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Swisa A, Kieckhaefer J, Daniel SG, El-Mekkoussi H, Kolev HM, Tigue M, Jin C, Assenmacher CA, Dohnalová L, Thaiss CA, Karlsson NG, Bittinger K, Kaestner KH. The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation. Dev Cell 2024; 59:2069-2084.e8. [PMID: 38821056 PMCID: PMC11338728 DOI: 10.1016/j.devcel.2024.05.006] [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: 11/16/2022] [Revised: 12/19/2023] [Accepted: 05/09/2024] [Indexed: 06/02/2024]
Abstract
Evolutionary adaptation of multicellular organisms to a closed gut created an internal microbiome differing from that of the environment. Although the composition of the gut microbiome is impacted by diet and disease state, we hypothesized that vertebrates promote colonization by commensal bacteria through shaping of the apical surface of the intestinal epithelium. Here, we determine that the evolutionarily ancient FOXA transcription factors control the composition of the gut microbiome by establishing favorable glycosylation on the colonic epithelial surface. FOXA proteins bind to regulatory elements of a network of glycosylation enzymes, which become deregulated when Foxa1 and Foxa2 are deleted from the intestinal epithelium. As a direct consequence, microbial composition shifts dramatically, and spontaneous inflammatory bowel disease ensues. Microbiome dysbiosis was quickly reversed upon fecal transplant into wild-type mice, establishing a dominant role for the host epithelium, in part mediated by FOXA factors, in controlling symbiosis in the vertebrate holobiont.
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Affiliation(s)
- Avital Swisa
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Julia Kieckhaefer
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hilana El-Mekkoussi
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Hannah M Kolev
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Mark Tigue
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Chunsheng Jin
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Charles-Antoine Assenmacher
- Comparative Pathology Core, Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Lenka Dohnalová
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christoph A Thaiss
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, 0130 Oslo, Norway
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA.
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2
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Verhagen MP, Joosten R, Schmitt M, Välimäki N, Sacchetti A, Rajamäki K, Choi J, Procopio P, Silva S, van der Steen B, van den Bosch TPP, Seinstra D, de Vries AC, Doukas M, Augenlicht LH, Aaltonen LA, Fodde R. Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation. Nat Genet 2024; 56:1456-1467. [PMID: 38902475 PMCID: PMC11250264 DOI: 10.1038/s41588-024-01801-y] [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: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/22/2024]
Abstract
According to conventional views, colon cancer originates from stem cells. However, inflammation, a key risk factor for colon cancer, has been shown to suppress intestinal stemness. Here, we used Paneth cells as a model to assess the capacity of differentiated lineages to trigger tumorigenesis in the context of inflammation in mice. Upon inflammation, Paneth cell-specific Apc mutations led to intestinal tumors reminiscent not only of those arising in patients with inflammatory bowel disease, but also of a larger fraction of human sporadic colon cancers. The latter is possibly because of the inflammatory consequences of western-style dietary habits, a major colon cancer risk factor. Machine learning methods designed to predict the cell-of-origin of cancer from patient-derived tumor samples confirmed that, in a substantial fraction of sporadic cases, the origins of colon cancer reside in secretory lineages and not in stem cells.
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Affiliation(s)
- Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rosalie Joosten
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark Schmitt
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Andrea Sacchetti
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Paola Procopio
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Sara Silva
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Danielle Seinstra
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie C de Vries
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leonard H Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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3
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Langerud J, Eilertsen IA, Moosavi SH, Klokkerud SMK, Reims HM, Backe IF, Hektoen M, Sjo OH, Jeanmougin M, Tejpar S, Nesbakken A, Lothe RA, Sveen A. Multiregional transcriptomics identifies congruent consensus subtypes with prognostic value beyond tumor heterogeneity of colorectal cancer. Nat Commun 2024; 15:4342. [PMID: 38773143 PMCID: PMC11109119 DOI: 10.1038/s41467-024-48706-2] [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: 08/23/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Intra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for classifications less vulnerable to heterogeneity in a single-hospital series of 1093 tumor samples from 692 patients, including multiregional samples from 98 primary tumors and 35 primary-metastasis sets. We show that intra-tumor heterogeneity of the consensus molecular subtypes (CMS) is frequent and has poor-prognostic associations independently of tumor microenvironment markers. Multiregional transcriptomics uncover cancer cell-intrinsic and low-heterogeneity signals that recapitulate the intrinsic CMSs proposed by single-cell sequencing. Further subclassification identifies congruent CMSs that explain a larger proportion of variation in patient survival than intra-tumor heterogeneity. Plasticity is indicated by discordant intrinsic phenotypes of matched primary and metastatic tumors. We conclude that multiregional sampling reconciles the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.
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Affiliation(s)
- Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Solveig M K Klokkerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ingeborg F Backe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ole H Sjo
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Arild Nesbakken
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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4
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Naser AN, Xing T, Tatum R, Lu Q, Boyer PJ, Chen YH. Colonic crypt stem cell functions are controlled by tight junction protein claudin-7 through Notch/Hippo signaling. Ann N Y Acad Sci 2024; 1535:92-108. [PMID: 38598500 PMCID: PMC11111361 DOI: 10.1111/nyas.15137] [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: 07/13/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The tight junction protein claudin-7 is essential for tight junction function and intestinal homeostasis. Cldn7 deletion in mice leads to an inflammatory bowel disease-like phenotype exhibiting severe intestinal epithelial damage, weight loss, inflammation, mucosal ulcerations, and epithelial hyperplasia. Claudin-7 has also been shown to be involved in cancer metastasis and invasion. Here, we test our hypothesis that claudin-7 plays an important role in regulating colonic intestinal stem cell function. Conditional knockout of Cldn7 in the colon led to impaired epithelial cell differentiation, hyperproliferative epithelium, a decrease in active stem cells, and dramatically altered gene expression profiles. In 3D colonoid culture, claudin-7-deficient crypts were unable to survive and form spheroids, emphasizing the importance of claudin-7 in stem cell survival. Inhibition of the Hippo pathway or activation of Notch signaling partially rescued the defective stem cell behavior. Concurrent Notch activation and Hippo inhibition resulted in restored colonoid survival, growth, and differentiation to the level comparable to those of wild-type derived crypts. In this study, we highlight the essential role of claudin-7 in regulating Notch and Hippo signaling-dependent colonic stem cell functions, including survival, self-renewal, and differentiation. These new findings may shed light on potential avenues to explore for drug development in colorectal cancer.
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Affiliation(s)
- Amna N. Naser
- Department of Anatomy and Cell Biology, University of South Carolina, Columbia, South Carolina, USA
| | - Tiaosi Xing
- Department of Anatomy and Cell Biology, University of South Carolina, Columbia, South Carolina, USA
- Neural and Behavioral Science Department, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Rodney Tatum
- Department of Anatomy and Cell Biology, University of South Carolina, Columbia, South Carolina, USA
| | - Qun Lu
- Department of Anatomy and Cell Biology, University of South Carolina, Columbia, South Carolina, USA
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Philip J. Boyer
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Yan-Hua Chen
- Department of Anatomy and Cell Biology, University of South Carolina, Columbia, South Carolina, USA
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
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5
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Wang K, Liu Y, Li H, Liang X, Hao M, Yuan D, Ding L. Claudin-7 is essential for the maintenance of colonic stem cell homoeostasis via the modulation of Wnt/Notch signalling. Cell Death Dis 2024; 15:284. [PMID: 38654000 PMCID: PMC11039680 DOI: 10.1038/s41419-024-06658-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: 10/01/2023] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Intestinal stem cells (ISCs) play a crucial role in the continuous self-renewal and recovery of the intestinal epithelium. In previous studies, we have revealed that the specific absence of Claudin-7 (Cldn-7) in intestinal epithelial cells (IECs) can lead to the development of spontaneous colitis. However, the mechanisms by which Cldn-7 maintains homeostasis in the colonic epithelium remain unclear. Therefore, in the present study, we used IEC- and ISC-specific Cldn-7 knockout mice to investigate the regulatory effects of Cldn-7 on colonic Lgr5+ stem cells in the mediation of colonic epithelial injury and repair under physiological and inflammatory conditions. Notably, our findings reveal that Cldn-7 deletion disrupts the self-renewal and differentiation of colonic stem cells alongside the formation of colonic organoids in vitro. Additionally, these Cldn-7 knockout models exhibited heightened susceptibility to experimental colitis, limited epithelial repair and regeneration, and increased differentiation toward the secretory lineage. Mechanistically, we also established that Cldn-7 facilitates the proliferation, differentiation, and organoid formation of Lgr5+ stem cells through the maintenance of Wnt and Notch signalling pathways in the colonic epithelium. Overall, our study provides new insights into the maintenance of ISC function and colonic epithelial homoeostasis.
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Affiliation(s)
- Kun Wang
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Ultrasound, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yin Liu
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Huimin Li
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xiaoqing Liang
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mengdi Hao
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Dajin Yuan
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Lei Ding
- Gastrointestinal Oncology Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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6
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Shin JH, Park J, Lim J, Jeong J, Dinesh RK, Maher SE, Hong JY, Wysolmerski J, Choi J, Bothwell ALM. Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589235. [PMID: 38659853 PMCID: PMC11042192 DOI: 10.1101/2024.04.12.589235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in homeostatic conditions, but the underlying mechanisms of cancer stem cell niche development are unclear. Here we report that Dickkopf-2 (DKK2) is essential for the generation of cancer cells with Paneth cell properties during colon cancer metastasis. Splenic injection of Dkk2-knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases. Transcriptome analysis showed reduction of Paneth cell markers such as lysozymes in KO organoids. Single cell RNA sequencing analyses of murine metastasized colon cancer cells and patient samples identified the presence of lysozyme positive cells with Paneth cell properties including enhanced glycolysis. Further analyses of transcriptome and chromatin accessibility suggested Hepatocyte nuclear factor 4-alpha (HNF4A) as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing analysis revealed that HNF4A binds to the promoter region of Sox9, a well-known transcription factor for Paneth cell differentiation. In the liver metastatic foci, DKK2 knockout rescued HNF4A protein levels followed by reduction of lysozyme positive cancer cells. Taken together, DKK2-mediated reduction of HNF4A protein promotes the generation of lysozyme positive cancer cells with Paneth cell properties in the metastasized colon cancers.
