1
|
Yu X, Wang S, Ji Z, Meng J, Mou Y, Wu X, Yang X, Xiong P, Li M, Guo Y. Ferroptosis: An important mechanism of disease mediated by the gut-liver-brain axis. Life Sci 2024; 347:122650. [PMID: 38631669 DOI: 10.1016/j.lfs.2024.122650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/27/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
AIMS As a unique iron-dependent non-apoptotic cell death, Ferroptosis is involved in the pathogenesis and development of many human diseases and has become a research hotspot in recent years. However, the regulatory role of ferroptosis in the gut-liver-brain axis has not been elucidated. This paper summarizes the regulatory role of ferroptosis and provides theoretical basis for related research. MATERIALS AND METHODS We searched PubMed, CNKI and Wed of Science databases on ferroptosis mediated gut-liver-brain axis diseases, summarized the regulatory role of ferroptosis on organ axis, and explained the adverse effects of related regulatory effects on various diseases. KEY FINDINGS According to our summary, the main way in which ferroptosis mediates the gut-liver-brain axis is oxidative stress, and the key cross-talk of ferroptosis affecting signaling pathway network is Nrf2/HO-1. However, there were no specific marker between different organ axes mediate by ferroptosis. SIGNIFICANCE Our study illustrates the main ways and key cross-talk of ferroptosis mediating the gut-liver-brain axis, providing a basis for future research.
Collapse
Affiliation(s)
- Xinxin Yu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Shihao Wang
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Zhongjie Ji
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Jiaqi Meng
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Yunying Mou
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Xinyi Wu
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Xu Yang
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Panyang Xiong
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China
| | - Mingxia Li
- Nursing School, Shandong University of Traditional Chinese Medicine, Jinan, 250355, Shandong, China
| | - Yinghui Guo
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China.
| |
Collapse
|
2
|
McConnell BB, Liang Z, Xu C, Han Y, Yun CC. LPA 5-Dependent signaling regulates regeneration of the intestinal epithelium following irradiation. Am J Physiol Gastrointest Liver Physiol 2024; 326:G631-G642. [PMID: 38593468 DOI: 10.1152/ajpgi.00269.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/20/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
Lysophosphatidic acid (LPA) is a bioactive lipid molecule that regulates a wide array of cellular functions, including proliferation, differentiation, and survival, via activation of cognate receptors. The LPA5 receptor is highly expressed in the intestinal epithelium, but its function in restoring intestinal epithelial integrity following injury has not been examined. Here, we use a radiation-induced injury model to study the role of LPA5 in regulating intestinal epithelial regeneration. Control mice (Lpar5f/f) and mice with an inducible, epithelial cell-specific deletion of Lpar5 in the small intestine (Lpar5IECKO) were subjected to 10 Gy total body X-ray irradiation and analyzed during recovery. Repair of the intestinal mucosa was delayed in Lpar5IECKO mice with reduced epithelial proliferation and increased crypt cell apoptosis. These effects were accompanied by reduced numbers of OLFM4+ intestinal stem cells (ISCs). The effects of LPA5 on ISCs were corroborated by studies using organoids derived from Lgr5-lineage tracking reporter mice with deletion of Lpar5 in Lgr5+-stem cells (Lgr5Cont or Lgr5ΔLpar5). Irradiation of organoids resulted in fewer numbers of Lgr5ΔLpar5 organoids retaining Lgr5+-derived progenitor cells compared with Lgr5Cont organoids. Finally, we observed that impaired regeneration in Lpar5IECKO mice was associated with reduced numbers of Paneth cells and decreased expression of Yes-associated protein (YAP), a critical factor for intestinal epithelial repair. Our study highlights a novel role for LPA5 in regeneration of the intestinal epithelium following irradiation and its effect on the maintenance of Paneth cells that support the stem cell niche.NEW & NOTEWORTHY We used mice lacking expression of the lysophosphatidic acid receptor 5 (LPA5) in intestinal epithelial cells and intestinal organoids to show that the LPA5 receptor protects intestinal stem cells and progenitors from radiation-induced injury. We show that LPA5 induces YAP signaling and regulates Paneth cells.
Collapse
Affiliation(s)
- Beth B McConnell
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Zhongxing Liang
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Chad Xu
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Yiran Han
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
| | - C Chris Yun
- Division of Digestive Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States
- Gastroenterology Research, Atlanta Veterans Administration Medical Center, Decatur, Georgia, United States
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States
| |
Collapse
|
3
|
Kessler S, Burke B, Andrieux G, Schinköthe J, Hamberger L, Kacza J, Zhan S, Reasoner C, Dutt TS, Kaukab Osman M, Henao-Tamayo M, Staniek J, Villena Ossa JF, Frank DT, Ma W, Ulrich R, Cathomen T, Boerries M, Rizzi M, Beer M, Schwemmle M, Reuther P, Schountz T, Ciminski K. Deciphering bat influenza H18N11 infection dynamics in male Jamaican fruit bats on a single-cell level. Nat Commun 2024; 15:4500. [PMID: 38802391 PMCID: PMC11130286 DOI: 10.1038/s41467-024-48934-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Jamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected male Jamaican fruit bats with the bat-derived influenza A virus (IAV) H18N11. Using comparative single-cell RNA sequencing, we generated single-cell atlases of the Jamaican fruit bat intestine and mesentery. Gene expression profiling showed that H18N11 infection resulted in a moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. H18N11 infection was predominant in various leukocytes, including macrophages, B cells, and NK/T cells. Confirming these findings, human leukocytes, particularly macrophages, were also susceptible to H18N11, highlighting the zoonotic potential of this bat-derived IAV. Our study provides insight into a natural virus-host relationship and thus serves as a fundamental resource for future in-depth characterization of bat immunology.
Collapse
Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bradly Burke
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jan Schinköthe
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Lea Hamberger
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Kacza
- BioImaging Core Facility, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Shijun Zhan
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Clara Reasoner
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Taru S Dutt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marcela Henao-Tamayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Julian Staniek
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Jose Francisco Villena Ossa
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Dalit T Frank
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Toni Cathomen
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tony Schountz
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Kevin Ciminski
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
4
|
Liang Y, Luo C, Sun L, Feng T, Yin W, Zhang Y, Mulholland MW, Zhang W, Yin Y. Reduction of specific enterocytes from loss of intestinal LGR4 improves lipid metabolism in mice. Nat Commun 2024; 15:4393. [PMID: 38782937 PMCID: PMC11116434 DOI: 10.1038/s41467-024-48622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Whether intestinal Leucine-rich repeat containing G-protein-coupled receptor 4 (LGR4) impacts nutrition absorption and energy homeostasis remains unknown. Here, we report that deficiency of Lgr4 (Lgr4iKO) in intestinal epithelium decreased the proportion of enterocytes selective for long-chain fatty acid absorption, leading to reduction in lipid absorption and subsequent improvement in lipid and glucose metabolism. Single-cell RNA sequencing demonstrates the heterogeneity of absorptive enterocytes, with a decrease in enterocytes selective for long-chain fatty acid-absorption and an increase in enterocytes selective for carbohydrate absorption in Lgr4iKO mice. Activation of Notch signaling and concurrent inhibition of Wnt signaling are observed in the transgenes. Associated with these alterations is the substantial reduction in lipid absorption. Decrement in lipid absorption renders Lgr4iKO mice resistant to high fat diet-induced obesity relevant to wild type littermates. Our study thus suggests that targeting intestinal LGR4 is a potential strategy for the intervention of obesity and liver steatosis.
Collapse
Affiliation(s)
- Yuan Liang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China
| | - Chao Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China
| | - Lijun Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China
| | - Tiange Feng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China
| | - Wenzhen Yin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China
| | - Yunhua Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China
| | - Michael W Mulholland
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, 48109-0346, USA
| | - Weizhen Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China.
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, 48109-0346, USA.
| | - Yue Yin
- Department of Pharmacology, School of Basic Medical Sciences, and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 100191, Beijing, China.
| |
Collapse
|
5
|
Tan S, Santolaya JL, Wright TF, Liu Q, Fujikawa T, Chi S, Bergstrom CP, Lopez A, Chen Q, Vale G, McDonald JG, Schmidt A, Vo N, Kim J, Baniasadi H, Li L, Zhu G, He TC, Zhan X, Obata Y, Jin A, Jia D, Elmquist JK, Sifuentes-Dominguez L, Burstein E. Interaction between the gut microbiota and colonic enteroendocrine cells regulates host metabolism. Nat Metab 2024:10.1038/s42255-024-01044-5. [PMID: 38777856 DOI: 10.1038/s42255-024-01044-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/09/2024] [Indexed: 05/25/2024]
Abstract
Nutrient handling is an essential function of the gastrointestinal tract. Hormonal responses of small intestinal enteroendocrine cells (EECs) have been extensively studied but much less is known about the role of colonic EECs in metabolic regulation. To address this core question, we investigated a mouse model deficient in colonic EECs. Here we show that colonic EEC deficiency leads to hyperphagia and obesity. Furthermore, colonic EEC deficiency results in altered microbiota composition and metabolism, which we found through antibiotic treatment, germ-free rederivation and transfer to germ-free recipients, to be both necessary and sufficient for the development of obesity. Moreover, studying stool and blood metabolomes, we show that differential glutamate production by intestinal microbiota corresponds to increased appetite and that colonic glutamate administration can directly increase food intake. These observations shed light on an unanticipated host-microbiota axis in the colon, part of a larger gut-brain axis, that regulates host metabolism and body weight.
Collapse
Affiliation(s)
- Shuai Tan
- Department of Endocrinology Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing, P. R. China.
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Jacobo L Santolaya
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tiffany Freeney Wright
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qi Liu
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Teppei Fujikawa
- Center for Hypothalamic Research, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sensen Chi
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Colin P Bergstrom
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adam Lopez
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qing Chen
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Goncalo Vale
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Schmidt
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nguyen Vo
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hamid Baniasadi
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Li Li
- Department of Endocrinology Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing, P. R. China
| | - Gaohui Zhu
- Department of Endocrinology Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing, P. R. China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuuki Obata
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aishun Jin
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Joel K Elmquist
- Center for Hypothalamic Research, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Ezra Burstein
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
6
|
Tang W, Ni Z, Wei Y, Hou K, Valencak TG, Wang H. Extracellular vesicles of Bacteroides uniformis induce M1 macrophage polarization and aggravate gut inflammation during weaning. Mucosal Immunol 2024:S1933-0219(24)00045-X. [PMID: 38777177 DOI: 10.1016/j.mucimm.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/01/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Weaning process is commonly associated with gastrointestinal inflammation and dysbiosis of the intestinal microbes. In particular, the impact of gut bacteria and of extracellular vesicles (EV) on the etiology of intestinal inflammation during weaning is not well understand. We have uncovered a potential link between gut inflammation and the corresponding variation of macrophage bacterial sensing and pro-inflammatory polarization during the weaning process of piglet through single-cell transcriptomic analyses. We conducted a comprehensive analysis of bacterial distribution across the gastrointestinal tract and pinpointed Bacteroides uniformis (B. uniformis) enriching in piglets undergoing weaning. Next, we found out that exposure to B. uniformis-derived EVs (BEVs) exacerbated gut inflammation in a murine colitis model while recruiting and polarizing intestinal macrophages towards a pro-inflammatory phenotype. BEVs modulated the function of macrophages cultured in vitro by suppressing the GM-CSF/STAT5/ARG1 pathway, thereby affecting polarization towards an M1-like state. The effects of BEVs were verified both in the macrophage-clearance murine model and by using an adoptive transfer assay. Our findings highlight the involvement of BEVs in facilitating the polarization of pro-inflammatory macrophages and promoting gut inflammation during weaning.
