12938/bmfh.33.91] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/28/2014] [Indexed: 11/05/2022]
Abstract
Intestinal M (microfold or membranous) cells are an enigmatic lineage of intestinal epithelial cells that initiate mucosal immune responses through the uptake and transcytosis of luminal antigens. Due to their rarity, the mechanisms of M-cell function and differentiation are poorly understood. To overcome this problem, experimental strategies to enrich for M-cells have been established. Transcriptome analyses have provided valuable insight, especially on the receptors for antigen uptake, and such studies have broadened our knowledge of M-cell function. In another line of investigation, we and others have begun to dissect the molecular pathways of M-cell differentiation. Among them, receptor activator of NF-κB ligand (RANKL) has been identified as an essential factor for M-cell differentiation. We have focused on the M-cell inducible activity of RANKL and have been able to observe temporal transitions during M-cell differentiation by using in vivo ectopic M-cell differentiation induced by exogenous RANKL treatment. We have found that the ets-family transcription factor Spi-B is essential for functional maturation of M cells. In the absence of Spi-B, the immune response to Salmonella Typhimurium is severely impaired, suggesting that M cells are important for maintaining intestinal homeostasis.
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Affiliation(s)
- Takashi Kanaya
- Laboratory for Intestinal Ecosystem, RCAI, Riken Center for Integrative Medical Sciences (IMS-RCAI), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RCAI, Riken Center for Integrative Medical Sciences (IMS-RCAI), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Murine norovirus transcytosis across an in vitro polarized murine intestinal epithelial monolayer is mediated by M-like cells. J Virol 2013; 87:12685-93. [PMID: 24049163 DOI: 10.1128/jvi.02378-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noroviruses (NoVs) are the causative agent of the vast majority of nonbacterial gastroenteritis worldwide. Due to the inability to culture human NoVs and the inability to orally infect a small animal model, little is known about the initial steps of viral entry. One particular step that is not understood is how NoVs breach the intestinal epithelial barrier. Murine NoV (MNV) is the only NoV that can be propagated in vitro by infecting murine macrophages and dendritic cells, making this virus an attractive model for studies of different aspects of NoV biology. Polarized murine intestinal epithelial mICcl2 cells were used to investigate how MNV interacts with and crosses the intestinal epithelium. In this in vitro model of the follicle-associated epithelium (FAE), MNV is transported across the polarized cell monolayer in the absence of viral replication or disruption of tight junctions by a distinct epithelial cell with microfold (M) cell properties. In addition to transporting MNV, these M-like cells also transcytose microbeads and express an IgA receptor. Interestingly, B myeloma cells cultured in the basolateral compartment underlying the epithelial monolayer did not alter the number of M-like cells but increased their transcytotic activity. Our data demonstrate that MNV can cross an intact intestinal epithelial monolayer in vitro by hijacking the M-like cells' intrinsic transcytotic pathway and suggest a potential mechanism for MNV entry into the host.
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