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Affiliation(s)
- Jae Hun Shin
- Integrative Science and Engineering Division, Underwood International College, Yonsei University, Incheon 21983, Korea
| | - Jooyoung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Jaechul Lim
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jaekwang Jeong
- Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
| | - Ravi K. Dinesh
- Department of Pathology, Stanford University, Stanford, California 94305, U.S
| | - Stephen E. Maher
- Department of Urology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
| | - Jun Young Hong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - John Wysolmerski
- Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Alfred L. M. Bothwell
- Dept. of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, 505 S. 45 Street., Omaha, NE 68198, U.S
- Dept. of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S
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7
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Forsyth CB, Shaikh M, Engen PA, Preuss F, Naqib A, Palmen BA, Green SJ, Zhang L, Bogin ZR, Lawrence K, Sharma D, Swanson GR, Bishehsari F, Voigt RM, Keshavarzian A. Evidence that the loss of colonic anti-microbial peptides may promote dysbiotic Gram-negative inflammaging-associated bacteria in aging mice. FRONTIERS IN AGING 2024; 5:1352299. [PMID: 38501032 PMCID: PMC10945560 DOI: 10.3389/fragi.2024.1352299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/02/2024] [Indexed: 03/20/2024]
Abstract
Introduction: Aging studies in humans and mice have played a key role in understanding the intestinal microbiome and an increased abundance of "inflammaging" Gram-negative (Gn) bacteria. The mechanisms underlying this inflammatory profile in the aging microbiome are unknown. We tested the hypothesis that an aging-related decrease in colonic crypt epithelial cell anti-microbial peptide (AMP) gene expression could promote colonic microbiome inflammatory Gn dysbiosis and inflammaging. Methods: As a model of aging, C57BL/6J mice fecal (colonic) microbiota (16S) and isolated colonic crypt epithelial cell gene expression (RNA-seq) were assessed at 2 months (mth) (human: 18 years old; yo), 15 mth (human: 50 yo), and 25 mth (human: 84 yo). Informatics examined aging-related microbial compositions, differential colonic crypt epithelial cell gene expressions, and correlations between colonic bacteria and colonic crypt epithelial cell gene expressions. Results: Fecal microbiota exhibited significantly increased relative abundances of pro-inflammatory Gn bacteria with aging. Colonic crypt epithelial cell gene expression analysis showed significant age-related downregulation of key AMP genes that repress the growth of Gn bacteria. The aging-related decrease in AMP gene expressions is significantly correlated with an increased abundance in Gn bacteria (dysbiosis), loss of colonic barrier gene expression, and senescence- and inflammation-related gene expression. Conclusion: This study supports the proposed model that aging-related loss of colonic crypt epithelial cell AMP gene expression promotes increased relative abundances of Gn inflammaging-associated bacteria and gene expression markers of colonic inflammaging. These data may support new targets for aging-related therapies based on intestinal genes and microbiomes.
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Affiliation(s)
- Christopher B. Forsyth
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Maliha Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Phillip A. Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Fabian Preuss
- Department of Biological Sciences, University of Wisconsin Parkside, Kenosha, WI, United States
| | - Ankur Naqib
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, United States
| | - Breanna A. Palmen
- Department of Biological Sciences, University of Wisconsin Parkside, Kenosha, WI, United States
| | - Stefan J. Green
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, United States
| | - Lijuan Zhang
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Zlata R. Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Kristi Lawrence
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Deepak Sharma
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Garth R. Swanson
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Faraz Bishehsari
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Robin M. Voigt
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Ali Keshavarzian
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
- Department of Physiology, Rush University Medical Center, Chicago, IL, United States
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8
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Buijs JT, van Beijnum R, Anijs RJS, Laghmani EH, Sensuk L, Minderhoud C, Ünlü B, Klok FA, Kuppen PJK, Cannegieter SC, Versteeg HH. The association of tumor-expressed REG4, SPINK4 and alpha-1 antitrypsin with cancer-associated thrombosis in colorectal cancer. J Thromb Thrombolysis 2024; 57:370-380. [PMID: 38066386 PMCID: PMC10961291 DOI: 10.1007/s11239-023-02907-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 03/26/2024]
Abstract
Novel biomarkers are needed to improve current imperfect risk prediction models for cancer-associated thrombosis (CAT). We recently identified an RNA-sequencing profile that associates with CAT in colorectal cancer (CRC) patients, with REG4, SPINK4, and SERPINA1 as the top-3 upregulated genes at mRNA level. In the current study, we investigated whether protein expression of REG4, SPINK4 and alpha-1 antitrypsin (A1AT, encoded by SERPINA1) in the tumor associated with CAT in an independent cohort of CRC patients. From 418 patients with resected CRC, 18 patients who developed CAT were age, sex, and tumor stage-matched to 18 CRC patients without CAT. Protein expression was detected by immunohistochemical staining and scored blindly by assessing the H-score (percentage positive cells*scoring intensity). The association with CAT was assessed by means of logistic regression, using patients with an H-score below 33 as reference group. The odds ratios (ORs) for developing CAT for patients with A1AThigh, REG4high, SPINK4high tumors were 3.5 (95%CI 0.8-14.5), 2.0 (95%CI 0.5-7.6) and 2.0 (95%CI 0.5-7.4) when compared to A1ATlow, REG4low, SPINK4low, respectively. The OR was increased to 24.0 (95%CI 1.1-505.1) when two proteins were combined (A1AThigh/REG4high). This nested case-control study shows that combined protein expression of A1AT and REG4 associate with CAT in patients with colorectal cancer. Therefore, REG4/A1AT are potential biomarkers to improve the identification of patients with CRC who may benefit from thromboprophylaxis.
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Affiliation(s)
- Jeroen T Buijs
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands.
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Robin van Beijnum
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Rayna J S Anijs
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - El Houari Laghmani
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Lily Sensuk
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Cas Minderhoud
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Betül Ünlü
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Frederikus A Klok
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Suzanne C Cannegieter
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Epidemiology, LUMC, Leiden, The Netherlands
| | - Henri H Versteeg
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
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9
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Hensel IV, Éliás S, Steinhauer M, Stoll B, Benfatto S, Merkt W, Krienke S, Lorenz HM, Haas J, Wildemann B, Resnik-Docampo M. SLE serum induces altered goblet cell differentiation and leakiness in human intestinal organoids. EMBO Mol Med 2024; 16:547-574. [PMID: 38316934 PMCID: PMC10940301 DOI: 10.1038/s44321-024-00023-3] [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: 10/04/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Human intestinal epithelial cells are the interface between luminal content and basally residing immune cells. They form a tight monolayer that constantly secretes mucus creating a multilayered protective barrier. Alterations in this barrier can lead to increased permeability which is common in systemic lupus erythematosus (SLE) patients. However, it remains unexplored how the barrier is affected. Here, we present an in vitro model specifically designed to examine the effects of SLE on epithelial cells. We utilize human colon organoids that are stimulated with serum from SLE patients. Combining transcriptomic with functional analyses revealed that SLE serum induced an expression profile marked by a reduction of goblet cell markers and changed mucus composition. In addition, organoids exhibited imbalanced cellular composition along with enhanced permeability, altered mitochondrial function, and an interferon gene signature. Similarly, transcriptomic analysis of SLE colon biopsies revealed a downregulation of secretory markers. Our work uncovers a crucial connection between SLE and intestinal homeostasis that might be promoted in vivo through the blood, offering insights into the causal connection of barrier dysfunction and autoimmune diseases.
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Affiliation(s)
| | | | | | | | | | - Wolfgang Merkt
- Division of Rheumatology, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Krienke
- Division of Rheumatology, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Hanns-Martin Lorenz
- Division of Rheumatology, Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Jürgen Haas
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Brigitte Wildemann
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
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10
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Yang X, Wu X, Wang Y, Li W, Wu X, Yuan L, Yu T, Li N, Zhang S, Hua J. Induction of lung progenitor cell-like organoids by porcine pluripotent stem cells. FASEB J 2024; 38:e23481. [PMID: 38334430 DOI: 10.1096/fj.202302402r] [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: 11/22/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
Organoids are in vitro 3D models that are generated using stem cells to study organ development and regeneration. Despite the extensive research on lung organoids, there is limited information on pig lung cell generation or development. Here, we identified five epithelial cell types along with their characteristic markers using scRNA-seq. Additionally, we found that NKX2.1 and FOXA2 acted as the crucial core transcription factors in porcine lung development. The presence of SOX9/SOX2 double-positive cells was identified as a key marker for lung progenitor cells. The Monocle algorithm was used to create a pseudo-temporal differentiation trajectory of epithelial cells, leading to the identification of signaling pathways related to porcine lung development. Moreover, we established the differentiation method from porcine pluripotent stem cells (pPSCs) to SOX17+ FOXA2+ definitive endoderm (DE) and NKX2.1+ FOXA2+ CDX2- anterior foregut endoderm (AFE). The AFE is further differentiated into lung organoids while closely monitoring the differentiation process. We showed that NKX2.1 overexpression facilitated the induction of lung organoids and supported subsequent lung differentiation and maturation. This model offers valuable insights into studying the interaction patterns between cells and the signaling pathways during the development of the porcine lung.
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Affiliation(s)
- Xinchun Yang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaolong Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuqi Wang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenhao Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojie Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Liming Yuan
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Taiyong Yu
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Na Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
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11
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Kwon SJ, Khan MS, Kim SG. Intestinal Inflammation and Regeneration-Interdigitating Processes Controlled by Dietary Lipids in Inflammatory Bowel Disease. Int J Mol Sci 2024; 25:1311. [PMID: 38279309 PMCID: PMC10816399 DOI: 10.3390/ijms25021311] [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: 12/12/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a disease of chronic inflammatory conditions of the intestinal tract due to disturbance of the inflammation and immune system. Symptoms of IBD include abdominal pain, diarrhea, bleeding, reduced weight, and fatigue. In IBD, the immune system attacks the intestinal tract's inner wall, causing chronic inflammation and tissue damage. In particular, interlukin-6 and interlukin-17 act on immune cells, including T cells and macrophages, to amplify the immune responses so that tissue damage and morphological changes occur. Of note, excessive calorie intake and obesity also affect the immune system due to inflammation caused by lipotoxicity and changes in lipids supply. Similarly, individuals with IBD have alterations in liver function after sustained high-fat diet feeding. In addition, excess dietary fat intake, along with alterations in primary and secondary bile acids in the colon, can affect the onset and progression of IBD because inflammatory cytokines contribute to insulin resistance; the factors include the release of inflammatory cytokines, oxidative stress, and changes in intestinal microflora, which may also contribute to disease progression. However, interfering with de novo fatty acid synthase by deleting the enzyme acetyl-CoA-carboxylase 1 in intestinal epithelial cells (IEC) leads to the deficiency of epithelial crypt structures and tissue regeneration, which seems to be due to Lgr5+ intestinal stem cell function. Thus, conflicting reports exist regarding high-fat diet effects on IBD animal models. This review will focus on the pathological basis of the link between dietary lipids intake and IBD and will cover the currently available pharmacological approaches.
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Affiliation(s)
| | | | - Sang Geon Kim
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang-si 10326, Gyeonggi-do, Republic of Korea; (S.J.K.); (M.S.K.)
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12
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Sakahara M, Okamoto T, Srivastava U, Natsume Y, Yamanaka H, Suzuki Y, Obama K, Nagayama S, Yao R. Paneth-like cells produced from OLFM4 + stem cells support OLFM4 + stem cell growth in advanced colorectal cancer. Commun Biol 2024; 7:27. [PMID: 38182890 PMCID: PMC10770338 DOI: 10.1038/s42003-023-05504-8] [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: 11/15/2022] [Accepted: 10/25/2023] [Indexed: 01/07/2024] Open
Abstract
Tumor tissues consist of heterogeneous cells that originate from stem cells; however, their cell fate determination program remains incompletely understood. Using patient-derived organoids established from patients with advanced colorectal cancer (CRC), we evaluated the potential of olfactomedin 4 (OLFM4)+ stem cells to produce a bifurcated lineage of progenies with absorptive and secretory properties. In the early phases of organoid reconstruction, OLFM4+ cells preferentially gave rise to secretory cells. Additionally, we found that Paneth-like cells, which do not exist in the normal colon, were induced in response to Notch signaling inhibition. Video recordings of single OLFM4+ cells revealed that organoids containing Paneth-like cells were effectively propagated and that their selective ablation led to organoid collapse. In tumor tissues, Paneth-like cells were identified only in the region where tumor cells lost cell adhesion. These findings indicate that Paneth-like cells are directly produced by OLFM4+ stem cells and that their interaction contributes to tumor formation by providing niche factors. This study reveals the importance of the cell fate specification program for building a complete tumor cellular ecosystem, which might be targeted with novel therapeutics.