Collapse
Affiliation(s)
- Wenjie Tang
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Zhixiang Ni
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Yusen Wei
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Kangwei Hou
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Teresa G Valencak
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Haifeng Wang
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China.
| |
Collapse
|
7
|
Hoo R, Ruiz-Morales ER, Kelava I, Rawat M, Mazzeo CI, Tuck E, Sancho-Serra C, Chelaghma S, Predeus AV, Murray S, Fernandez-Antoran D, Waller RF, Álvarez-Errico D, Lee MCS, Vento-Tormo R. Acute response to pathogens in the early human placenta at single-cell resolution. Cell Syst 2024; 15:425-444.e9. [PMID: 38703772 DOI: 10.1016/j.cels.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
Abstract
The placenta is a selective maternal-fetal barrier that provides nourishment and protection from infections. However, certain pathogens can attach to and even cross the placenta, causing pregnancy complications with potential lifelong impacts on the child's health. Here, we profiled at the single-cell level the placental responses to three pathogens associated with intrauterine complications-Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We found that upon exposure to the pathogens, all placental lineages trigger inflammatory responses that may compromise placental function. Additionally, we characterized the responses of fetal macrophages known as Hofbauer cells (HBCs) to each pathogen and propose that they are the probable niche for T. gondii. Finally, we revealed how P. falciparum adapts to the placental microenvironment by modulating protein export into the host erythrocyte and nutrient uptake pathways. Altogether, we have defined the cellular networks and signaling pathways mediating acute placental inflammatory responses that could contribute to pregnancy complications.
Collapse
Affiliation(s)
- Regina Hoo
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Iva Kelava
- Wellcome Sanger Institute, Cambridge, UK
| | - Mukul Rawat
- Wellcome Sanger Institute, Cambridge, UK; Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | | | | | | | - Sara Chelaghma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - David Fernandez-Antoran
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Marcus C S Lee
- Wellcome Sanger Institute, Cambridge, UK; Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK.
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| |
Collapse
|
8
|
Yang L, He H, Guo XK, Wang J, Wang W, Li D, Liang S, Shao F, Liu W, Hu X. Intraepithelial mast cells drive gasdermin C-mediated type 2 immunity. Immunity 2024; 57:1056-1070.e5. [PMID: 38614091 DOI: 10.1016/j.immuni.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/31/2023] [Accepted: 03/19/2024] [Indexed: 04/15/2024]
Abstract
A specialized population of mast cells residing within epithelial layers, currently known as intraepithelial mast cells (IEMCs), was originally observed over a century ago, yet their physiological functions have remained enigmatic. In this study, we unveil an unexpected and crucial role of IEMCs in driving gasdermin C-mediated type 2 immunity. During helminth infection, αEβ7 integrin-positive IEMCs engaged in extensive intercellular crosstalk with neighboring intestinal epithelial cells (IECs). Through the action of IEMC-derived proteases, gasdermin C proteins intrinsic to the epithelial cells underwent cleavage, leading to the release of a critical type 2 cytokine, interleukin-33 (IL-33). Notably, mast cell deficiency abolished the gasdermin C-mediated immune cascade initiated by epithelium. These findings shed light on the functions of IEMCs, uncover a previously unrecognized phase of type 2 immunity involving mast cell-epithelial cell crosstalk, and advance our understanding of the cellular mechanisms underlying gasdermin C activation.
Collapse
Affiliation(s)
- Liu Yang
- Institute for Immunology, Tsinghua University, Beijing, China; School of Basic Medical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Huabin He
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Kun Guo
- Chinese Institutes for Medical Research, Beijing, China
| | - Jiali Wang
- Institute for Immunology, Tsinghua University, Beijing, China; School of Basic Medical Sciences, Tsinghua University, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Wenwen Wang
- Institute for Immunology, Tsinghua University, Beijing, China; School of Basic Medical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Da Li
- National Institute of Biological Sciences, Beijing, China
| | - Shaonan Liang
- Institute for Immunology, Tsinghua University, Beijing, China; School of Basic Medical Sciences, Tsinghua University, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences, Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Wanli Liu
- Institute for Immunology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China; The State Key Laboratory of Membrane Biology, Beijing, China
| | - Xiaoyu Hu
- Institute for Immunology, Tsinghua University, Beijing, China; School of Basic Medical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China; The State Key Laboratory of Membrane Biology, Beijing, China.
| |
Collapse
|
9
|
Singh A, Khiabanian H. Feature selection followed by a novel residuals-based normalization simplifies and improves single-cell gene expression analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.02.530891. [PMID: 38328133 PMCID: PMC10849523 DOI: 10.1101/2023.03.02.530891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Normalization is a crucial step in the analysis of single-cell RNA-sequencing (scRNA-seq) counts data. Its principal objectives are to reduce the systematic biases primarily introduced through technical sources and to transform the data to make it more amenable for application of established statistical frameworks. In the standard workflows, normalization is followed by feature selection to identify highly variable genes (HVGs) that capture most of the biologically meaningful variation across the cells. Here, we make the case for a revised workflow by proposing a simple feature selection method and showing that we can perform feature selection before normalization by relying on observed counts. We highlight that the feature selection step can be used to not only select HVGs but to also identify stable genes. We further propose a novel variance stabilization transformation inclusive residuals-based normalization method that in fact relies on the stable genes to inform the reduction of systematic biases. We demonstrate significant improvements in downstream clustering analyses through the application of our proposed methods on biological truth-known as well as simulated counts datasets. We have implemented this novel workflow for analyzing high-throughput scRNA-seq data in an R package called Piccolo.
Collapse
Affiliation(s)
- Amartya Singh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| |
Collapse
|
10
|
Ndjim M, Gasmi I, Herbert F, Joséphine C, Bas J, Lamrani A, Coutry N, Henry S, Zimmermann VS, Dardalhon V, Campillo Poveda M, Turtoi E, Thirard S, Forichon L, Giordano A, Ciancia C, Homayed Z, Pannequin J, Britton C, Devaney E, McNeilly TN, Berrard S, Turtoi A, Maizels RM, Gerbe F, Jay P. Tuft cell acetylcholine is released into the gut lumen to promote anti-helminth immunity. Immunity 2024:S1074-7613(24)00223-1. [PMID: 38744292 DOI: 10.1016/j.immuni.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 11/26/2023] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Upon parasitic helminth infection, activated intestinal tuft cells secrete interleukin-25 (IL-25), which initiates a type 2 immune response during which lamina propria type 2 innate lymphoid cells (ILC2s) produce IL-13. This causes epithelial remodeling, including tuft cell hyperplasia, the function of which is unknown. We identified a cholinergic effector function of tuft cells, which are the only epithelial cells that expressed choline acetyltransferase (ChAT). During parasite infection, mice with epithelial-specific deletion of ChAT had increased worm burden, fitness, and fecal egg counts, even though type 2 immune responses were comparable. Mechanistically, IL-13-amplified tuft cells release acetylcholine (ACh) into the gut lumen. Finally, we demonstrated a direct effect of ACh on worms, which reduced their fecundity via helminth-expressed muscarinic ACh receptors. Thus, tuft cells are sentinels in naive mice, and their amplification upon helminth infection provides an additional type 2 immune response effector function.
Collapse
Affiliation(s)
- Marième Ndjim
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Imène Gasmi
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Fabien Herbert
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Charlène Joséphine
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Julie Bas
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Ali Lamrani
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Nathalie Coutry
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Sylvain Henry
- Montpellier Alliance for Metabolomics and Metabolism Analysis, Platform for Translational Oncometabolomics (PLATON), Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Valérie S Zimmermann
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Valérie Dardalhon
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marta Campillo Poveda
- Centre for Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK
| | - Evgenia Turtoi
- Montpellier Alliance for Metabolomics and Metabolism Analysis, Platform for Translational Oncometabolomics (PLATON), Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Steeve Thirard
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Luc Forichon
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Alicia Giordano
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Claire Ciancia
- Centre for Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK
| | - Zeinab Homayed
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Julie Pannequin
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Collette Britton
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Eileen Devaney
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Tom N McNeilly
- Disease Control Department, Moredun Research Institute, Penicuik, UK
| | - Sylvie Berrard
- University Paris Cité, Inserm, NeuroDiderot, Paris, France
| | - Andrei Turtoi
- Montpellier Alliance for Metabolomics and Metabolism Analysis, Platform for Translational Oncometabolomics (PLATON), Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France; Cancer Research Institute of Montpellier (IRCM), University of Montpellier, Inserm, Montpellier, France
| | - Rick M Maizels
- Centre for Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK
| | - François Gerbe
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France.
| | - Philippe Jay
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, Inserm, Montpellier, France.
| |
Collapse
|
11
|
Engevik KA, Scribano FJ, Gebert JT, Hyser JM. Purinergic Signaling Drives Multiple Aspects of Rotavirus Pathophysiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592953. [PMID: 38765995 PMCID: PMC11100750 DOI: 10.1101/2024.05.07.592953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rotavirus causes life-threatening diarrhea in children, resulting in ∼200,000 deaths/year. The current treatment during infection is Oral Rehydration Solution which successfully replenishes fluids but does not alleviate diarrhea volume or severity. As a result, there is an urgent need to better understand rotavirus pathophysiology and develop more effective pediatric therapeutics. Rotavirus primarily infects the tips of small intestinal villi, yet has far-reaching effects on cell types distant from infected cells. We recently identified that rotavirus infected cells release the purinergic signaling molecule ADP, which activates P2Y1 receptors on nearby uninfected cells in vitro . To elucidate the role of purinergic signaling via P2Y1 receptors during rotavirus infection in vivo , we used the mouse-like rotavirus strain D6/2 which generates a severe infection in mice. C57BL/6J mouse pups were given an oral gavage of D6/2 rotavirus and assessed over the course of 5-7 days. Beginning at day 1 post infection, infected pups were treated daily by oral gavage with saline or 4 mg/kg MRS2500, a selective P2Y1 antagonist. Mice were monitored for diarrhea severity, diarrhea incidence, and viral shedding. Neonatal mice were euthanized at days 3 and 5 post-infection and small intestine was collected to observe infection. MRS2500 treatment decreased the severity, prevalence, and incidence of rotavirus diarrhea. Viral stool shedding, assessed by qPCR for rotavirus gene levels, revealed that MRS2500 treated pups had significantly lower viral shedding starting at day 4 post infection compared to saline treated pups, which suggests P2Y1 signaling may enhance rotavirus replication. Finally, we found that inhibition of P2Y1 with MRS2500 limited transmitted rotavirus diarrhea to uninfected pups within a litter. Together, these results suggest that P2Y1 signaling is involved in the pathogenesis of a homologous murine rotavirus strain, making P2Y1 receptors a promising anti-diarrheal, anti-viral therapeutic target to reduce rotavirus disease burden.