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Affiliation(s)
- Mizuho Sakahara
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Upasna Srivastava
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Nagayama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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13
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Hopton RE, Jahahn NJ, Zemper AE. Lrig1 drives cryptogenesis and restrains proliferation during colon development. Am J Physiol Gastrointest Liver Physiol 2023; 325:G570-G581. [PMID: 37873577 PMCID: PMC11192189 DOI: 10.1152/ajpgi.00094.2023] [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: 05/03/2023] [Revised: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023]
Abstract
Growth and specification of the mouse intestine occurs in utero and concludes after birth. Although numerous studies have examined this developmental process in the small intestine, far less is known about the cellular and molecular cues required for colon development. In this study, we examine the morphological events leading to crypt formation, epithelial cell differentiation, proliferation, and the emergence and expression of a stem and progenitor cell marker Lrig1. Through multicolor lineage tracing, we show Lrig1-expressing cells are present at birth and behave as stem cells to establish clonal crypts within 3 wk of life. In addition, we use an inducible knockout mouse to eliminate Lrig1 and show Lrig1 restrains proliferation within a critical developmental time window, without impacting colonic epithelial cell differentiation. Our study illustrates morphological changes during crypt development and the importance of Lrig1 in the developing colon.NEW & NOTEWORTHY Our studies define the importance of studying Lrig1 in colon development. We address a critical gap in the intestinal development literature and provide new information about the molecular cues that guide colon development. Using a novel, inducible knockout of Lrig1, we show Lrig1 is required for appropriate colon epithelial growth and illustrate the importance of Lrig1-expressing cells in the establishment of colonic crypts.
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Affiliation(s)
- Rachel E Hopton
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States
- Department of Biology, University of Oregon, Eugene, Oregon, United States
| | - Nicholas J Jahahn
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States
- Department of Biology, University of Oregon, Eugene, Oregon, United States
| | - Anne E Zemper
- Department of Biology, University of Oregon, Eugene, Oregon, United States
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14
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Schumacher MA. The emerging roles of deep crypt secretory cells in colonic physiology. Am J Physiol Gastrointest Liver Physiol 2023; 325:G493-G500. [PMID: 37697924 PMCID: PMC10887841 DOI: 10.1152/ajpgi.00093.2023] [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: 05/02/2023] [Revised: 08/18/2023] [Accepted: 09/03/2023] [Indexed: 09/13/2023]
Abstract
Deep crypt secretory (DCS) cells are a population of epithelial cells located at the colonic crypt base that share some similarities to Paneth and goblet cells. They were initially defined as c-Kit expressing cells, though subsequent work showed that they are more specifically marked by Reg4 in the murine colon. The best-understood function of DCS cells at present is supporting the stem cell niche by generating Notch and EGF ligands. However, as these cells also express immunoregulatory (e.g., Ccl6) and host defense (e.g., Retnlb) genes, it is likely they have additional functions in maintaining colonic health outside of maintenance of the stem niche. Recent advances in single-cell transcriptomic profiling hint at additional epithelial and immune roles that may exist for these cells and have aided in elucidating their developmental lineage. This review highlights the emerging evidence supporting a crucial role for DCS cells in intestinal physiology, the current understanding of how these cells are regulated, and their potential role(s) in colonic disease.
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Affiliation(s)
- Michael A Schumacher
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California, United States
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States
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15
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Endo R, Sugimoto S, Shirosaki K, Kato H, Wada M, Kanai T, Sato T. Clinical challenges of short bowel syndrome and the path forward for organoid-based regenerative medicine. Regen Ther 2023; 24:64-73. [PMID: 37868721 PMCID: PMC10584670 DOI: 10.1016/j.reth.2023.06.001] [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: 03/31/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 10/24/2023] Open
Abstract
Short bowel syndrome (SBS) is a rare condition, the main symptom of which is malabsorption following extensive resection of the small intestine. Treatment for SBS is mainly supportive, consisting of supplementation, prevention and treatment of complications, and promotion of intestinal adaptation. While development of parenteral nutrition and drugs promoting intestinal adaptation has improved clinical outcomes, the prognosis of patients with SBS remains poor. Intestinal transplantation is the only curative therapy but its outcome is unsatisfactory. In the absence of definitive therapy, novel treatment is urgently needed. With the advent of intestinal organoids, research on the intestine has developed remarkably in recent years. Concepts such as the "tissue-engineered small intestine" and "small intestinalized colon," which create a functional small intestine by combining organoids with other technologies, are potentially novel regenerative therapeutic approaches for SBS. Although they are still under development and there are substantial issues to be resolved, the problems that have prevented establishment of the complex function and structure of the small intestine are gradually being overcome. This review discusses the current treatments for SBS, the fundamentals of the intestine and organoids, the current status of these new technologies, and future perspectives.
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Affiliation(s)
- Ryoma Endo
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Pediatric Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Shinya Sugimoto
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Koji Shirosaki
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hirochika Kato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Motoshi Wada
- Department of Pediatric Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
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16
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Abo H, Sultana MF, Kawashima H. Dual function of angiogenin-4 inducing intestinal stem cells and apoptosis. Front Cell Dev Biol 2023; 11:1181145. [PMID: 38020881 PMCID: PMC10651741 DOI: 10.3389/fcell.2023.1181145] [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: 03/07/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The intestinal epithelium is the first line of host defense, and its homeostasis is dependent on soluble factors that comprise the crypt niche. Antimicrobial proteins are one of the mediators to maintain gut homeostasis. Angiogenin-4 (Ang4) is a member of the ribonuclease A superfamily and plays a pivotal role in antimicrobial activity against gut microbiota. However, the functions of Ang4 within the intestinal crypt niche, particularly its involvement in the development of intestinal epithelial cells (IECs), remain unknown. Here, we demonstrate that Ang4 plays a significant role in maintaining Lgr5+ intestinal stem cells (ISCs) and induces apoptosis of IECs in a concentration-dependent manner. We revealed that Ang4 is highly expressed by Paneth cells in the small intestine, as well as regenerating islet-derived family member-4 (Reg4) expressing goblet cells in the colon, and both cell subsets highly contribute to ISC maintenance. Functional analysis using intestinal organoids revealed that Ang4 induces Wnt and Notch signaling, increases Lgr5+ stem cell expansion, and promotes organoid growth. Furthermore, high concentrations of Ang4 induced apoptosis in the IEC cell line and organoids. Collectively, we propose that Ang4 is a dual functional protein and is a novel member of the crypt niche factor that promotes the expansion of ISCs and induces apoptosis.
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Affiliation(s)
- Hirohito Abo
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Mst. Farzana Sultana
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hiroto Kawashima
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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17
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Verhagen MP, Joosten R, Schmitt M, Valimaki N, Sacchetti A, Rajamaki K, Choi J, Procopio P, Silva S, van der Steen B, van den Bosch TPP, Seinstra D, Doukas M, Augenlicht LH, Aaltonen LA, Fodde R. The origin of intestinal cancer in the context of inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560432. [PMID: 37873142 PMCID: PMC10592905 DOI: 10.1101/2023.10.02.560432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
According to conventional views, colon cancer originates from stem cells. However, inflammation, a key risk factor for colon cancer, was shown to suppress intestinal stemness. Here, we employed Paneth cells (PCs) as a model to assess the capacity of differentiated lineages to trigger tumorigenesis in the context of inflammation. Upon inflammation, PC-specific Apc mutations led to intestinal tumors reminiscent not only of those arising in inflammatory bowel disease (IBD) patients but also of a larger fraction of sporadic colon cancers. The latter is likely due to the inflammatory consequences of Western-style dietary habits, the major colon cancer risk factor. Computational methods designed to predict the cell-of-origin of cancer confirmed that, in a substantial fraction of sporadic colon cancers the cells-of-origin are secretory lineages and not stem cells.
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18
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Brügger MD, Basler K. The diverse nature of intestinal fibroblasts in development, homeostasis, and disease. Trends Cell Biol 2023; 33:834-849. [PMID: 37080817 DOI: 10.1016/j.tcb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023]
Abstract
Only in recent years have we begun to appreciate the involvement of fibroblasts in intestinal development, tissue homeostasis, and disease. These insights followed the advent of single-cell transcriptomics that allowed researchers to explore the heterogeneity of intestinal fibroblasts in unprecedented detail. Since researchers often defined cell types and their associated function based on the biological process they studied, there are a plethora of partially overlapping markers for different intestinal fibroblast populations. This ambiguity complicates putting different research findings into context. Here, we provide a census on the function and identity of intestinal fibroblasts in mouse and human. We propose a simplified framework consisting of three colonic and four small intestinal fibroblast populations to aid navigating the diversity of intestinal fibroblasts.
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Affiliation(s)
- Michael David Brügger
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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19
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Qi Y, He J, Zhang Y, Ge Q, Wang Q, Chen L, Xu J, Wang L, Chen X, Jia D, Lin Y, Xu C, Zhang Y, Hou T, Si J, Chen S, Wang L. Heat-inactivated Bifidobacterium adolescentis ameliorates colon senescence through Paneth-like-cell-mediated stem cell activation. Nat Commun 2023; 14:6121. [PMID: 37777508 PMCID: PMC10542354 DOI: 10.1038/s41467-023-41827-0] [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: 06/14/2022] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Declined numbers and weakened functions of intestinal stem cells (ISCs) impair the integrity of the intestinal epithelium during aging. However, the impact of intestinal microbiota on ISCs in this process is unclear. Here, using premature aging mice (telomerase RNA component knockout, Terc-/-), natural aging mice, and in vitro colonoid models, we explore how heat-inactivated Bifidobacterium adolescentis (B. adolescentis) affects colon senescence. We find that B. adolescentis could mitigate colonic senescence-related changes by enhancing intestinal integrity and stimulating the regeneration of Lgr5+ ISCs via Wnt/β-catenin signaling. Furthermore, we uncover the involvement of Paneth-like cells (PLCs) within the colonic stem-cell-supporting niche in the B. adolescentis-induced ISC regeneration. In addition, we identify soluble polysaccharides (SPS) as potential effective components of B. adolescentis. Overall, our findings reveal the role of heat-inactivated B. adolescentis in maintaining the ISCs regeneration and intestinal barrier, and propose a microbiota target for ameliorating colon senescence.
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Affiliation(s)
- Yadong Qi
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiamin He
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yawen Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiwei Ge
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiwen Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luyi Chen
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jilei Xu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lan Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xueqin Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dingjiacheng Jia
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yifeng Lin
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chaochao Xu
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tongyao Hou
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianmin Si
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Shujie Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Liangjing Wang
- Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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20
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Przybylla R, Krohn M, Sellin ML, Frank M, Oswald S, Linnebacher M. Novel In Vitro Models for Cell Differentiation and Drug Transport Studies of the Human Intestine. Cells 2023; 12:2371. [PMID: 37830585 PMCID: PMC10572004 DOI: 10.3390/cells12192371] [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: 08/28/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
The most common in vitro model for absorption, distribution, metabolism, and excretion (ADME) purposes is currently the Caco-2 cell line. However, clear differences in gene and protein expression towards the small intestine and an, at best, fair prediction accuracy of intestinal drug absorption restrict the usefulness of a model for intestinal epithelial cells. To overcome these limitations, we evaluated a panel of low-passaged patient-derived colorectal cancer cell lines of the HROC collection concerning similarities to small intestinal epithelial cells and their potential to predict intestinal drug absorption. After initial screening of a larger panel, ten cell lines with confluent outgrowth and long-lasting barrier-forming potential were further characterized in close detail. Tight junctional complexes and microvilli structures were detected in all lines, anda higher degree of differentiation was observed in 5/10 cell lines. All lines expressed multiple transporter molecules, with the expression levels in three lines being close to those of small intestinal epithelial cells. Compared with the Caco-2 model, three HROC lines demonstrated both higher similarity to jejunal epithelial tissue cells and higher regulatory potential of relevant drug transporters. In summary, these lines would be better-suited human small intestinal epithelium models for basic and translational research, especially for ADME studies.
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Affiliation(s)
- Randy Przybylla
- Molecular Oncology and Immunotherapy, Clinic of General Surgery, Rostock University Medical Centre, 18057 Rostock, Germany; (R.P.); (M.K.)
| | - Mathias Krohn
- Molecular Oncology and Immunotherapy, Clinic of General Surgery, Rostock University Medical Centre, 18057 Rostock, Germany; (R.P.); (M.K.)
| | - Marie-Luise Sellin
- Research Laboratory for Biomechanics and Implant Technology, Department of Orthopedics, Rostock University Medical Centre, 18057 Rostock, Germany;
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre, 18057 Rostock, Germany;
- Department Life, Light and Matter, University of Rostock, 18059 Rostock, Germany
| | - Stefan Oswald
- Institute of Pharmacology and Toxicology, Rostock University Medical Centre, 18057 Rostock, Germany;
| | - Michael Linnebacher
- Molecular Oncology and Immunotherapy, Clinic of General Surgery, Rostock University Medical Centre, 18057 Rostock, Germany; (R.P.); (M.K.)
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21
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Salm F, Znalesniak EB, Laskou A, Harder S, Schlüter H, Hoffmann W. Expression Profiling along the Murine Intestine: Different Mucosal Protection Systems and Alterations in Tff1-Deficient Animals. Int J Mol Sci 2023; 24:12684. [PMID: 37628863 PMCID: PMC10454331 DOI: 10.3390/ijms241612684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Tff1 is a typical gastric peptide secreted together with the mucin, Muc5ac. Tff1-deficient (Tff1KO) mice are well known for their prominent gastric phenotype and represent a recognized model for antral tumorigenesis. Notably, intestinal abnormalities have also been reported in the past in these animals. Here, we have compared the expression of selected genes in Tff1KO mice and their corresponding wild-type littermates (RT-PCR analyses), focusing on different mucosal protection systems along the murine intestine. As hallmarks, genes were identified with maximum expression in the proximal colon and/or the duodenum: Agr2, Muc6/A4gnt/Tff2, Tff1, Fut2, Gkn2, Gkn3, Duox2/Lpo, Nox1. This is indicative of different protection systems such as Tff2/Muc6, Tff1-Fcgbp, gastrokines, fucosylation, and reactive oxygen species (ROS) in the proximal colon and/or duodenum. Few significant transcriptional changes were observed in the intestine of Tff1KO mice when compared with wild-type littermates, Clca1 (Gob5), Gkn1, Gkn2, Nox1, Tff2. We also analyzed the expression of Tff1, Tff2, and Tff3 in the pancreas, liver, and lung of Tff1KO and wild-type animals, indicating a cross-regulation of Tff gene expression. Furthermore, on the protein level, heteromeric Tff1-Fcgbp and various monomeric Tff1 forms were identified in the duodenum and a high-molecular-mass Tff2/Muc6 complex was identified in the proximal colon (FPLC, proteomics).
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Affiliation(s)
- Franz Salm
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Eva B. Znalesniak
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Aikaterini Laskou
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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22
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Kolev HM, Kaestner KH. Mammalian Intestinal Development and Differentiation-The State of the Art. Cell Mol Gastroenterol Hepatol 2023; 16:809-821. [PMID: 37507088 PMCID: PMC10520362 DOI: 10.1016/j.jcmgh.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
The development of the mammalian intestine, from its earliest origins as a morphologically uniform sheet of endoderm cells during gastrulation into the complex organ system that is essential for the life of the organism, is a truly fascinating process. During midgestation development, reciprocal interactions between endoderm-derived epithelium and mesoderm-derived mesenchyme enable villification, or the conversion of a radially symmetric pseudostratified epithelium into the functional subdivision of crypts and villi. Once a mature crypt-villus axis is established, proliferation and differentiation of new epithelial cells continue throughout life. Spatially localized signals including the wingless and Int-1, fibroblast growth factor, and Hippo systems, among others, ensure that new cells are being born continuously in the crypt. As cells exit the crypt compartment, a gradient of bone morphogenetic protein signaling limits proliferation to allow for the specification of multiple mature cell types. The first major differentiation decision is dependent on Notch signaling, which specifies epithelial cells into absorptive and secretory lineages. The secretory lineage is subdivided further into Paneth, goblet, tuft, and enteroendocrine cells via a complex network of transcription factors. Although some of the signaling molecules are produced by epithelial cells, critical components are derived from specialized crypt-adjacent mesenchymal cells termed telocytes, which are marked by Forkhead box l1, GLI Family Zinc Finger 1, and platelet-derived growth factor receptor α. The crucial nature of these processes is evidenced by the multitude of intestinal disorders such as colorectal cancer, short-bowel syndrome, and inflammatory bowel disease, which all reflect perturbations of the development and/or differentiation of the intestine.
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Affiliation(s)
- Hannah M Kolev
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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23
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Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams TS, Kaminski N, Macosko EZ, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Rep 2023; 42:112412. [PMID: 37086403 PMCID: PMC10242439 DOI: 10.1016/j.celrep.2023.112412] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/26/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Abstract
Most cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at the cell population level, where cells divide labor and specialize in different functions. Division of labor can arise due to instruction by tissue environment or through self-organization. Here, we develop a computational framework to investigate the contribution of these mechanisms to division of labor within a cell-type population. By optimizing collective cellular task performance under trade-offs, we find that distinguishable expression patterns can emerge from cell-cell interactions versus instructive signals. We propose a method to construct ligand-receptor networks between specialist cells and use it to infer division-of-labor mechanisms from single-cell RNA sequencing (RNA-seq) and spatial transcriptomics data of stromal, epithelial, and immune cells. Our framework can be used to characterize the complexity of cell interactions within tissues.
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Affiliation(s)
- Miri Adler
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Noa Moriel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aleksandrina Goeva
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Inbal Avraham-Davidi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Simon Mages
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Evan Z Macosko
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | - Aviv Regev
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ruslan Medzhitov
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, CT, USA; Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel; Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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24
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Cadinu P, Sivanathan KN, Misra A, Xu RJ, Mangani D, Yang E, Rone JM, Tooley K, Kye YC, Bod L, Geistlinger L, Lee T, 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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539701. [PMID: 37214800 PMCID: PMC10197602 DOI: 10.1101/2023.05.08.539701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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 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.
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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
- These authors contributed equally
| | - Kisha N Sivanathan
- Evergrande Center for Immunologic Diseases and 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
- These authors contributed equally
| | - Aditya Misra
- Evergrande Center for Immunologic Diseases and 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
- Evergrande Center for Immunologic Diseases and 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
- Evergrande Center for Immunologic Diseases and 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
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yoon-Chul Kye
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lloyd Bod
- Evergrande Center for Immunologic Diseases and 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
| | - 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
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francisco J Quintana
- Evergrande Center for Immunologic Diseases and 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
- Evergrande Center for Immunologic Diseases and 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
- Evergrande Center for Immunologic Diseases and 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
- Evergrande Center for Immunologic Diseases and 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
- Lead contact
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25
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Hopton RE, Jahahn NJ, Zemper AE. The Role of Lrig1 in the Development of the Colonic Epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539114. [PMID: 37205411 PMCID: PMC10187246 DOI: 10.1101/2023.05.02.539114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Growth and specification of the mouse intestine occurs in utero and concludes after birth. While numerous studies have examined this developmental process in the small intestine, far less is known about the cellular and molecular cues required for colon development. In this study, we examine the morphological events leading to crypt formation, epithelial cell differentiation, areas of proliferation, and the emergence and expression of a stem and progenitor cell marker Lrig1. Through multicolor lineage tracing, we show Lrig1 expressing cells are present at birth and behave as stem cells to establish clonal crypts within three weeks after birth. In addition, we use an inducible knockout mouse to eliminate Lrig1 during colon development and show loss of Lrig1 restrains proliferation within a critical developmental time window, without impacting colonic epithelial cell differentiation. Our study illustrates the morphological changes that occur during crypt development and the importance of Lrig1 in the developing colon.
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26
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Hsu NY, Nayar S, Gettler K, Talware S, Giri M, Alter I, Argmann C, Sabic K, Thin TH, Ko HBM, Werner R, Tastad C, Stappenbeck T, Azabdaftari A, Uhlig HH, Chuang LS, Cho JH. NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell signatures. Gut 2023; 72:654-662. [PMID: 36191961 PMCID: PMC9998338 DOI: 10.1136/gutjnl-2021-326305] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/20/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Loss-of-function mutations in genes generating reactive oxygen species (ROS), such as NOX1, are associated with IBD. Mechanisms whereby loss of ROS drive IBD are incompletely defined. DESIGN ROS measurements and single-cell transcriptomics were performed on colonoids stratified by NOX1 genotype and TNFα stimulation. Clustering of epithelial cells from human UC (inflamed and uninflamed) scRNASeq was performed. Validation of M cell induction was performed by immunohistochemistry using UEA1 (ulex europaeus agglutin-1 lectin) and in vivo with DSS injury. RESULTS TNFα induces ROS production more in NOX1-WT versus NOX1-deficient murine colonoids under a range of Wnt-mediated and Notch-mediated conditions. scRNASeq from inflamed and uninflamed human colitis versus TNFα stimulated, in vitro colonoids defines substantially shared, induced transcription factors; NOX1-deficient colonoids express substantially lower levels of STAT3 (signal transducer and activator of transcription 3), CEBPD (CCAAT enhancer-binding protein delta), DNMT1 (DNA methyltransferase) and HIF1A (hypoxia-inducible factor) baseline. Subclustering unexpectedly showed marked TNFα-mediated induction of M cells (sentinel cells overlying lymphoid aggregates) in NOX1-deficient colonoids. M cell induction by UEA1 staining is rescued with H2O2 and paraquat, defining extra- and intracellular ROS roles in maintenance of LGR5+ stem cells. DSS injury demonstrated GP2 (glycoprotein-2), basal lymphoplasmacytosis and UEA1 induction in NOX1-deficiency. Principal components analyses of M cell genes and decreased DNMT1 RNA velocity correlate with UC inflammation. CONCLUSIONS NOX1 deficiency plus TNFα stimulation contribute to colitis through dysregulation of the stem cell niche and altered cell differentiation, enhancing basal lymphoplasmacytosis. Our findings prioritise ROS modulation for future therapies.