Collapse
|
12
|
Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024:S1934-5909(24)00142-5. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
Collapse
Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| |
Collapse
|
13
|
Billipp TE, Fung C, Webeck LM, Sargent DB, Gologorsky MB, Chen Z, McDaniel MM, Kasal DN, McGinty JW, Barrow KA, Rich LM, Barilli A, Sabat M, Debley JS, Wu C, Myers R, Howitt MR, von Moltke J. Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance. Immunity 2024:S1074-7613(24)00144-4. [PMID: 38744291 DOI: 10.1016/j.immuni.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 02/05/2024] [Accepted: 03/29/2024] [Indexed: 05/16/2024]
Abstract
Epithelial cells secrete chloride to regulate water release at mucosal barriers, supporting both homeostatic hydration and the "weep" response that is critical for type 2 immune defense against parasitic worms (helminths). Epithelial tuft cells in the small intestine sense helminths and release cytokines and lipids to activate type 2 immune cells, but whether they regulate epithelial secretion is unknown. Here, we found that tuft cell activation rapidly induced epithelial chloride secretion in the small intestine. This response required tuft cell sensory functions and tuft cell-derived acetylcholine (ACh), which acted directly on neighboring epithelial cells to stimulate chloride secretion, independent of neurons. Maximal tuft cell-induced chloride secretion coincided with immune restriction of helminths, and clearance was delayed in mice lacking tuft cell-derived ACh, despite normal type 2 inflammation. Thus, we have uncovered an epithelium-intrinsic response unit that uses ACh to couple tuft cell sensing to the secretory defenses of neighboring epithelial cells.
Collapse
Affiliation(s)
- Tyler E Billipp
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Connie Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lily M Webeck
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Derek B Sargent
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Matthew B Gologorsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Margaret M McDaniel
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Darshan N Kasal
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - John W McGinty
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Kaitlyn A Barrow
- Center for Respiratory Biology and Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA
| | - Lucille M Rich
- Center for Respiratory Biology and Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Mark Sabat
- Takeda Pharmaceuticals, San Diego, CA, USA
| | - Jason S Debley
- Center for Respiratory Biology and Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Michael R Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jakob von Moltke
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
| |
Collapse
|
14
|
Jiang Q, Chen S, Chen X, Jiang R. scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism. Bioinformatics 2024; 40:btae265. [PMID: 38625746 PMCID: PMC11076148 DOI: 10.1093/bioinformatics/btae265] [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: 12/07/2023] [Revised: 04/06/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024] Open
Abstract
MOTIVATION With the rapid advancement of single-cell sequencing technology, it becomes gradually possible to delve into the cellular responses to various external perturbations at the gene expression level. However, obtaining perturbed samples in certain scenarios may be considerably challenging, and the substantial costs associated with sequencing also curtail the feasibility of large-scale experimentation. A repertoire of methodologies has been employed for forecasting perturbative responses in single-cell gene expression. However, existing methods primarily focus on the average response of a specific cell type to perturbation, overlooking the single-cell specificity of perturbation responses and a more comprehensive prediction of the entire perturbation response distribution. RESULTS Here, we present scPRAM, a method for predicting perturbation responses in single-cell gene expression based on attention mechanisms. Leveraging variational autoencoders and optimal transport, scPRAM aligns cell states before and after perturbation, followed by accurate prediction of gene expression responses to perturbations for unseen cell types through attention mechanisms. Experiments on multiple real perturbation datasets involving drug treatments and bacterial infections demonstrate that scPRAM attains heightened accuracy in perturbation prediction across cell types, species, and individuals, surpassing existing methodologies. Furthermore, scPRAM demonstrates outstanding capability in identifying differentially expressed genes under perturbation, capturing heterogeneity in perturbation responses across species, and maintaining stability in the presence of data noise and sample size variations. AVAILABILITY AND IMPLEMENTATION https://github.com/jiang-q19/scPRAM and https://doi.org/10.5281/zenodo.10935038.
Collapse
Affiliation(s)
- Qun Jiang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shengquan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China
| | - Xiaoyang Chen
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| |
Collapse
|
15
|
Emanuel E, Arifuzzaman M, Artis D. Epithelial-neuronal-immune cell interactions: Implications for immunity, inflammation, and tissue homeostasis at mucosal sites. J Allergy Clin Immunol 2024; 153:1169-1180. [PMID: 38369030 PMCID: PMC11070312 DOI: 10.1016/j.jaci.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
The epithelial lining of the respiratory tract and intestine provides a critical physical barrier to protect host tissues against environmental insults, including dietary antigens, allergens, chemicals, and microorganisms. In addition, specialized epithelial cells communicate directly with hematopoietic and neuronal cells. These epithelial-immune and epithelial-neuronal interactions control host immune responses and have important implications for inflammatory conditions associated with defects in the epithelial barrier, including asthma, allergy, and inflammatory bowel diseases. In this review, we discuss emerging research that identifies the mechanisms and impact of epithelial-immune and epithelial-neuronal cross talk in regulating immunity, inflammation, and tissue homeostasis at mucosal barrier surfaces. Understanding the regulation and impact of these pathways could provide new therapeutic targets for inflammatory diseases at mucosal sites.
Collapse
Affiliation(s)
- Elizabeth Emanuel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY; Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY; Allen Discovery Center for Neuroimmune Interactions, New York, NY; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY.
| |
Collapse
|
16
|
Zhou HY, Wang YC, Wang T, Wu W, Cao YY, Zhang BC, Wang MD, Mao P. CCNA2 and NEK2 regulate glioblastoma progression by targeting the cell cycle. Oncol Lett 2024; 27:206. [PMID: 38516683 PMCID: PMC10956385 DOI: 10.3892/ol.2024.14339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/05/2024] [Indexed: 03/23/2024] Open
Abstract
Glioblastoma (GBM) is characterized by significant heterogeneity, leading to poor survival outcomes for patients, despite the implementation of comprehensive treatment strategies. The roles of cyclin A2 (CCNA2) and NIMA related kinase 2 (NEK2) have been extensively studied in numerous cancers, but their specific functions in GBM remain to be elucidated. The present study aimed to investigate the potential molecular mechanisms of CCNA2 and NEK2 in GBM. CCNA2 and NEK2 expression and prognosis in glioma were evaluated by bioinformatics methods. In addition, the distribution of CCNA2 and NEK2 expression in GBM subsets was determined using pseudo-time analysis and tricycle position of single-cell sequencing. Gene Expression Omnibus and Kyoto Encyclopedia of Genes and Genome databases were employed and enrichment analyses were conducted to investigate potential signaling pathways in GBM subsets and a nomogram was established to predict 1-, 2- and 3-year overall survival probability in GBM. CCNA2 and NEK2 expression levels were further validated by western blot analysis and immunohistochemical staining in GBM samples. High expression of CCNA2 and NEK2 in glioma indicates poor clinical outcomes. Single-cell sequencing of GBM revealed that these genes were upregulated in a subset of positive neural progenitor cells (P-NPCs), which showed significant proliferation and progression properties and may activate G2M checkpoint pathways. A comprehensive nomogram predicts 1-, 2- and 3-year overall survival probability in GBM by considering P-NPCs, age, chemotherapy and radiotherapy scores. CCNA2 and NEK2 regulate glioblastoma progression by targeting the cell cycle, thus indicating the potential of novel therapy directed to CCNA2 and NEK2 in GBM.
Collapse
Affiliation(s)
- Hao-Yu Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yi-Chang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Wei Wu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yi-Yang Cao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Bei-Chen Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Mao-De Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Ping Mao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| |
Collapse
|
17
|
Sanchez JG, Rankin S, Paul E, McCauley HA, Kechele DO, Enriquez JR, Jones NH, Greeley SAW, Letourneau-Friedberg L, Zorn AM, Krishnamurthy M, Wells JM. RFX6 regulates human intestinal patterning and function upstream of PDX1. Development 2024; 151:dev202529. [PMID: 38587174 PMCID: PMC11128285 DOI: 10.1242/dev.202529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/09/2024]
Abstract
The gastrointestinal (GI) tract is complex and consists of multiple organs with unique functions. Rare gene variants can cause congenital malformations of the human GI tract, although the molecular basis of these has been poorly studied. We identified a patient with compound-heterozygous variants in RFX6 presenting with duodenal malrotation and atresia, implicating RFX6 in development of the proximal intestine. To identify how mutations in RFX6 impact intestinal patterning and function, we derived induced pluripotent stem cells from this patient to generate human intestinal organoids (HIOs). We identified that the duodenal HIOs and human tissues had mixed regional identity, with gastric and ileal features. CRISPR-mediated correction of RFX6 restored duodenal identity. We then used gain- and loss-of-function and transcriptomic approaches in HIOs and Xenopus embryos to identify that PDX1 is a downstream transcriptional target of RFX6 required for duodenal development. However, RFX6 had additional PDX1-independent transcriptional targets involving multiple components of signaling pathways that are required for establishing early regional identity in the GI tract. In summary, we have identified RFX6 as a key regulator in intestinal patterning that acts by regulating transcriptional and signaling pathways.
Collapse
Affiliation(s)
- J. Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Scott Rankin
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Emily Paul
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Heather A. McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Daniel O. Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Jacob R. Enriquez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Nana-Hawa Jones
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Siri A. W. Greeley
- Division of Endocrinology, University of Chicago, Chicago, IL 60637, USA
| | | | - Aaron M. Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Mansa Krishnamurthy
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - James M. Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| |
Collapse
|
18
|
Griffin JD, Zhu Y, Reeves A, Buhman KK, Greenberg AS. Intestinal Acyl-CoA synthetase 5 (ACSL5) deficiency potentiates postprandial GLP-1 & PYY secretion, reduces food intake, and protects against diet-induced obesity. Mol Metab 2024; 83:101918. [PMID: 38499083 PMCID: PMC10990902 DOI: 10.1016/j.molmet.2024.101918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/15/2024] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
OBJECTIVE In the small intestine, the products of digestion of dietary triacylglycerol (TAG), fatty acids (FA) and monoacylglycerol, are taken up by absorptive cells, enterocytes, for systemic energy delivery. These digestion products can also bind receptors on endocrine cells to stimulate the release of hormones capable of influencing systemic energy metabolism. The initial phase of intestinal FA absorption involves the acylation of FAs to acyl-CoA by the acyl-CoA long chain synthetase (ACSL) enzymes. ACSL5 is abundantly expressed in the small intestinal epithelium where it is the major ACSL isoform, contributing approximately 80% of total ACSL activity. In mice with whole body deficiency of ACSL5, the rate of dietary fat absorption is reduced and energy expenditure is increased. However, the mechanisms by which intestinal ACSL5 contributes to intestinal FA metabolism, enteroendocrine signaling, and regulation of energy expenditure remain undefined. Here, we test the hypothesis that intestinal ACSL5 regulates energy metabolism by influencing dietary fat absorption and enteroendocrine signaling. METHODS To explore the role of intestinal ACSL5 in energy balance and intestinal dietary fat absorption, a novel mouse model of intestine specific ACSL5 deficiency (ACSL5IKO) was generated by breeding ACSL5 floxed (ACSL5loxP/loxP) to mice harboring the tamoxifen inducible, villin-Cre recombinase. ACSL5IKO and control, ACSL5loxP/loxP mice were fed chow (low in fat) or a 60% high fat diet (HFD), and metabolic phenotyping was performed including, body weight, body composition, insulin and glucose tolerance tests, energy expenditure, physical activity, and food intake studies. Pair-feeding studies were performed to determine the role of food intake in regulating development of obesity. Studies of dietary fat absorption, fecal lipid excretion, intestinal mucosal FA content, and circulating levels of glucagon like peptide 1 (GLP-1) and peptide YY (PYY) in response to a TAG challenge were performed. Treatment with a GLP-1 receptor antagonist was performed to determine the contribution of GLP-1 to acute regulation of food intake. RESULTS We found that ACSL5IKO mice experienced rapid and sustained protection from body weight and fat mass accumulation during HFD feeding. While intestine specific deficiency of ACSL5 delayed gastric emptying and reduced dietary fat secretion, it did not result in increased excretion of dietary lipid in feces. Energy expenditure and physical activity were not increased in ACSL5IKO mice. Mice deficient in intestinal ACSL5 display significantly reduced energy intake during HFD, but not chow feeding. When HFD intake of control mice was matched to ACSL5IKO during pair-feeding studies, no differences in body weight or fat mass gain were observed between groups. Postprandial GLP-1 and PYY were significantly elevated in ACSL5IKO mice secondary to increased FA content in the distal small intestine. Blockade of GLP-1 signaling by administration of a long-acting GLP-1 receptor antagonist partially restored HFD intake of ACSL5IKO. CONCLUSIONS These data indicate that intestinal ACSL5 serves as a critical regulator of energy balance, protecting mice from diet-induced obesity exclusively by increasing satiety and reducing food intake during HFD feeding. The reduction in food intake observed in ACSL5IKO mice is driven, in part, by increased postprandial GLP-1 and PYY secretion. These effects are only observed during HFD feeding, suggesting that altered processing of dietary fat following intestinal ACSL5 ablation contributes to GLP-1 and PYY mediated increases in satiety.
Collapse
Affiliation(s)
- John D Griffin
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, USA
| | - Ying Zhu
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, USA
| | - Andrew Reeves
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, USA
| | | | - Andrew S Greenberg
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, USA; Tufts University School of Medicine, USA; Friedman School of Nutrition Science and Policy at Tufts University, USA.
| |
Collapse
|
19
|
Zindl CL, Wilson CG, Chadha AS, Duck LW, Cai B, Harbour SN, Nagaoka-Kamata Y, Hatton RD, Gao M, Figge DA, Weaver CT. Distal colonocytes targeted by C. rodentium recruit T-cell help for barrier defence. Nature 2024; 629:669-678. [PMID: 38600382 PMCID: PMC11096101 DOI: 10.1038/s41586-024-07288-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Interleukin 22 (IL-22) has a non-redundant role in immune defence of the intestinal barrier1-3. T cells, but not innate lymphoid cells, have an indispensable role in sustaining the IL-22 signalling that is required for the protection of colonic crypts against invasion during infection by the enteropathogen Citrobacter rodentium4 (Cr). However, the intestinal epithelial cell (IEC) subsets targeted by T cell-derived IL-22, and how T cell-derived IL-22 sustains activation in IECs, remain undefined. Here we identify a subset of absorptive IECs in the mid-distal colon that are specifically targeted by Cr and are differentially responsive to IL-22 signalling. Major histocompatibility complex class II (MHCII) expression by these colonocytes was required to elicit sustained IL-22 signalling from Cr-specific T cells, which was required to restrain Cr invasion. Our findings explain the basis for the regionalization of the host response to Cr and demonstrate that epithelial cells must elicit MHCII-dependent help from IL-22-producing T cells to orchestrate immune protection in the intestine.
Collapse
Affiliation(s)
- Carlene L Zindl
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - C Garrett Wilson
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Awalpreet S Chadha
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lennard W Duck
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Baiyi Cai
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stacey N Harbour
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yoshiko Nagaoka-Kamata
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robin D Hatton
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Min Gao
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David A Figge
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey T Weaver
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
20
|
Pardy RD, Walzer KA, Wallbank BA, Byerly JH, O’Dea KM, Cohn IS, Haskins BE, Roncaioli JL, Smith EJ, Buenconsejo GY, Striepen B, Hunter CA. Analysis of intestinal epithelial cell responses to Cryptosporidium highlights the temporal effects of IFN-γ on parasite restriction. PLoS Pathog 2024; 20:e1011820. [PMID: 38718306 PMCID: PMC11078546 DOI: 10.1371/journal.ppat.1011820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/14/2024] [Indexed: 05/12/2024] Open
Abstract
The production of IFN-γ is crucial for control of multiple enteric infections, but its impact on intestinal epithelial cells (IEC) is not well understood. Cryptosporidium parasites exclusively infect epithelial cells and the ability of interferons to activate the transcription factor STAT1 in IEC is required for parasite clearance. Here, the use of single cell RNA sequencing to profile IEC during infection revealed an increased proportion of mid-villus enterocytes during infection and induction of IFN-γ-dependent gene signatures that was comparable between uninfected and infected cells. These analyses were complemented by in vivo studies, which demonstrated that IEC expression of the IFN-γ receptor was required for parasite control. Unexpectedly, treatment of Ifng-/- mice with IFN-γ showed the IEC response to this cytokine correlates with a delayed reduction in parasite burden but did not affect parasite development. These data sets provide insight into the impact of IFN-γ on IEC and suggest a model in which IFN-γ signalling to uninfected enterocytes is important for control of Cryptosporidium.
Collapse
Affiliation(s)
- Ryan D. Pardy
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katelyn A. Walzer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Bethan A. Wallbank
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jessica H. Byerly
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Keenan M. O’Dea
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ian S. Cohn
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Breanne E. Haskins
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Justin L. Roncaioli
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eleanor J. Smith
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gracyn Y. Buenconsejo
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christopher A. Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
21
|
Bustamante-Madrid P, Barbáchano A, Albandea-Rodríguez D, Rodríguez-Cobos J, Rodríguez-Salas N, Prieto I, Burgos A, Martínez de Villarreal J, Real FX, González-Sancho JM, Larriba MJ, Lafarga M, Muñoz A, Fernández-Barral A. Vitamin D opposes multilineage cell differentiation induced by Notch inhibition and BMP4 pathway activation in human colon organoids. Cell Death Dis 2024; 15:301. [PMID: 38684650 PMCID: PMC11058856 DOI: 10.1038/s41419-024-06680-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Understanding the mechanisms involved in colonic epithelial differentiation is key to unraveling the alterations causing inflammatory conditions and cancer. Organoid cultures provide an unique tool to address these questions but studies are scarce. We report a differentiation system toward enterocytes and goblet cells, the two major colonic epithelial cell lineages, using colon organoids generated from healthy tissue of colorectal cancer patients. Culture of these organoids in medium lacking stemness agents resulted in a modest ultrastructural differentiation phenotype with low-level expression of enterocyte (KLF4, KRT20, CA1, FABP2) and goblet cell (TFF2, TFF3, AGR2) lineage markers. BMP pathway activation through depletion of Noggin and addition of BMP4 resulted in enterocyte-biased differentiation. Contrarily, blockade of the Notch pathway using the γ-secretase inhibitor dibenzazepine (DBZ) favored goblet cell differentiation. Combination treatment with BMP4 and DBZ caused a balanced strong induction of both lineages. In contrast, colon tumor organoids responded poorly to BMP4 showing only weak signals of cell differentiation, and were unresponsive to DBZ. We also investigated the effects of 1α,25-dihydroxyvitamin D3 (calcitriol) on differentiation. Calcitriol attenuated the effects of BMP4 and DBZ on colon normal organoids, with reduced expression of differentiation genes and phenotype. Consistently, in normal organoids, calcitriol inhibited early signaling by BMP4 as assessed by reduction of the level of phospho-SMAD1/5/8. Our results show that BMP and Notch signaling play key roles in human colon stem cell differentiation to the enterocytic and goblet cell lineages and that calcitriol modulates these processes favoring stemness features.
Collapse
Affiliation(s)
- Pilar Bustamante-Madrid
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Antonio Barbáchano
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - David Albandea-Rodríguez
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Javier Rodríguez-Cobos
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Nuria Rodríguez-Salas
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Isabel Prieto
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
- Servicio de Cirugía General, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Aurora Burgos
- Servicio de Digestivo, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Jaime Martínez de Villarreal
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Francisco X Real
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - José Manuel González-Sancho
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - María Jesús Larriba
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Miguel Lafarga
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IDIVAL, 39008, Santander, Spain
| | - Alberto Muñoz
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain.
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain.
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain.
| | - Asunción Fernández-Barral
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain.
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain.
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain.
| |
Collapse
|
22
|
Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, Vickovic S. Tissue and cellular spatiotemporal dynamics in colon aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590125. [PMID: 38712088 PMCID: PMC11071407 DOI: 10.1101/2024.04.22.590125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.
Collapse
Affiliation(s)
- Aidan C. Daly
- New York Genome Center, New York, NY, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Britta Lötstedt
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nemanja Marjanovic
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olena Kuksenko
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | | | - Eugene Drokhlyansky
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel K Griffin
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Center for Data Science, New York University, New York, NY, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Sanja Vickovic
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden
| |
Collapse
|
23
|
Díez-Sánchez A, Lindholm HT, Vornewald PM, Ostrop J, Yao R, Single AB, Marstad A, Parmar N, Shaw TN, Martín-Alonso M, Oudhoff MJ. LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model. Nat Commun 2024; 15:3412. [PMID: 38649356 PMCID: PMC11035651 DOI: 10.1038/s41467-024-47815-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Postnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, the acquisition of immune tolerance via a balanced immune cell composition, and maturation of the intestinal epithelium. While studies have uncovered an interplay between the first two, less is known about the role of the maturing epithelium. Here we show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium and maintenance of this developed state during adulthood. Using microbiota-depleted mice, we find plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to depend on LSD1-controlled epithelial maturation. We propose that LSD1 controls the expression of epithelial-derived chemokines, such as Cxcl16, and that this is a mode of action for this epithelial-immune cell interplay in local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.