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Affiliation(s)
- Nai-Yun Hsu
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kyle Gettler
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sayali Talware
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai Department of Medicine, New York, New York, USA
- The Icahn Genomic Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Isaac Alter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ksenija Sabic
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tin Htwe Thin
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Huai-Bin Mabel Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Robert Werner
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christopher Tastad
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thaddeus Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, Ohio, USA
| | - Aline Azabdaftari
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Ling-Shiang Chuang
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy H Cho
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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27
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Bastian D, Sui X, Choi HJ, Wu Y, Tian L, Yang K, Liu C, Liu Y, Yu XZ. The Absence of IL-12Rβ2 Expression on Recipient Nonhematopoietic Cells Diminishes Acute Graft-versus-Host Disease in the Gastrointestinal Tract. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:486-495. [PMID: 36548465 PMCID: PMC9938950 DOI: 10.4049/jimmunol.2200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
The gastrointestinal (GI) tract is a frequent target organ in acute graft-versus-host disease (aGVHD), which can determine the morbidity and nonrelapse mortality after allogeneic hematopoietic cell transplantation (allo-HCT). Donor T cells recognize allogeneic Ags presented by host APCs, proliferate, and differentiate into Th1 and Th17 cells that drive GVHD pathogenesis. IL-12 has been shown to play an important role in amplifying the allogeneic response in preclinical and clinical studies. This study demonstrates that IL-12Rβ2 expression on recipient nonhematopoietic cells is required for optimal development of aGVHD in murine models of allo-HCT. aGVHD attenuation by genetic depletion of IL-12R signaling is associated with reduced MHC class II expression by intestinal epithelial cells and maintenance of intestinal integrity. We verified IL-12Rβ2 expression on activated T cells and in the GI tract. This study, to our knowledge, reveals a novel function of IL-12Rβ2 in GVHD pathogenesis and suggests that selectively targeting IL-12Rβ2 on host nonhematopoietic cells may preserve the GI tract after allo-HCT.
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Affiliation(s)
- David Bastian
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Xiaohui Sui
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Hee-Jin Choi
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yongxia Wu
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Linlu Tian
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kaipo Yang
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Yuejun Liu
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Xue-Zhong Yu
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
- The Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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28
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Stromal regulation of the intestinal barrier. Mucosal Immunol 2023; 16:221-231. [PMID: 36708806 DOI: 10.1016/j.mucimm.2023.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/27/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023]
Abstract
The intestinal barrier is a complex structure that allows the absorption of nutrients while ensuring protection against intestinal pathogens and balanced immunity. The development and maintenance of a functional intestinal barrier is a multifactorial process that is only partially understood. Here we review novel findings on the emerging role of mesenchymal cells in this process using insights gained from lineage tracing approaches, Cre-based gene deletion, and single-cell transcriptomics. The current evidence points toward a key organizer role for distinct mesenchymal lineages in intestinal development and homeostasis, regulating both epithelial and immune components of the intestinal barrier. We further discuss recent findings on functional mesenchymal heterogeneity and implications for intestinal regeneration and inflammatory intestinal pathologies.
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29
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Abstract
Reprogrammed metabolism is a hallmark of colorectal cancer (CRC). CRC cells are geared toward rapid proliferation, requiring nutrients and the removal of cellular waste in nutrient-poor environments. Intestinal stem cells (ISCs), the primary cell of origin for CRCs, must adapt their metabolism along the adenoma-carcinoma sequence to the unique features of their complex microenvironment that include interactions with intestinal epithelial cells, immune cells, stromal cells, commensal microbes, and dietary components. Emerging evidence implicates modifiable risk factors related to the environment, such as diet, as important in CRC pathogenesis. Here, we focus on describing the metabolism of ISCs, diets that influence CRC initiation, CRC genetics and metabolism, and the tumor microenvironment. The mechanistic links between environmental factors, metabolic adaptations, and the tumor microenvironment in enhancing or supporting CRC tumorigenesis are becoming better understood. Thus, greater knowledge of CRC metabolism holds promise for improved prevention and treatment.
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Affiliation(s)
- Joseph C Sedlak
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, Massachusetts, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Massachusetts General Hospital, Department of Pathology, Boston, Massachusetts, USA
| | - Jatin Roper
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina, USA;
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
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30
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Verhagen MP, Joosten R, Schmitt M, Sacchetti A, Choi J, Välimäki N, Aaltonen LA, Augenlicht LH, Fodde R. Paneth cells as the origin of intestinal cancer in the context of inflammation. RESEARCH SQUARE 2023:rs.3.rs-2458794. [PMID: 36711533 PMCID: PMC9882659 DOI: 10.21203/rs.3.rs-2458794/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Paneth cells (PCs), responsible for the secretion of antimicrobial peptides in the small intestine and for niche support to Lgr5+ crypt-base columnar stem cells (CBCs), have been shown to respond to inflammation by dedifferentiating into stem-like cells in order to sustain a regenerative response1,2. Therefore, PCs may represent the cells-of-origin of intestinal cancer in the context of inflammation. To test this hypothesis, we targeted Apc, Kras, and Tp53 mutations in Paneth cells by Cre-Lox technology and modelled inflammation by dextran sodium sulfate (DSS) administration. PC-specific loss of Apc resulted in multiple small intestinal tumors, whereas Kras or Tp53 mutations did not. Compound Apc and Kras mutations in PCs resulted in a striking increase in tumor multiplicity even in the absence of the inflammatory insult. By combining scRNAseq with lineage tracing to capture the conversion of PCs into bona fide tumor cells, we show that they progress through a "revival stem cell" (RSC) state characterized by high Clusterin (Clu) expression and Yap1 signaling, reminiscent of what has been previously observed upon irradiation of the mouse digestive tract3. Accordingly, comparison of PC- and Lgr5-derived murine intestinal tumors revealed differences related to Wnt signaling and inflammatory pathways which match the dichotomy of CBCs and injury-induced RSCs4 between human sporadic colon cancers and those arising in the context of inflammatory bowel diseases. Last, we show that western-style dietary habits, known to trigger a low-grade inflammation throughout the intestinal tract, underlie the analogous dedifferentiation of Paneth cells and their acquisition of stem-like features. Taken together, our results show that intestinal cancer arises in the context of inflammation through the dedifferentiation of committed secretory lineages such as Paneth cells and the activation of the revival stem cell state. As such, a true quiescent stem cell identity may be hidden in fully committed and postmitotic lineages which, upon inflammation, support the regenerative response by re-entering the cell cycle and dedifferentiating into RSCs. The chronic nature of the tissue insult in inflammatory bowel diseases and even in the context of western-style dietary habits is likely to result in the expansion of cell targets for tumor initiation and progression.
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Affiliation(s)
- Mathijs P. Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rosalie Joosten
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark Schmitt
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Institute of Pharmacology, University of Marburg, Germany
| | - Andrea Sacchetti
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, U.S.A
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Lauri A. Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Wiarda JE, Becker SR, Sivasankaran SK, Loving CL. Regional epithelial cell diversity in the small intestine of pigs. J Anim Sci 2023; 101:skac318. [PMID: 36183288 PMCID: PMC9831138 DOI: 10.1093/jas/skac318] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023] Open
Abstract
Understanding regional distribution and specialization of small intestinal epithelial cells is crucial for developing methods to control appetite, stress, and nutrient uptake in swine. To establish a better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. EE cells were divided into two subsets based on the level of expression of the EE lineage commitment gene, NEUROD1. NEUROD1hi EE cells had minimal expression of hormone-encoding genes and were dissimilar to EE cells in humans and mice, indicating a subset of EE cells unique to pigs. Recently discovered BEST4 enterocytes were detected in both crypts and villi throughout the small intestine via in situ staining, unlike in humans, where BEST4 enterocytes are found only in small intestinal villi. Proximal-to-distal gradients of expression were noted for hormone-encoding genes in EE cells and nutrient transport genes in enterocytes via scRNA-seq, demonstrating regional specialization. Regional gene expression in EE cells and enterocytes was validated via quantitative PCR (qPCR) analysis of RNA isolated from epithelial cells of different small intestinal locations. Though many genes had similar patterns of regional expression when assessed by qPCR of total epithelial cells, some regional expression was only detected via scRNA-seq, highlighting advantages of scRNA-seq to deconvolute cell type-specific regional gene expression when compared to analysis of bulk samples. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.
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Affiliation(s)
- Jayne E Wiarda
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
- Immunobiology Graduate Program, Iowa State University, Ames, IA, USA
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, USA
| | - Sage R Becker
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
- Immunobiology Graduate Program, Iowa State University, Ames, IA, USA
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Sathesh K Sivasankaran
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
- Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Crystal L Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
- Immunobiology Graduate Program, Iowa State University, Ames, IA, USA
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32
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Videlock EJ, Hatami A, Zhu C, Kawaguchi R, Chen H, Khan T, Yehya AHS, Stiles L, Joshi S, Hoffman JM, Law KM, Rankin CR, Chang L, Maidment NT, John V, Geschwind DH, Pothoulakis C. Distinct Patterns of Gene Expression Changes in the Colon and Striatum of Young Mice Overexpressing Alpha-Synuclein Support Parkinson's Disease as a Multi-System Process. JOURNAL OF PARKINSON'S DISEASE 2023; 13:1127-1147. [PMID: 37638450 PMCID: PMC10657720 DOI: 10.3233/jpd-223568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Evidence supports a role for the gut-brain axis in Parkinson's disease (PD). Mice overexpressing human wild type α- synuclein (Thy1-haSyn) exhibit slow colonic transit prior to motor deficits, mirroring prodromal constipation in PD. Identifying molecular changes in the gut could provide both biomarkers for early diagnosis and gut-targeted therapies to prevent progression. OBJECTIVE To identify early molecular changes in the gut-brain axis in Thy1-haSyn mice through gene expression profiling. METHODS Gene expression profiling was performed on gut (colon) and brain (striatal) tissue from Thy1-haSyn and wild-type (WT) mice aged 1 and 3 months using 3' RNA sequencing. Analysis included differential expression, gene set enrichment and weighted gene co-expression network analysis (WGCNA). RESULTS At one month, differential expression (Thy1-haSyn vs. WT) of mitochondrial genes and pathways related to PD was discordant between gut and brain, with negative enrichment in brain (enriched in WT) but positive enrichment in gut. Linear regression of WGCNA modules showed partial independence of gut and brain gene expression changes. Thy1-haSyn-associated WGCNA modules in the gut were enriched for PD risk genes and PD-relevant pathways including inflammation, autophagy, and oxidative stress. Changes in gene expression were modest at 3 months. CONCLUSIONS Overexpression of haSyn acutely disrupts gene expression in the colon. While changes in colon gene expression are highly related to known PD-relevant mechanisms, they are distinct from brain changes, and in some cases, opposite in direction. These findings are in line with the emerging view of PD as a multi-system disease.
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Affiliation(s)
- Elizabeth J. Videlock
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Asa Hatami
- The Drug Discovery Lab, Mary S. Easton Center for Alzheimer’s Disease Research, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chunni Zhu
- The Drug Discovery Lab, Mary S. Easton Center for Alzheimer’s Disease Research, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Riki Kawaguchi
- The Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Han Chen
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Tasnin Khan
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ashwaq Hamid Salem Yehya
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Linsey Stiles
- Department of Medicine, Division of Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Swapna Joshi
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Jill M. Hoffman
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ka Man Law
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Carl Robert Rankin
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Lin Chang
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Nigel T. Maidment
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Varghese John
- The Drug Discovery Lab, Mary S. Easton Center for Alzheimer’s Disease Research, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Daniel H. Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Charalabos Pothoulakis
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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McCarthy H, Keely S. Re-evaluating the Role of Deep Crypt Secretory Cells in Intestinal Homeostasis. Cell Mol Gastroenterol Hepatol 2023; 15:1020-1021. [PMID: 36781071 PMCID: PMC10040954 DOI: 10.1016/j.jcmgh.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023]
Affiliation(s)
- Huw McCarthy
- School of Biomedical Science and Pharmacy, NHMCR Centre for Research Excellence, University of Newcastle, Callaghan, NSW, Australia; Immune Health Program Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Simon Keely
- School of Biomedical Science and Pharmacy, NHMCR Centre for Research Excellence, University of Newcastle, Callaghan, NSW, Australia; Immune Health Program Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
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Su X, Jin M, Xu C, Gao Y, Yang Y, Qi H, Zhang Q, Yang X, Ya W, Zhang Y, Yang R. FABP4 in Paneth cells regulates antimicrobial protein expression to reprogram gut microbiota. Gut Microbes 2022; 14:2139978. [PMID: 36519446 PMCID: PMC9635462 DOI: 10.1080/19490976.2022.2139978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial proteins possess a broad spectrum of bactericidal activity and play an important role in shaping the composition of gut microbiota, which is related to multiple diseases such as metabolic syndrome. However, it is incompletely known for the regulation of defensin expression in the gut Paneth cells. Here, we found that FABP4 in the Paneth cells of gut epithelial cells and organoids can downregulate the expression of defensins. FABP4fl/flpvillinCreT mice were highly resistance to Salmonella Typhimurium (S.T) infection and had increased bactericidal ability to pathogens. The FABP4-mediated downregulation of defensins is through degrading PPARγ after K48 ubiquitination. We also demonstrate that high-fat diet (HFD)-mediated downregulation of defensins is through inducing a robust FABP4 in Paneth cells. Firmicutes/Bacteroidetes (F/B) ratio in FABP4fl/flpvillinCreT mice is lower than control mice, which is opposite to that in mice fed HFD, indicating that FABP4 in the Paneth cells could reprogram gut microbiota. Interestingly, FABP4-mediated downregulation of defensins in Paneth cells not only happens in mice but also in human. A better understanding of the regulation of defensins, especially HFD-mediated downregulation of defensin in Paneth cells will provide insights into factor(s) underlying modern diseases.Abbreviations: FABP4: Fatty acid binding protein 4; S. T: Salmonella Typhimurium; HFD: High-fat diet; Defa: α-defensin; 930 HD5: Human α-defensin 5; HD6: Human α-defensin 6; F/B: Firmicutes/Bacteroidetes; SFB: Segmental filamentous bacteria; AMPs: Antimicrobial peptides; PPARγ: Peroxisome proliferator-activated receptor γ; P-PPAR: Phosphorylated PPAR; Dhx15: DEAD-box helicase 15; 935 EGF: Epidermal growth factor; ENR: Noggin and R-spondin 1; CFU: Colony forming unit; Lyz1: Lysozyme 1; Saa1: Serum amyoid A 1; Pla2g2a: Phospholipase A2, group IIA; MMP-7: Matrix metalloproteinase; AU-PAGE: Acid-urea polyacrylamide gel electrophoresis; PA: Palmitic 940 acid; GPR40: G-protein-coupled receptor; GF: Germ-free; EGF: Epidermal growth factor; LP: Lamina propria; KO: Knock out; WT: Wild-type.
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Affiliation(s)
- Xiaomin Su
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China
| | - Mengli Jin
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Chen Xu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Yunhuan Gao
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Yazheng Yang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Houbao Qi
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Qianjing Zhang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Xiaorong Yang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Wang Ya
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China
| | - Yuan Zhang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Rongcun Yang
- Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin, China,Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Tianjin, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China,CONTACT Rongcun Yang Department of Immunology, Nankai University School of Medicine; Nankai University, Tianjin300071, China
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Schumacher MA, Liu CY, Katada K, Thai MH, Hsieh JJ, Hansten BJ, Waddell A, Rosen MJ, Frey MR. Deep Crypt Secretory Cell Differentiation in the Colonic Epithelium Is Regulated by Sprouty2 and Interleukin 13. Cell Mol Gastroenterol Hepatol 2022; 15:971-984. [PMID: 36414210 PMCID: PMC9982040 DOI: 10.1016/j.jcmgh.2022.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND & AIMS Deep crypt secretory (DCS) cells are a critical component of the colonic stem cell niche. However, the regulatory mechanisms controlling DCS cell numbers and function are not well understood. Sprouty2 is an inflammation-responsive regulator of intracellular signaling that influences colonic secretory cell numbers in colitis via an epithelial-stromal interleukin (IL)33/IL13 signaling loop. Here, we tested the hypothesis that IL13, induced by epithelial Sprouty2 down-regulation, promotes DCS cell differentiation and function. METHODS Distal colons from mice with an intestinal epithelial-specific Sprouty2 deletion (Spry2ΔIE) and littermate controls were analyzed by in situ hybridization for Reg4+ DCS cells. Single-cell RNA sequencing and immunostaining were used to identify DCS cell-derived host defense peptides (HDPs) and localization of IL13 and IL13 receptor; bulk RNA sequencing and quantitative polymerase chain reaction were used to quantify changes in expression of identified HDPs. Cytokine-treated colonoids were assessed for DCS cells. A requirement for an IL33/IL13 signaling loop in the regulation of DCS cells was assessed in vivo using IL13 null mice. RESULTS Reg4+ DCS cell numbers were increased 2-fold in distal colons of Spry2ΔIE mice with a concomitant overall increase in DCS cell marker expression (Reg4, Spink4, and Agr2). Single-cell transcriptomics showed the HDP Retnlb/Resistin Like Beta (RELMβ) is highly enriched in DCS cells. Retnlb/RELMβ expression was increased in Spry2ΔIE colons. IL13, but not IL33, induced Reg4 and Retnlb expression in colonic epithelial organoids, and IL33-mediated expansion of the DCS cell population in vivo was dependent on IL13, which was expressed predominantly by type II innate lymphoid cells in the colonic mucosa. CONCLUSIONS Sprouty2 limits colonic DCS cell differentiation through suppression of IL13 signaling. At homeostasis, DCS cells are marked by high levels of the HDP RELMβ. Loss of epithelial Sprouty2 activates type II innate lymphoid cells to release IL13, promoting expansion of the DCS cell population and increased colonic RELMβ levels.
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Affiliation(s)
- Michael A Schumacher
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California; The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California.
| | - Cambrian Y Liu
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kay Katada
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Megan H Thai
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Jonathan J Hsieh
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Britany J Hansten
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Amanda Waddell
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Michael J Rosen
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Mark R Frey
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California; The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, California.
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36
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Fujishita T, Kojima Y, Kajino-Sakamoto R, Mishiro-Sato E, Shimizu Y, Hosoda W, Yamaguchi R, Taketo MM, Aoki M. The cAMP/PKA/CREB and TGFβ/SMAD4 Pathways Regulate Stemness and Metastatic Potential in Colorectal Cancer Cells. Cancer Res 2022; 82:4179-4190. [PMID: 36066360 DOI: 10.1158/0008-5472.can-22-1369] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/28/2022] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE This study identifies signaling pathways essential for maintaining the stemness and metastatic potential of colorectal cancer cells and proposes CREB as a therapeutic target in metastatic colorectal cancer.
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Affiliation(s)
- Teruaki Fujishita
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Yasushi Kojima
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Rie Kajino-Sakamoto
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Emi Mishiro-Sato
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Yasuhiro Shimizu
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Aichi, Japan
| | - Waki Hosoda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Aichi, Japan
| | - Rui Yamaguchi
- Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan.,Department of Cancer Informatics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Makoto Mark Taketo
- Colon Cancer Project, Kyoto University Hospital-iACT, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Masahiro Aoki
- Division of Pathophysiology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan.,Department of Cancer Physiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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37
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Jelinsky SA, Derksen M, Bauman E, Verissimo CS, van Dooremalen WTM, Roos JL, Higuera Barón C, Caballero-Franco C, Johnson BG, Rooks MG, Pott J, Oldenburg B, Vries RGJ, Boj SF, Kasaian MT, Pourfarzad F, Rosadini CV. Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier. Inflamm Bowel Dis 2022; 29:195-206. [PMID: 36356046 PMCID: PMC9890212 DOI: 10.1093/ibd/izac212] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Patient-derived organoid (PDO) models offer potential to transform drug discovery for inflammatory bowel disease (IBD) but are limited by inconsistencies with differentiation and functional characterization. We profiled molecular and cellular features across a range of intestinal organoid models and examined differentiation and establishment of a functional epithelial barrier. METHODS Patient-derived organoids or monolayers were generated from control or IBD patient-derived colon or ileum and were molecularly or functionally profiled. Biological or technical replicates were examined for transcriptional responses under conditions of expansion or differentiation. Cell-type composition was determined by deconvolution of cell-associated gene signatures and histological features. Differentiated control or IBD-derived monolayers were examined for establishment of transepithelial electrical resistance (TEER), loss of barrier integrity in response to a cocktail of interferon (IFN)-γ and tumor necrosis factor (TNF)-α, and prevention of cytokine-induced barrier disruption by the JAK inhibitor, tofacitinib. RESULTS In response to differentiation media, intestinal organoids and monolayers displayed gene expression patterns consistent with maturation of epithelial cell types found in the human gut. Upon differentiation, both colon- and ileum-derived monolayers formed functional barriers, with sustained TEER. Barrier integrity was compromised by inflammatory cytokines IFN-γ and TNF-α, and damage was inhibited in a dose-dependent manner by tofacitinib. CONCLUSIONS We describe the generation and characterization of human colonic or ileal organoid models capable of functional differentiation to mature epithelial cell types. In monolayer culture, these cells formed a robust epithelial barrier with sustained TEER and responses to pharmacological modulation. Our findings demonstrate that control and IBD patient-derived organoids possess consistent transcriptional and functional profiles that can enable development of epithelial-targeted therapies.