Collapse
Affiliation(s)
- Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Håvard T Lindholm
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Pia M Vornewald
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jenny Ostrop
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rouan Yao
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andrew B Single
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Marstad
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tovah N Shaw
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mara Martín-Alonso
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno J Oudhoff
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Health Sciences, Carleton University, Ottawa, Ontario, ON, Canada.
| |
Collapse
|
24
|
Ran R, Muñoz Briones J, Jena S, Anderson NL, Olson MR, Green LN, Brubaker DK. Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics. iScience 2024; 27:109383. [PMID: 38523788 PMCID: PMC10959667 DOI: 10.1016/j.isci.2024.109383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
The co-culture of two adult human colorectal cancer cell lines, Caco-2 and HT29, on Transwell is commonly used as an in vitro gut mimic, yet the translatability of insights from such a system to adult human physiological contexts is not fully characterized. Here, we used single-cell RNA sequencing on the co-culture to obtain a detailed survey of cell type heterogeneity in the system and conducted a holistic comparison with human physiology. We identified the intestinal stem cell-, transit amplifying-, enterocyte-, goblet cell-, and enteroendocrine-like cells in the system. In general, the co-culture was fetal intestine-like, with less variety of gene expression compared to the adult human gut. Transporters for major types of nutrients were found in the majority of the enterocytes-like cells in the system. TLR 4 was not expressed in the sample, indicating that the co-culture model is incapable of mimicking the innate immune aspect of the human epithelium.
Collapse
Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Javier Muñoz Briones
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Purdue Interdisciplinary Life Science Program, West Lafayette, IN, USA
| | - Smrutiti Jena
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Nicole L. Anderson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew R. Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Leopold N. Green
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH, USA
| |
Collapse
|
25
|
Tan B, Xiao D, Wang J, Tan B. The Roles of Polyamines in Intestinal Development and Function in Piglets. Animals (Basel) 2024; 14:1228. [PMID: 38672376 PMCID: PMC11047586 DOI: 10.3390/ani14081228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The gastrointestinal tract plays crucial roles in the digestion and absorption of nutrients, as well as in maintenance of a functional barrier. The development and maturation of the intestine is important for piglets to maintain optimal growth and health. Polyamines are necessary for the proliferation and growth of enterocytes, which play a key role in differentiation, migration, remodeling and integrity of the intestinal mucosa after injury. This review elaborates the development of the structure and function of the intestine of piglets during embryonic, suckling and weaning periods, the utilization and metabolism of polyamines in the intestine, as well as the role of polyamines in intestinal development and mucosal repair. The nutritional intervention to improve intestinal development and functions by modulating polyamine metabolism in piglets is also put forward. These results may help to promote the adaption to weaning in pigs and provide useful information for the development and health of piglets.
Collapse
Affiliation(s)
- Bihui Tan
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Dingfu Xiao
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Jing Wang
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Bi’e Tan
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
- Hunan Linxi Biological Technology Co., Ltd. Expert Workstation, Changsha 410202, China
| |
Collapse
|
26
|
Prochera A, Muppirala AN, Kuziel GA, Soualhi S, Shepherd A, Sun L, Issac B, Rosenberg HJ, Karim F, Perez K, Smith KH, Archibald TH, Rakoff-Nahoum S, Hagen SJ, Rao M. Enteric glia regulate Paneth cell secretion and intestinal microbial ecology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589545. [PMID: 38659931 PMCID: PMC11042301 DOI: 10.1101/2024.04.15.589545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions [1]. To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express PLP1 in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1+ cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1+ glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.
Collapse
Affiliation(s)
- Aleksandra Prochera
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Anoohya N Muppirala
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Gavin A Kuziel
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Salima Soualhi
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Amy Shepherd
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Biju Issac
- Research Computing, Department of Information Technology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Harry J Rosenberg
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Farah Karim
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Kristina Perez
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Kyle H Smith
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tonora H Archibald
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Seth Rakoff-Nahoum
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Susan J Hagen
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Meenakshi Rao
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| |
Collapse
|
27
|
Ding J, Garber JJ, Uchida A, Lefkovith A, Carter GT, Vimalathas P, Canha L, Dougan M, Staller K, Yarze J, Delorey TM, Rozenblatt-Rosen O, Ashenberg O, Graham DB, Deguine J, Regev A, Xavier RJ. An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nat Commun 2024; 15:3344. [PMID: 38637492 PMCID: PMC11026436 DOI: 10.1038/s41467-024-47647-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Coordinated cell interactions within the esophagus maintain homeostasis, and disruption can lead to eosinophilic esophagitis (EoE), a chronic inflammatory disease with poorly understood pathogenesis. We profile 421,312 individual cells from the esophageal mucosa of 7 healthy and 15 EoE participants, revealing 60 cell subsets and functional alterations in cell states, compositions, and interactions that highlight previously unclear features of EoE. Active disease displays enrichment of ALOX15+ macrophages, PRDM16+ dendritic cells expressing the EoE risk gene ATP10A, and cycling mast cells, with concomitant reduction of TH17 cells. Ligand-receptor expression uncovers eosinophil recruitment programs, increased fibroblast interactions in disease, and IL-9+IL-4+IL-13+ TH2 and endothelial cells as potential mast cell interactors. Resolution of inflammation-associated signatures includes mast and CD4+ TRM cell contraction and cell type-specific downregulation of eosinophil chemoattractant, growth, and survival factors. These cellular alterations in EoE and remission advance our understanding of eosinophilic inflammation and opportunities for therapeutic intervention.
Collapse
Affiliation(s)
- Jiarui Ding
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John J Garber
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| | - Amiko Uchida
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ariel Lefkovith
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Grace T Carter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Praveen Vimalathas
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Lauren Canha
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Michael Dougan
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Kyle Staller
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Joseph Yarze
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Genentech, South San Francisco, CA, 94080, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel B Graham
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jacques Deguine
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Genentech, South San Francisco, CA, 94080, USA.
| | - Ramnik J Xavier
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| |
Collapse
|
28
|
Zeinali S, Sutton K, Zefreh MG, Mabbott N, Vervelde L. Discrimination of distinct chicken M cell subsets based on CSF1R expression. Sci Rep 2024; 14:8795. [PMID: 38627516 PMCID: PMC11021470 DOI: 10.1038/s41598-024-59368-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
In mammals, a subset of follicle-associated epithelial (FAE) cells, known as M cells, conduct the transcytosis of antigens across the epithelium into the underlying lymphoid tissues. We previously revealed that M cells in the FAE of the chicken lung, bursa of Fabricius (bursa), and caecum based on the expression of CSF1R. Here, we applied RNA-seq analysis on highly enriched CSF1R-expressing bursal M cells to investigate their transcriptome and identify novel chicken M cell-associated genes. Our data show that, like mammalian M cells, those in the FAE of the chicken bursa also express SOX8, MARCKSL1, TNFAIP2 and PRNP. Immunohistochemical analysis also confirmed the expression of SOX8 in CSF1R-expressing cells in the lung, bursa, and caecum. However, we found that many other mammalian M cell-associated genes such as SPIB and GP2 were not expressed by chicken M cells or represented in the chicken genome. Instead, we show bursal M cells express high levels of related genes such as SPI1. Whereas our data show that bursal M cells expressed CSF1R-highly, the M cells in the small intestine lacked CSF1R and both expressed SOX8. This study offers insights into the transcriptome of chicken M cells, revealing the expression of CSF1R in M cells is tissue-specific.
Collapse
Affiliation(s)
- Safieh Zeinali
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Kate Sutton
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| | - Masoud Ghaderi Zefreh
- Division of Genetics and Genomics, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Neil Mabbott
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Lonneke Vervelde
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| |
Collapse
|
29
|
Kim GD, Shin SI, Jung SW, An H, Choi SY, Eun M, Jun CD, Lee S, Park J. Cell Type- and Age-Specific Expression of lncRNAs across Kidney Cell Types. J Am Soc Nephrol 2024:00001751-990000000-00292. [PMID: 38621182 DOI: 10.1681/asn.0000000000000354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
Key Points
We constructed a single-cell long noncoding RNA atlas of various tissues, including normal and aged kidneys.We identified age- and cell type–specific expression changes of long noncoding RNAs in kidney cells.
Background
Accumulated evidence demonstrates that long noncoding RNAs (lncRNAs) regulate cell differentiation and homeostasis, influencing kidney aging and disease. Despite their versatility, the function of lncRNA remains poorly understood because of the lack of a reference map of lncRNA transcriptome in various cell types.
Methods
In this study, we used a targeted single-cell RNA sequencing method to enrich and characterize lncRNAs in individual cells. We applied this method to various mouse tissues, including normal and aged kidneys.
Results
Through tissue-specific clustering analysis, we identified cell type–specific lncRNAs that showed a high correlation with known cell-type marker genes. Furthermore, we constructed gene regulatory networks to explore the functional roles of differentially expressed lncRNAs in each cell type. In the kidney, we observed dynamic expression changes of lncRNAs during aging, with specific changes in glomerular cells. These cell type– and age-specific expression patterns of lncRNAs suggest that lncRNAs may have a potential role in regulating cellular processes, such as immune response and energy metabolism, during kidney aging.
Conclusions
Our study sheds light on the comprehensive landscape of lncRNA expression and function and provides a valuable resource for future analysis of lncRNAs (https://gist-fgl.github.io/sc-lncrna-atlas/).
Collapse
Affiliation(s)
- Gyeong Dae Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Su Woong Jung
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hyunsu An
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sin Young Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Minho Eun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sangho Lee
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| |
Collapse
|
30
|
Cadinu P, Sivanathan KN, Misra A, Xu RJ, Mangani D, Yang E, Rone JM, Tooley K, Kye YC, Bod L, Geistlinger L, Lee T, Mertens RT, Ono N, Wang G, Sanmarco L, Quintana FJ, Anderson AC, Kuchroo VK, Moffitt JR, Nowarski R. Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling. Cell 2024; 187:2010-2028.e30. [PMID: 38569542 PMCID: PMC11017707 DOI: 10.1016/j.cell.2024.03.013] [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: 04/20/2023] [Revised: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used multiplexed error-robust fluorescence in situ hybridization (MERFISH) to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations, charted their spatial organization, and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.
Collapse
Affiliation(s)
- Paolo Cadinu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kisha N Sivanathan
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Aditya Misra
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rosalind J Xu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Davide Mangani
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Evan Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph M Rone
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Tooley
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yoon-Chul Kye
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lloyd Bod
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Tyrone Lee
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Randall T Mertens
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77030, USA
| | - Gang Wang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Liliana Sanmarco
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francisco J Quintana
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ana C Anderson
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vijay K Kuchroo
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Roni Nowarski
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| |
Collapse
|
31
|
Ren X, Liu Q, Zhou P, Zhou T, Wang D, Mei Q, Flavell RA, Liu Z, Li M, Pan W, Zhu S. DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells. Nat Commun 2024; 15:3080. [PMID: 38594251 PMCID: PMC11004185 DOI: 10.1038/s41467-024-47235-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Epithelial barrier dysfunction and crypt destruction are hallmarks of inflammatory bowel disease (IBD). Intestinal stem cells (ISCs) residing in the crypts play a crucial role in the continuous self-renewal and rapid recovery of intestinal epithelial cells (IECs). However, how ISCs are dysregulated in IBD remains poorly understood. Here, we observe reduced DHX9 protein levels in IBD patients, and mice with conditional DHX9 depletion in the intestinal epithelium (Dhx9ΔIEC) exhibit an increased susceptibility to experimental colitis. Notably, Dhx9ΔIEC mice display a significant reduction in the numbers of ISCs and Paneth cells. Further investigation using ISC-specific or Paneth cell-specific Dhx9-deficient mice demonstrates the involvement of ISC-expressed DHX9 in maintaining epithelial homeostasis. Mechanistically, DHX9 deficiency leads to abnormal R-loop accumulation, resulting in genomic instability and the cGAS-STING-mediated inflammatory response, which together impair ISC function and contribute to the pathogenesis of IBD. Collectively, our findings highlight R-loop-mediated genomic instability in ISCs as a risk factor in IBD.
Collapse
Affiliation(s)
- Xingxing Ren
- Hefei National Research Center for Physical Sciences at the Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145, Guangzhou, China
| | - Qiuyuan Liu
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Peirong Zhou
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145, Guangzhou, China
| | - Tingyue Zhou
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Decai Wang
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qiao Mei
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Mingsong Li
- Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, 510145, Guangzhou, China.
| | - Wen Pan
- Hefei National Research Center for Physical Sciences at the Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Shu Zhu
- Hefei National Research Center for Physical Sciences at the Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- School of Data Science, University of Science and Technology of China, Hefei, 230026, China.
| |
Collapse
|
32
|
Bianco V, Svecla M, Vingiani GB, Kolb D, Schwarz B, Buerger M, Beretta G, Norata GD, Kratky D. Regional Differences in the Small Intestinal Proteome of Control Mice and of Mice Lacking Lysosomal Acid Lipase. J Proteome Res 2024; 23:1506-1518. [PMID: 38422518 PMCID: PMC7615810 DOI: 10.1021/acs.jproteome.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
The metabolic contribution of the small intestine (SI) is still unclear despite recent studies investigating the involvement of single cells in regional differences. Using untargeted proteomics, we identified regional characteristics of the three intestinal tracts of C57BL/6J mice and found that proteins abundant in the mouse ileum correlated with the high ileal expression of the corresponding genes in humans. In the SI of C57BL/6J mice, we also detected an increasing abundance of lysosomal acid lipase (LAL), which is responsible for degrading triacylglycerols and cholesteryl esters within the lysosome. LAL deficiency in patients and mice leads to lipid accumulation, gastrointestinal disturbances, and malabsorption. We previously demonstrated that macrophages massively infiltrated the SI of Lal-deficient (KO) mice, especially in the duodenum. Using untargeted proteomics (ProteomeXchange repository, data identifier PXD048378), we revealed a general inflammatory response and a common lipid-associated macrophage phenotype in all three intestinal segments of Lal KO mice, accompanied by a higher expression of GPNMB and concentrations of circulating sTREM2. However, only duodenal macrophages activated a metabolic switch from lipids to other pathways, which were downregulated in the jejunum and ileum of Lal KO mice. Our results provide new insights into the process of absorption in control mice and possible novel markers of LAL-D and/or systemic inflammation in LAL-D.
Collapse
Affiliation(s)
- Valentina Bianco
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
| | - Monika Svecla
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Giovanni Battista Vingiani
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Dagmar Kolb
- Core
Facility Ultrastructural Analysis, Medical
University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Gottfried
Schatz Research Center, Cell Biology, Histology and Embryology, Medical University of Graz, 8010 Graz, Austria
| | - Birgit Schwarz
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
| | - Martin Buerger
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
| | - Giangiacomo Beretta
- Department
of Environmental Science and Policy, Università
degli Studi di Milano, 20133 Milan, Italy
| | - Giuseppe Danilo Norata
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
- Centro
SISA per lo studio dell’Aterosclerosi, Ospedale Bassini, 20092 Cinisello Balsamo, Italy
| | - Dagmar Kratky
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| |
Collapse
|
33
|
Ding W, Li X, Zhang J, Ji M, Zhang M, Zhong X, Cao Y, Liu X, Li C, Xiao C, Wang J, Li T, Yu Q, Mo F, Zhang B, Qi J, Yang JC, Qi J, Tian L, Xu X, Peng Q, Zhou WZ, Liu Z, Fu A, Zhang X, Zhang JJ, Sun Y, Hu B, An NA, Zhang L, Li CY. Adaptive functions of structural variants in human brain development. SCIENCE ADVANCES 2024; 10:eadl4600. [PMID: 38579006 DOI: 10.1126/sciadv.adl4600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.
Collapse
Affiliation(s)
- Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiangshang Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Xiaoming Zhong
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119S Fourth Ring Rd W, Fengtai District, Beijing, China
| | - Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunqiong Li
- Chinese Institute for Brain Research, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ting Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qing Yu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jianhuan Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie-Chun Yang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Juntian Qi
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Lu Tian
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qi Peng
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory, Wuhan, China
| | - Xiuqin Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jian-Jun Zhang
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, National International Joint Research Center for Molecular Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
- Southwest United Graduate School, Kunming 650092, China
| |
Collapse
|
34
|
Barr J, Xu L, Li R, Verheyden J, Sun X. Airway Microfold Cells Emerge in the Post-Influenza Lung. Am J Respir Cell Mol Biol 2024; 70:322-325. [PMID: 38127584 DOI: 10.1165/rcmb.2023-0351le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Justinn Barr
- University of California, San Diego La Jolla, California
| | - Le Xu
- University of California, San Diego La Jolla, California
| | - Rongbo Li
- University of California, San Diego La Jolla, California
| | | | - Xin Sun
- University of California, San Diego La Jolla, California
| |
Collapse
|
35
|
Didriksen BJ, Eshleman EM, Alenghat T. Epithelial regulation of microbiota-immune cell dynamics. Mucosal Immunol 2024; 17:303-313. [PMID: 38428738 DOI: 10.1016/j.mucimm.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
The mammalian gastrointestinal tract hosts a diverse community of trillions of microorganisms, collectively termed the microbiota, which play a fundamental role in regulating tissue physiology and immunity. Recent studies have sought to dissect the cellular and molecular mechanisms mediating communication between the microbiota and host immune system. Epithelial cells line the intestine and form an initial barrier separating the microbiota from underlying immune cells, and disruption of epithelial function has been associated with various conditions ranging from infection to inflammatory bowel diseases and cancer. From several studies, it is now clear that epithelial cells integrate signals from commensal microbes. Importantly, these non-hematopoietic cells also direct regulatory mechanisms that instruct the recruitment and function of microbiota-sensitive immune cells. In this review, we discuss the central role that has emerged for epithelial cells in orchestrating intestinal immunity and highlight epithelial pathways through which the microbiota can calibrate tissue-intrinsic immune responses.
Collapse
Affiliation(s)
- Bailey J Didriksen
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Emily M Eshleman
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
| |
Collapse
|
36
|
Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition. Nat Microbiol 2024; 9:922-937. [PMID: 38503977 PMCID: PMC10994852 DOI: 10.1038/s41564-024-01628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.
Collapse
Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kali M Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Chemistry, University of California, Davis, CA, USA
| | - Nikita P Balcazo
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
37
|
Gu Y, Bartolomé-Casado R, Xu C, Bertocchi A, Janney A, Heuberger C, Pearson CF, Teichmann SA, Thornton EE, Powrie F. Immune microniches shape intestinal T reg function. Nature 2024; 628:854-862. [PMID: 38570678 PMCID: PMC11041794 DOI: 10.1038/s41586-024-07251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The intestinal immune system is highly adapted to maintaining tolerance to the commensal microbiota and self-antigens while defending against invading pathogens1,2. Recognizing how the diverse network of local cells establish homeostasis and maintains it in the complex immune environment of the gut is critical to understanding how tolerance can be re-established following dysfunction, such as in inflammatory disorders. Although cell and molecular interactions that control T regulatory (Treg) cell development and function have been identified3,4, less is known about the cellular neighbourhoods and spatial compartmentalization that shapes microorganism-reactive Treg cell function. Here we used in vivo live imaging, photo-activation-guided single-cell RNA sequencing5-7 and spatial transcriptomics to follow the natural history of T cells that are reactive towards Helicobacter hepaticus through space and time in the settings of tolerance and inflammation. Although antigen stimulation can occur anywhere in the tissue, the lamina propria-but not embedded lymphoid aggregates-is the key microniche that supports effector Treg (eTreg) cell function. eTreg cells are stable once their niche is established; however, unleashing inflammation breaks down compartmentalization, leading to dominance of CD103+SIRPα+ dendritic cells in the lamina propria. We identify and validate the putative tolerogenic interaction between CD206+ macrophages and eTreg cells in the lamina propria and identify receptor-ligand pairs that are likely to govern the interaction. Our results reveal a spatial mechanism of tolerance in the lamina propria and demonstrate how knowledge of local interactions may contribute to the next generation of tolerance-inducing therapies.
Collapse
Affiliation(s)
- Yisu Gu
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Raquel Bartolomé-Casado
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alice Bertocchi
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Alina Janney
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Cornelia Heuberger
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
- Roche Innovation Center Zurich, Pharma Research and Early Development, F. Hoffmann-La Roche, Schlieren, Switzerland
| | - Claire F Pearson
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Emily E Thornton
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK.
- MRC Translational Immune Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK.
| |
Collapse
|
38
|
Spencer NJ, Kyloh MA, Travis L, Hibberd TJ. Mechanisms underlying the gut-brain communication: How enterochromaffin (EC) cells activate vagal afferent nerve endings in the small intestine. J Comp Neurol 2024; 532:e25613. [PMID: 38625817 DOI: 10.1002/cne.25613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/02/2024] [Accepted: 03/24/2024] [Indexed: 04/18/2024]
Abstract
How the gastrointestinal tract communicates with the brain, via sensory nerves, is of significant interest for our understanding of human health and disease. Enterochromaffin (EC) cells in the gut mucosa release a variety of neurochemicals, including the largest quantity of 5-hydroxytryptamine (5-HT) in the body. How 5-HT and other substances released from EC cells activate sensory nerve endings in the gut wall remains a major unresolved mystery. We used in vivo anterograde tracing from nodose ganglia to determine the spatial relationship between 5-HT synthesizing and peptide-YY (PYY)-synthesizing EC cells and their proximity to vagal afferent nerve endings that project to the mucosa of mouse small intestine. The shortest mean distances between single 5-HT- and PYY-synthesizing EC cells and the nearest vagal afferent nerve endings in the mucosa were 33.1 ± 14.4 µm (n = 56; N = 6) and 70.3 ± 32.3 µm (n = 16; N = 6). No morphological evidence was found to suggest that 5-HT- or PYY-containing EC cells form close morphological associations with vagal afferents endings, or varicose axons of passage. The large distances between EC cells and vagal afferent endings are many hundreds of times greater than those known to underlie synaptic transmission in the nervous system (typically 10-15 nm). Taken together, the findings lead to the inescapable conclusion that communication between 5-HT-containing EC cells and vagal afferent nerve endings in the mucosa of the mouse small intestinal occurs in a paracrine fashion, via diffusion. New and Noteworthy None of the findings here are consistent with a view that close physical contacts occur between 5-HT-containing EC cells and vagal afferent nerve endings in mouse small intestine. Rather, the findings suggest that gut-brain communication between EC cells and vagal afferent endings occurs via passive diffusion. The morphological data presented do not support the view that EC cells are physically close enough to vagal afferent endings to communicate via fast synaptic transmission.