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Affiliation(s)
| | | | - Eric Bauman
- Pfizer Worldwide Research, Development, and Medical, Cambridge, MA, USA
| | | | | | | | | | | | - Bryce G Johnson
- Pfizer Worldwide Research, Development, and Medical, Cambridge, MA, USA
| | - Michelle G Rooks
- Pfizer Worldwide Research, Development, and Medical, Cambridge, MA, USA
| | | | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | | | - Marion T Kasaian
- Pfizer Worldwide Research, Development, and Medical, Cambridge, MA, USA
| | | | - Charles V Rosadini
- Address correspondence to: Charles V. Rosadini, PhD, Inflammation and Immunology, Research Unit, Pfizer Worldwide Research, Development, and Medical, 1 Portland Street, Cambridge, MA, 02139, USA ()
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38
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Liu TC, Kalugin PN, Wilding JL, Bodmer WF. GMMchi: gene expression clustering using Gaussian mixture modeling. BMC Bioinformatics 2022; 23:457. [PMID: 36324085 PMCID: PMC9632092 DOI: 10.1186/s12859-022-05006-0] [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: 02/22/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Cancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer types suggests the existence of certain "driver mutations," which likely make up the major contribution to tumors' selective advantages over surrounding normal tissue and as such are responsible for the most consequential aspects of the cancer cells' gene expression patterns and phenotypes. We hypothesize that such mutations are likely to cluster with specific dichotomous shifts in the expression of the genes they most closely control, and propose GMMchi, a Python package that leverages Gaussian Mixture Modeling to detect and characterize bimodal gene expression patterns across cancer samples, as a tool to analyze such correlations using 2 × 2 contingency table statistics. RESULTS Using well-defined simulated data, we were able to confirm the robust performance of GMMchi, reaching 85% accuracy with a sample size of n = 90. We were also able to demonstrate a few examples of the application of GMMchi with respect to its capacity to characterize background florescent signals in microarray data, filter out uninformative background probe sets, as well as uncover novel genetic interrelationships and tumor characteristics. Our approach to analysing gene expression analysis in cancers provides an additional lens to supplement traditional continuous-valued statistical analysis by maximizing the information that can be gathered from bulk gene expression data. CONCLUSIONS We confirm that GMMchi robustly and reliably extracts bimodal patterns from both colorectal cancer (CRC) cell line-derived microarray and tumor-derived RNA-Seq data and verify previously reported gene expression correlates of some well-characterized CRC phenotypes. AVAILABILITY The Python package GMMchi and our cell line microarray data used in this paper is available for downloading on GitHub at https://github.com/jeffliu6068/GMMchi .
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Affiliation(s)
- Ta-Chun Liu
- grid.4991.50000 0004 1936 8948Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - Peter N. Kalugin
- grid.4991.50000 0004 1936 8948Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA 02115 USA
| | - Jennifer L. Wilding
- grid.4991.50000 0004 1936 8948Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - Walter F. Bodmer
- grid.4991.50000 0004 1936 8948Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
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Zheng L, Duan SL, Wen XL, Dai YC. Molecular regulation after mucosal injury and regeneration in ulcerative colitis. Front Mol Biosci 2022; 9:996057. [PMID: 36310594 PMCID: PMC9606627 DOI: 10.3389/fmolb.2022.996057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/26/2022] [Indexed: 12/02/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic nonspecific inflammatory disease with a complex etiology. Intestinal mucosal injury is an important pathological change in individuals with UC. Leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5+) intestinal stem cells (ISCs) exhibit self-renewal and high differentiation potential and play important roles in the repair of intestinal mucosal injury. Moreover, LGR5+ ISCs are intricately regulated by both the Wnt/β-catenin and Notch signaling pathways, which jointly maintain the function of LGR5+ ISCs. Combination therapy targeting multiple signaling pathways and transplantation of LGR5+ ISCs may lead to the development of new clinical therapies for UC.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an, Shaanxi Province, China
| | - Sheng-Lei Duan
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an, Shaanxi Province, China
| | - Xin-Li Wen
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an, Shaanxi Province, China
| | - Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yan-Cheng Dai,
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40
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Xiang LW, Xue H, Ha MW, Yu DY, Xiao LJ, Zheng HC. The effects of REG4 expression on chemoresistance of ovarian cancer. J OBSTET GYNAECOL 2022; 42:3149-3157. [PMID: 35929918 DOI: 10.1080/01443615.2022.2106834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Although ovarian cancer usually responds well to platinum- and taxane-based first-line chemotherapy, most patients develop recurrence and chemoresistance. Regenerating gene 4 (REG4) is a secretory protein involved in cell differentiation and proliferation. We found higher REG4 expression in ovarian cancer than in normal tissues (p < .05). Regenerating gene 4 expression was negatively associated with overall, progression-free or post-progression survival rates of patients with ovarian cancer receiving platinum or paclitaxel treatment (p < .05) according to a Kaplan-Meier plotter. Regenerating gene 4 overexpression resulted in either cisplatin or paclitaxel resistance, and apoptosis resistance in CAOV3 ovarian cancer cells (p < .05). REG4-transfected ovarian cancer cells showed stronger migration and invasion treated with cisplatin or paclitaxel (p < .05). Additionally, cisplatin or paclitaxel exposure led to the overexpression of phosphorylated phosphoinositide 3-kinase (p-PI3K), p-Akt, phosphorylated mammalian target of rapamycin (p-mTOR), glutathione S-transferase-π, survivin, and B-cell lymphoma 2 in REG4 transfectants compared with control cells (p < .05). These findings suggested that REG4 expression was up-regulated in ovarian cancer, and associated with poor survival and chemotherapy resistance. REG4 promoted the occurrence, development, and chemotherapy resistance of ovarian cancer by regulating cell proliferation, apoptosis, migration, and invasion, and PI3K/Akt/m-TOR signalling pathways. IMPACT STATEMENTWhat is already known on this subject? REG4 mRNA expression is up-regulated in many digestive cancers. High REG4 expression was associated with an adverse prognosis, high tumour and nodal stages, poor differentiation, and hepatic and peritoneal metastases of digestive cancers. REG4 expression conferred cancer cells with increased resistance to chemoradiotherapy, especially 5-FU-based treatment, by activating the MAPK/Erk/Bim signalling pathway.What do the results of this study add? REG4 was highly expressed in ovarian cancer. The expression of p-PI3K, p-AKT, p-mTOR, GST-π, survivin, and Bcl-2 was increased in REG4-overexpressing cells. High REG4 expression was significantly associated with inferior OS, PFS, and PPS rates in patients with ovarian cancer receiving platinum chemotherapy. REG4 mediated cisplatin and paclitaxel resistance in CAOV3 ovarian cancer cells. The percentage of apoptotic cells was markedly lower in REG4-transfected compared to mock-transfected cells after cisplatin or paclitaxel treatment.What are the implications of these findings for clinical practice and/or further research? This study aimed to evaluate the prognostic significance of REG4 expression in ovarian cancer treated with platinum and paclitaxel, to explore REG4 chemoresistance mechanisms to platinum and paclitaxel, and to provide a scientific experimental basis for the clinical treatment and outcome evaluation of ovarian cancer. In order to provide comprehensive clinical treatment of ovarian cancer, it is helpful to improve our understanding of multi-drug resistance and identify new cancer diagnostic biomarkers.
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Affiliation(s)
- Li-Wei Xiang
- Department of Oncology and Experimental Center, The Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Hang Xue
- Department of Oncology and Experimental Center, The Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Min-Wen Ha
- Cancer Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Da-Yong Yu
- Department of Cell Biology, Basic Medicine College of Chengde Medical University, Chengde, China
| | - Li-Jun Xiao
- Department of Immunology, Basic Medicine College of Chengde Medical University, Chengde, China
| | - Hua-Chuan Zheng
- Department of Oncology and Experimental Center, The Affiliated Hospital of Chengde Medical University, Chengde, China
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Oda M, Hatano Y, Sato T. Intestinal epithelial organoids: regeneration and maintenance of the intestinal epithelium. Curr Opin Genet Dev 2022; 76:101977. [PMID: 36058061 DOI: 10.1016/j.gde.2022.101977] [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: 05/30/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022]
Abstract
Vital functions of the intestines: digestion, absorption, and surface barrier are performed by the intestinal epithelium, which consists of various differentiated cells and intestinal stem cells. Recent technological advances in sequencing technology, including single-cell transcriptomics and epigenetic analysis, have facilitated the genetic characterization of diverse intestinal epithelial cell types and surrounding mesenchymal niche environments. Organoids have allowed biological analysis of the human intestinal epithelium in coordination with genome engineering, genetic lineage tracing, and transplantation into orthotopic tissue. Together, these technologies have prompted the development of organoid-based regenerative therapies for intestinal diseases, including short-bowel syndrome. This article provides an overview of the current understanding of intestinal epithelial self-renewal during homeostasis and regeneration and provides a perspective for future organoid medicine.
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Affiliation(s)
- Mayumi Oda
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Yoshiko Hatano
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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Ectopically Localized Epithelial Cell Clumps in Ulcers Are Derived from Reserved Crypt Stem Cells in a Mouse Model of Ulcerative Colitis. Dig Dis Sci 2022; 67:4770-4779. [PMID: 35088188 DOI: 10.1007/s10620-021-07340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND We previously reported that clumps of a few epithelial cells were scattered in ulcer regions in a dextran sulfate sodium (DSS)-induced mouse model of ulcerative colitis (UC). AIMS To determine the ectopically localized epithelial clumps might be derived from stem cells or their daughter progenitor cells. METHODS Female BALB/c mice were administered DSS in drinking water for 6 days, followed by withdrawal of DSS for 6 days. Histological and immunohistochemical examinations were conducted in the distal region and proximal region of the colorectum to determine expression of stem cell markers in the epithelial clumps. RESULTS Similar to the characteristics of UC, the ulcers were more severe in the distal region close to the anus than in the proximal region of the colorectum. Quantitative analyses revealed that the epithelial clumps appeared in relation to the severity of the ulcer, and they expressed the cell adhesion molecules E-cadherin and β-catenin. Among stem cell markers, the epithelial clumps primarily expressed +5 cell marker Dll1 as reserved intestinal stem cells, followed by +4 cell marker Bmi1 and crypt stem cell marker Lgr5 in that order. Nuclear expression of Sox9, but not nuclear β-catenin, was identified in the clumps. CONCLUSION The present results suggest that most epithelial clumps comprised crypt-derived, reserved stem cells, which might have potential for mucosal healing.
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Zheng HC, Xue H, Zhang CY. REG4 promotes the proliferation and anti-apoptosis of cancer. Front Cell Dev Biol 2022; 10:1012193. [PMID: 36172286 PMCID: PMC9511136 DOI: 10.3389/fcell.2022.1012193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022] Open
Abstract
Regenerating islet-derived 4 (REG4) gene was discovered by high-throughput sequencing of ulcerative colitis cDNA libraries. REG4 is involved in infection and inflammation by enhancing macrophage polarization to M2, via activation of epidermal growth factor receptor (EGFR)/Akt/cAMP-responsive element binding and the killing inflammatory Escherichia coli, and closely linked to tumorigenesis. Its expression was transcriptionally activated by caudal type homeobox 2, GATA binding protein 6, GLI family zinc finger 1, SRY-box transcription factor 9, CD44 intracytoplasmic domain, activating transcription factor 2, and specificity protein 1, and translationally activated by miR-24. REG4 can interact with transmembrane CD44, G protein-coupled receptor 37, mannan and heparin on cancer cells. Its overexpression was observed in gastric, colorectal, pancreatic, gallbladder, ovarian and urothelial cancers, and is closely linked to their aggressive behaviors and a poor prognosis. Additionally, REG4 expression and recombinant REG4 aggravated such cellular phenotypes as tumorigenesis, proliferation, anti-apoptosis, chemoradioresistance, migration, invasion, peritoneal dissemination, tumor growth, and cancer stemness via EGFR/Akt/activator protein-1 and Akt/glycogen synthase kinase three β/β-catenin/transcription factor 4 pathways. Sorted REG4-positive deep crypt secretory cells promote organoid formation of single Lgr5 (+) colon stem cells by Notch inhibition and Wnt activation. Histologically, REG4 protein is specifically expressed in neuroendocrine tumors and signet ring cell carcinomas of the gastrointestinal tract, pancreas, ovary, and lung. It might support the histogenesis of gastric intestinal–metaplasia–globoid dysplasia–signet ring cell carcinoma. In this review, we summarized the structure, biological functions, and effects of REG4 on inflammation and cancer. We conclude that REG4 may be employed as a biomarker of tumorigenesis, subsequent progression and poor prognosis of cancer, and may be a useful target for gene therapy.