Collapse
Affiliation(s)
- Nick J Spencer
- Visceral Neurophysiology Laboratory, Flinders Health and Medical Research Institute & College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | - Melinda A Kyloh
- Visceral Neurophysiology Laboratory, Flinders Health and Medical Research Institute & College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | - Lee Travis
- Visceral Neurophysiology Laboratory, Flinders Health and Medical Research Institute & College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | - Timothy J Hibberd
- Visceral Neurophysiology Laboratory, Flinders Health and Medical Research Institute & College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia, Australia
| |
Collapse
|
39
|
Wang Z, Shen J. The role of goblet cells in Crohn' s disease. Cell Biosci 2024; 14:43. [PMID: 38561835 PMCID: PMC10985922 DOI: 10.1186/s13578-024-01220-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
The prevalence of Crohn's disease (CD), a subtype of inflammatory bowel disease (IBD), is increasing worldwide. The pathogenesis of CD is hypothesized to be related to environmental, genetic, immunological, and bacterial factors. Current studies have indicated that intestinal epithelial cells, including columnar, Paneth, M, tuft, and goblet cells dysfunctions, are strongly associated with these pathogenic factors. In particular, goblet cells dysfunctions have been shown to be related to CD pathogenesis by direct or indirect ways, according to the emerging studies. The mucus barrier was established with the help of mucins secreted by goblet cells. Not only do the mucins mediate the mucus barrier permeability and bacterium selection, but also, they are closely linked with the endothelial reticulum stress during the synthesis process. Goblet cells also play a vital role in immune response. It was indicated that goblet cells take part in the antigen presentation and cytokines secretion process. Disrupted goblet cells related immune process were widely discovered in CD patients. Meanwhile, dysbiosis of commensal and pathogenic microbiota can induce myriad immune responses through mucus and goblet cell-associated antigen passage. Microbiome dysbiosis lead to inflammatory reaction against pathogenic bacteria and abnormal tolerogenic response. All these three pathways, including the loss of mucus barrier function, abnormal immune reaction, and microbiome dysbiosis, may have independent or cooperative effect on the CD pathogenesis. However, many of the specific mechanisms underlying these pathways remain unclear. Based on the current understandings of goblet cell's role in CD pathogenesis, substances including butyrate, PPARγagonist, Farnesoid X receptor agonist, nuclear factor-Kappa B, nitrate, cytokines mediators, dietary and nutrient therapies were all found to have potential therapeutic effects on CD by regulating the goblet cells mediated pathways. Several monoclonal antibodies already in use for the treatment of CD in the clinical settings were also found to have some goblet cells related therapeutic targets. In this review, we introduce the disease-related functions of goblet cells, their relationship with CD, their possible mechanisms, and current CD treatments targeting goblet cells.
Collapse
Affiliation(s)
- Zichen Wang
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Ministry of Health, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, No.160 PuJian Road, Shanghai, 200127, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Ministry of Health, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, No.160 PuJian Road, Shanghai, 200127, China.
| |
Collapse
|
40
|
He Z, Zhou Q, Du J, Huang Y, Wu B, Xu Z, Wang C, Cheng X. Integrated single-cell and bulk RNA sequencing reveals CREM is involved in the pathogenesis of ulcerative colitis. Heliyon 2024; 10:e27805. [PMID: 38496850 PMCID: PMC10944264 DOI: 10.1016/j.heliyon.2024.e27805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
Background Ulcerative colitis (UC) is an inflammatory bowel disease characterized by persistent colonic inflammation. Here, we performed a systematic analysis to gain better insights into UC pathogenesis. Methods We analyzed two UC-related datasets extracted from the gene expression omnibus database using several bioinformatics tools. The primary cell types and key subgroups of primary cells associated with UC and differentially expressed genes (DEGs) between UC and control samples were identified. The molecular regulation of the key genes was also predicted. The gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses of marker genes of key cell subgroups and model genes were performed. The expression of key enriched genes was validated in 10 clinical samples using real-time quantitative polymerase chain reaction (RT-qPCR). Results Monocytes were identified as the major cell type. Ten differentially expressed marker genes were obtained by intersecting the 3121 DEGs, 38 marker genes in major cell types, and 104 marker genes in key cell subgroups. Four essential genes, associated with immune response, were obtained using support vector machine recursive feature elimination and least absolute shrinkage and selection operator analyses. The four essential genes were highly expressed in Cluster 0 during differentiation. Validation of the four key genes in colonic mucosal biopsy specimens from 10 normal and 10 UC patients revealed that CREM was highly expressed in both the lesion-free sites and lesion sites colonic mucosa of UC patients compared with normal adults. Conclusions We identified CREM involved in UC pathogenesis, which is expected to provide a new therapeutic target for UC.
Collapse
Affiliation(s)
- Zongqi He
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Qing Zhou
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210004, PR China
| | - Jun Du
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Yuyu Huang
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Bensheng Wu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Zhizhong Xu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Chao Wang
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Xudong Cheng
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| |
Collapse
|
41
|
Hu X, Chen F, Jia L, Long A, Peng Y, Li X, Huang J, Wei X, Fang X, Gao Z, Zhang M, Liu X, Chen YG, Wang Y, Zhang H, Wang Y. A gut-derived hormone regulates cholesterol metabolism. Cell 2024; 187:1685-1700.e18. [PMID: 38503280 DOI: 10.1016/j.cell.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/18/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
The reciprocal coordination between cholesterol absorption in the intestine and de novo cholesterol synthesis in the liver is essential for maintaining cholesterol homeostasis, yet the mechanisms governing the opposing regulation of these processes remain poorly understood. Here, we identify a hormone, Cholesin, which is capable of inhibiting cholesterol synthesis in the liver, leading to a reduction in circulating cholesterol levels. Cholesin is encoded by a gene with a previously unknown function (C7orf50 in humans; 3110082I17Rik in mice). It is secreted from the intestine in response to cholesterol absorption and binds to GPR146, an orphan G-protein-coupled receptor, exerting antagonistic downstream effects by inhibiting PKA signaling and thereby suppressing SREBP2-controlled cholesterol synthesis in the liver. Therefore, our results demonstrate that the Cholesin-GPR146 axis mediates the inhibitory effect of intestinal cholesterol absorption on hepatic cholesterol synthesis. This discovered hormone, Cholesin, holds promise as an effective agent in combating hypercholesterolemia and atherosclerosis.
Collapse
Affiliation(s)
- Xiaoli Hu
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fengyi Chen
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Liangjie Jia
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Aijun Long
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ying Peng
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xu Li
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Junfeng Huang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xueyun Wei
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xinlei Fang
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zihua Gao
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengxian Zhang
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Ye-Guang Chen
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Guangzhou Laboratory, Guangzhou 510005, China; School of Basic Medicine, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Yan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Huijie Zhang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Yiguo Wang
- State Key Laboratory of Membrane Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
42
|
Reina-Campos M, Monell A, Ferry A, Luna V, Cheung KP, Galletti G, Scharping NE, Takehara KK, Quon S, Boland B, Lin YH, Wong WH, Indralingam CS, Yeo GW, Chang JT, Heeg M, Goldrath AW. Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585130. [PMID: 38585842 PMCID: PMC10996520 DOI: 10.1101/2024.03.20.585130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Tissue-resident memory CD8 T cells (TRM) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) TRM cells consist of distinct subpopulations with higher expression of effector molecules or greater memory potential. We hypothesized that occupancy of diverse anatomical niches imprints these distinct TRM transcriptional programs. We leveraged human samples and a murine model of acute systemic viral infection to profile the location and transcriptome of pathogen-specific TRM cell differentiation at single-transcript resolution. We developed computational approaches to capture cellular locations along three anatomical axes of the small intestine and to visualize the spatiotemporal distribution of cell types and gene expression. TRM populations were spatially segregated: with more effector- and memory-like TRM preferentially localized at the villus tip or crypt, respectively. Modeling ligand-receptor activity revealed patterns of key cellular interactions and cytokine signaling pathways that initiate and maintain TRM differentiation and functional diversity, including different TGFβ sources. Alterations in the cellular networks induced by loss of TGFβRII expression revealed a model consistent with TGFβ promoting progressive TRM maturation towards the villus tip. Ultimately, we have developed a framework for the study of immune cell interactions with the spectrum of tissue cell types, revealing that T cell location and functional state are fundamentally intertwined.
Collapse
Affiliation(s)
- Miguel Reina-Campos
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Alexander Monell
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amir Ferry
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Vida Luna
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Kitty P. Cheung
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Giovanni Galletti
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Nicole E. Scharping
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Kennidy K. Takehara
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Sara Quon
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Brigid Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yun Hsuan Lin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maximilian Heeg
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Ananda W. Goldrath
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Allen Institute for Immunology, 615 Westlake Avenue N, Seattle, WA 98109, USA
| |
Collapse
|
43
|
Bao L, Fu L, Su Y, Chen Z, Peng Z, Sun L, Gonzalez FJ, Wu C, Zhang H, Shi B, Shi YB. Amino acid transporter SLC7A5 regulates cell proliferation and secretary cell differentiation and distribution in the mouse intestine. Int J Biol Sci 2024; 20:2187-2201. [PMID: 38617535 PMCID: PMC11008275 DOI: 10.7150/ijbs.94297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/16/2024] [Indexed: 04/16/2024] Open
Abstract
The intestine is critical for not only processing nutrients but also protecting the organism from the environment. These functions are mainly carried out by the epithelium, which is constantly being self-renewed. Many genes and pathways can influence intestinal epithelial cell proliferation. Among them is mTORC1, whose activation increases cell proliferation. Here, we report the first intestinal epithelial cell (IEC)-specific knockout (ΔIEC) of an amino acid transporter capable of activating mTORC1. We show that the transporter, SLC7A5, is highly expressed in mouse intestinal crypt and Slc7a5ΔIEC reduces mTORC1 signaling. Surprisingly, adult Slc7a5ΔIEC intestinal crypts have increased cell proliferation but reduced mature Paneth cells. Goblet cells, the other major secretory cell type in the small intestine, are increased in the crypts but reduced in the villi. Analyses with scRNA-seq and electron microscopy have revealed dedifferentiation of Paneth cells in Slc7a5ΔIEC mice, leading to markedly reduced secretory granules with little effect on Paneth cell number. Thus, SLC7A5 likely regulates secretory cell differentiation to affect stem cell niche and indirectly regulate cell proliferation.
Collapse
Affiliation(s)
- Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine. No.277, Yanta West Road, Xi'an, Shaanxi, 710061, P.R. China
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging and Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhaoyi Peng
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine. No.277, Yanta West Road, Xi'an, Shaanxi, 710061, P.R. China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine. No.277, Yanta West Road, Xi'an, Shaanxi, 710061, P.R. China
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
| |
Collapse
|
44
|
Eskiocak O, Chowdhury S, Shah V, Nnuji-John E, Chung C, Boyer JA, Harris AS, Habel J, Sadelain M, Beyaz S, Amor C. Senolytic CAR T cells reverse aging-associated defects in intestinal regeneration and fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585779. [PMID: 38529506 PMCID: PMC10962734 DOI: 10.1101/2024.03.19.585779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Intestinal stem cells (ISCs) drive the rapid regeneration of the gut epithelium to maintain organismal homeostasis. Aging, however, significantly reduces intestinal regenerative capacity. While cellular senescence is a key feature of the aging process, little is known about the in vivo effects of senescent cells on intestinal fitness. Here, we identify the accumulation of senescent cells in the aging gut and, by harnessing senolytic CAR T cells to eliminate them, we uncover their detrimental impact on epithelial integrity and overall intestinal homeostasis in natural aging, injury and colitis. Ablation of intestinal senescent cells with senolytic CAR T cells in vivo or in vitro is sufficient to promote the regenerative potential of aged ISCs. This intervention improves epithelial integrity and mucosal immune function. Overall, these results highlight the ability of senolytic CAR T cells to rejuvenate the intestinal niche and demonstrate the potential of targeted cell therapies to promote tissue regeneration in aging organisms.
Collapse
Affiliation(s)
- Onur Eskiocak
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University; NY, USA
| | | | - Vyom Shah
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Emmanuella Nnuji-John
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Charlie Chung
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Jacob A. Boyer
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University; Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA
| | | | - Jill Habel
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Corina Amor
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| |
Collapse
|
45
|
Strine MS, Fagerberg E, Darcy PW, Barrón GM, Filler RB, Alfajaro MM, D'Angelo-Gavrish N, Wang F, Graziano VR, Menasché BL, Damo M, Wang YT, Howitt MR, Lee S, Joshi NS, Mucida D, Wilen CB. Intestinal tuft cell immune privilege enables norovirus persistence. Sci Immunol 2024; 9:eadi7038. [PMID: 38517952 DOI: 10.1126/sciimmunol.adi7038] [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: 05/12/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
The persistent murine norovirus strain MNVCR6 is a model for human norovirus and enteric viral persistence. MNVCR6 causes chronic infection by directly infecting intestinal tuft cells, rare chemosensory epithelial cells. Although MNVCR6 induces functional MNV-specific CD8+ T cells, these lymphocytes fail to clear infection. To examine how tuft cells promote immune escape, we interrogated tuft cell interactions with CD8+ T cells by adoptively transferring JEDI (just EGFP death inducing) CD8+ T cells into Gfi1b-GFP tuft cell reporter mice. Unexpectedly, some intestinal tuft cells partially resisted JEDI CD8+ T cell-mediated killing-unlike Lgr5+ intestinal stem cells and extraintestinal tuft cells-despite seemingly normal antigen presentation. When targeting intestinal tuft cells, JEDI CD8+ T cells predominantly adopted a T resident memory phenotype with decreased effector and cytotoxic capacity, enabling tuft cell survival. JEDI CD8+ T cells neither cleared nor prevented MNVCR6 infection in the colon, the site of viral persistence, despite targeting a virus-independent antigen. Ultimately, we show that intestinal tuft cells are relatively resistant to CD8+ T cells independent of norovirus infection, representing an immune-privileged niche that can be leveraged by enteric microbes.
Collapse
Affiliation(s)
- Madison S Strine
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Fagerberg
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Patrick W Darcy
- Laboratory of Mucosal Immunology, Rockefeller University, New York, NY, USA
| | - Gabriel M Barrón
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Fang Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Vincent R Graziano
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, USA
| | - Bridget L Menasché
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Martina Damo
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ya-Ting Wang
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Tsinghua University School of Medicine, Beijing, China
| | - Michael R Howitt
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Sanghyun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nikhil S Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
46
|
Ren W, Chen J, Wang W, Li Q, Yin X, Zhuang G, Zhou H, Zeng W. Sympathetic nerve-enteroendocrine L cell communication modulates GLP-1 release, brain glucose utilization, and cognitive function. Neuron 2024; 112:972-990.e8. [PMID: 38242116 DOI: 10.1016/j.neuron.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/26/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Glucose homeostasis is controlled by brain-gut communications. Yet our understanding of the neuron-gut interface in the glucoregulatory system remains incomplete. Here, we find that sympathetic nerves elevate postprandial blood glucose but restrict brain glucose utilization by repressing the release of glucagon-like peptide-1 (GLP-1) from enteroendocrine L cells. Sympathetic nerves are in close apposition with the L cells. Importantly, sympathetic denervation or intestinal deletion of the adrenergic receptor α2 (Adra2a) augments postprandial GLP-1 secretion, leading to reduced blood glucose levels and increased brain glucose uptake. Conversely, sympathetic activation shows the opposite effects. At the cellular level, adrenergic signaling suppresses calcium flux to limit GLP-1 secretion upon sugar ingestion. Consequently, abrogation of adrenergic signal results in a significant improvement in learning and memory ability. Together, our results reveal a sympathetic nerve-enteroendocrine unit in constraining GLP-1 secretion, thus providing a therapeutic nexus of mobilizing endogenous GLP-1 for glucose management and cognitive improvement.
Collapse
Affiliation(s)
- Wenran Ren
- Institute for Immunology and School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
| | - Jianhui Chen
- Institute for Immunology and School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
| | - Wenjing Wang
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qingqing Li
- Institute for Immunology and School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China
| | - Xia Yin
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Guanglei Zhuang
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hong Zhou
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
| | - Wenwen Zeng
- Institute for Immunology and School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan 030001, Shanxi, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing 100084, China.
| |
Collapse
|
47
|
Silverman JB, Krystofiak EE, Caplan LR, Lau KS, Tyska MJ. Intestinal tuft cells assemble a cytoskeletal superstructure composed of co-aligned actin bundles and microtubules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585757. [PMID: 38562898 PMCID: PMC10983963 DOI: 10.1101/2024.03.19.585757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background & Aims All tissues consist of a distinct set of cell types, which collectively support organ function and homeostasis. Tuft cells are a rare epithelial cell type found in diverse epithelia, where they play important roles in sensing antigens and stimulating downstream immune responses. Exhibiting a unique polarized morphology, tuft cells are defined by an array of giant actin filament bundles that support ∼2 μm of apical membrane protrusion and extend over 7 μm towards the cell's perinuclear region. Despite their established roles in maintaining intestinal epithelial homeostasis, tuft cells remain understudied due to their rarity (e.g. ∼ 1% in the small intestinal epithelium). Details regarding the ultrastructural organization of the tuft cell cytoskeleton, the molecular components involved in building the array of giant actin bundles, and how these cytoskeletal structures support tuft cell biology remain unclear. Methods To begin to answer these questions, we used advanced light and electron microscopy to perform quantitative morphometry of the small intestinal tuft cell cytoskeleton. Results We found that tuft cell core bundles consist of actin filaments that are crosslinked in a parallel "barbed-end out" configuration. These polarized structures are also supported by a unique group of tuft cell enriched actin-binding proteins that are differentially localized along the giant core bundles. Furthermore, we found that tuft cell actin bundles are co-aligned with a highly ordered network of microtubules. Conclusions Tuft cells assemble a cytoskeletal superstructure that is well positioned to serve as a track for subcellular transport along the apical-basolateral axis and in turn, support the dynamic sensing functions that are critical for intestinal epithelial homeostasis. SYNOPSIS This research leveraged advanced light and electron microscopy to perform quantitative morphometry of the intestinal tuft cell cytoskeleton. Three-dimensional reconstructions of segmented image data revealed a co-aligned actin-microtubule superstructure that may play a fundamental role in tuft cell function.
Collapse
|
48
|
Minařík M, Modrell MS, Gillis JA, Campbell AS, Fuller I, Lyne R, Micklem G, Gela D, Pšenička M, Baker CVH. Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. Front Cell Dev Biol 2024; 12:1327924. [PMID: 38562141 PMCID: PMC10982350 DOI: 10.3389/fcell.2024.1327924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.
Collapse
Affiliation(s)
- Martin Minařík
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Melinda S. Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - J. Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Alexander S. Campbell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Isobel Fuller
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - David Gela
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Clare V. H. Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
49
|
Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system. Nat Commun 2024; 15:2230. [PMID: 38472198 PMCID: PMC10933491 DOI: 10.1038/s41467-024-46285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.
Collapse
Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094, Budapest, Hungary
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
50
|
López-Posadas R, Bagley DC, Pardo-Pastor C, Ortiz-Zapater E. The epithelium takes the stage in asthma and inflammatory bowel diseases. Front Cell Dev Biol 2024; 12:1258859. [PMID: 38529406 PMCID: PMC10961468 DOI: 10.3389/fcell.2024.1258859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024] Open
Abstract
The epithelium is a dynamic barrier and the damage to this epithelial layer governs a variety of complex mechanisms involving not only epithelial cells but all resident tissue constituents, including immune and stroma cells. Traditionally, diseases characterized by a damaged epithelium have been considered "immunological diseases," and research efforts aimed at preventing and treating these diseases have primarily focused on immuno-centric therapeutic strategies, that often fail to halt or reverse the natural progression of the disease. In this review, we intend to focus on specific mechanisms driven by the epithelium that ensure barrier function. We will bring asthma and Inflammatory Bowel Diseases into the spotlight, as we believe that these two diseases serve as pertinent examples of epithelium derived pathologies. Finally, we will argue how targeting the epithelium is emerging as a novel therapeutic strategy that holds promise for addressing these chronic diseases.
Collapse
Affiliation(s)
- Rocío López-Posadas
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universtiy Eralngen-Nürnberg, Erlangen, Germany
| | - Dustin C. Bagley
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, School of Basic and Medical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Carlos Pardo-Pastor
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, School of Basic and Medical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- Department of Biochemistry and Molecular Biology, Universitat de Valencia, Valencia, Spain
- Instituto Investigación Hospital Clínico-INCLIVA, Valencia, Spain
| |
Collapse
|