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Affiliation(s)
- Hua-Chuan Zheng
- Department of Oncology and Central Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, China
- *Correspondence: Hua-Chuan Zheng,
| | - Hang Xue
- Department of Oncology and Central Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Cong-Yu Zhang
- Cancer Center, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
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44
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Ferguson N, Cogswell A, Barker E. Contribution of Innate Lymphoid Cells in Supplementing Cytokines Produced by CD4 + T Cells During Acute and Chronic SIV Infection of the Colon. AIDS Res Hum Retroviruses 2022; 38:709-725. [PMID: 35459417 PMCID: PMC9514600 DOI: 10.1089/aid.2022.0007] [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] [Indexed: 01/25/2023] Open
Abstract
HIV/SIV (simian immunodeficiency virus) infection leads to a loss of CD4+ T helper (Th) cells in number and function that begins during the acute phase and persists through the chronic phase of infection. In particular, there is a drastic decrease of Th17 and Th22 cells in the HIV/SIV-infected gastrointestinal (GI) tract as a source of interleukin (IL)-17 and IL-22. These cytokines are vital in the immune response to extracellular pathogens and maintenance of the GI tract. However, innate lymphoid cells (ILCs) are a source of IL-17 and IL-22 during the early stages of an immune response in mucosal tissue and remain vital cytokine producers when the immune response is persistent. Here, we wanted to determine whether ILCs are a source of IL-17 and IL-22 in the SIV-infected colon and could compensate for the loss of Th17 and Th22 cells. As a control, we evaluated the frequency and number of ILCs expressing interferon-gamma (IFNγ) and tumor necrosis factor-alpha (TNFα). We determined the frequency and number of cytokine expressing ILC subsets and T cell subsets within leukocytes from the colons of uninfected as well as acute and chronic SIV-infected colons without in vitro mitogenic stimulation. In the present study, we find that: (1) the frequency of IL-22, IFNγ, and TNFα but not IL-17 producing ILCs is increased in the acutely infected colon and remains high during the chronically infected colon relative to cytokine expressing ILCs in the uninfected colon, (2) ILCs are a significant source of IL-22, IFNγ, and TNFα but not IL-17 when CD4+ T lymphocytes in the gut lose their capacity to secrete these cytokines during SIV infection, and (3) the changes in the cytokines expressed by ILCs relative to CD4+ T cells in the infected colon were not due to increases in the frequency or number of ILCs in relation to T lymphocytes found in the tissue.
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Affiliation(s)
- Natasha Ferguson
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, USA
| | - Andrew Cogswell
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, USA
| | - Edward Barker
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois, USA
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45
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Takasawa S, Tsuchida C, Sakuramoto-Tsuchida S, Uchiyama T, Makino M, Yamauchi A, Itaya-Hironaka A. Upregulation of REG IV gene in human intestinal epithelial cells by lipopolysaccharide via downregulation of microRNA-24. J Cell Mol Med 2022; 26:4710-4720. [PMID: 35946046 PMCID: PMC9443949 DOI: 10.1111/jcmm.17498] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 01/10/2023] Open
Abstract
The pathophysiology of inflammatory bowel diseases (IBD) reflects a balance between mucosal injury and reparative mechanisms. Some regenerating gene (Reg) family members (REG Iα, REG Iβ and REG IV) are expressed in Crohn's disease (CD) and ulcerative colitis (UC) and involved as proliferative mucosal factors in IBD. We revealed that REG Iα and REG Iβ were induced in cell culture system by IL‐6/IL‐22. Although REG IV was upregulated in IBD biopsy samples, the upregulation of REG IV was not at all induced in cell culture by autoimmune‐related cytokines such as IL‐6, IL‐22 and TNFα. Here, we analysed REG IV expression in LS‐174 T and HT‐29 human intestinal epithelial cells by real‐time RT–PCR and elisa. REG IV expression was induced by lipopolysaccharide (LPS). However, LPS did not activate REG IV promoter activity. As the LPS‐induced upregulation of REG IV was considered to be regulated post‐transcriptionally, we searched targeted microRNA (miR), which revealed that REG IV mRNA has a potential target sequence for miR‐24. We measured the miR‐24 level of LPS‐treated cells and found that the level was significantly lower. The LPS‐induced increase of REG IV mRNA was abolished by the introduction of miR‐24 mimic but not by non‐specific control RNA.
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Affiliation(s)
- Shin Takasawa
- Department of Biochemistry, Nara Medical University, Kashihara, Japan
| | | | | | - Tomoko Uchiyama
- Department of Biochemistry, Nara Medical University, Kashihara, Japan.,Department of Diagnostic Pathology, Nara Medical University, Kashihara, Japan
| | - Mai Makino
- Department of Biochemistry, Nara Medical University, Kashihara, Japan
| | - Akiyo Yamauchi
- Department of Biochemistry, Nara Medical University, Kashihara, Japan
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Goto N, Goto S, Imada S, Hosseini S, Deshpande V, Yilmaz ÖH. Lymphatics and fibroblasts support intestinal stem cells in homeostasis and injury. Cell Stem Cell 2022; 29:1246-1261.e6. [PMID: 35931033 PMCID: PMC9720889 DOI: 10.1016/j.stem.2022.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/20/2022] [Accepted: 06/22/2022] [Indexed: 01/19/2023]
Abstract
Lgr5+ intestinal stem cells (ISCs) depend on niche factors for their proper function. However, the source of these ISC niche factors and how they support ISCs in vivo remain controversial. Here, we report that ISCs depend on lymphatic endothelial cells (LECs) and RSPO3+GREM1+ fibroblasts (RGFs). In the intestine and colon, LECs are surrounded by RGFs and are located near ISCs at the crypt base. Both LECs and RGFs provide the critical ISC niche factor RSPO3 to support ISCs, where RSPO3 loss in both cell types drastically compromises ISC numbers, villi length, and repair after injury. In response to injury, LEC and RGF numbers expand and produce greater amounts of RSPO3 and other growth/angiocrine factors to foster intestinal repair. We propose that LECs represent a novel niche component for ISCs, which together with RGFs serve as the major in vivo RSPO3 source for ISCs in homeostasis and injury-mediated regeneration.
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Affiliation(s)
- Norihiro Goto
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA,Correspondence:
(N.G.), (Ö.H.Y.)
| | - Saori Goto
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA
| | - Shinya Imada
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA
| | - Sahar Hosseini
- Department of Pathology, Massachusetts General Hospital and
Harvard Medical School, Boston, MA 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and
Harvard Medical School, Boston, MA 02114, USA
| | - Ömer H. Yilmaz
- Department of Biology, The David H. Koch Institute for
Integrative Cancer Research at MIT, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital and
Harvard Medical School, Boston, MA 02114, USA,Lead contact,Correspondence:
(N.G.), (Ö.H.Y.)
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Villablanca EJ, Selin K, Hedin CRH. Mechanisms of mucosal healing: treating inflammatory bowel disease without immunosuppression? NATURE REVIEWS. GASTROENTEROLOGY & HEPATOLOGY 2022. [PMID: 35440774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Almost all currently available treatments for inflammatory bowel disease (IBD) act by inhibiting inflammation, often blocking specific inflammatory molecules. However, given the infectious and neoplastic disease burden associated with chronic immunosuppressive therapy, the goal of attaining mucosal healing without immunosuppression is attractive. The absence of treatments that directly promote mucosal healing and regeneration in IBD could be linked to the lack of understanding of the underlying pathways. The range of potential strategies to achieve mucosal healing is diverse. However, the targeting of regenerative mechanisms has not yet been achieved for IBD. Stem cells provide hope as a regenerative treatment and are used in limited clinical situations. Growth factors are available for the treatment of short bowel syndrome but have not yet been applied in IBD. The therapeutic application of organoid culture and stem cell therapy to generate new intestinal tissue could provide a novel mechanism to restore barrier function in IBD. Furthermore, blocking key effectors of barrier dysfunction (such as MLCK or damage-associated molecular pattern molecules) has shown promise in experimental IBD. Here, we review the diversity of molecular targets available to directly promote mucosal healing, experimental models to identify new potential pathways and some of the anticipated potential therapies for IBD.
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Affiliation(s)
- Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - Katja Selin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte R H Hedin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden. .,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
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48
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Villablanca EJ, Selin K, Hedin CRH. Mechanisms of mucosal healing: treating inflammatory bowel disease without immunosuppression? Nat Rev Gastroenterol Hepatol 2022; 19:493-507. [PMID: 35440774 DOI: 10.1038/s41575-022-00604-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Almost all currently available treatments for inflammatory bowel disease (IBD) act by inhibiting inflammation, often blocking specific inflammatory molecules. However, given the infectious and neoplastic disease burden associated with chronic immunosuppressive therapy, the goal of attaining mucosal healing without immunosuppression is attractive. The absence of treatments that directly promote mucosal healing and regeneration in IBD could be linked to the lack of understanding of the underlying pathways. The range of potential strategies to achieve mucosal healing is diverse. However, the targeting of regenerative mechanisms has not yet been achieved for IBD. Stem cells provide hope as a regenerative treatment and are used in limited clinical situations. Growth factors are available for the treatment of short bowel syndrome but have not yet been applied in IBD. The therapeutic application of organoid culture and stem cell therapy to generate new intestinal tissue could provide a novel mechanism to restore barrier function in IBD. Furthermore, blocking key effectors of barrier dysfunction (such as MLCK or damage-associated molecular pattern molecules) has shown promise in experimental IBD. Here, we review the diversity of molecular targets available to directly promote mucosal healing, experimental models to identify new potential pathways and some of the anticipated potential therapies for IBD.
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Affiliation(s)
- Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - Katja Selin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte R H Hedin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden. .,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
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Deng F, Wu Z, Zou F, Wang S, Wang X. The Hippo–YAP/TAZ Signaling Pathway in Intestinal Self-Renewal and Regeneration After Injury. Front Cell Dev Biol 2022; 10:894737. [PMID: 35927987 PMCID: PMC9343807 DOI: 10.3389/fcell.2022.894737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/23/2022] [Indexed: 11/23/2022] Open
Abstract
The Hippo pathway and its downstream effectors, the transcriptional coactivators Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), control stem cell fate and cell proliferation and differentiation and are essential for tissue self-renewal and regeneration. YAP/TAZ are the core components of the Hippo pathway and they coregulate transcription when localized in the nucleus. The intestinal epithelium undergoes well-regulated self-renewal and regeneration programs to maintain the structural and functional integrity of the epithelial barrier. This prevents luminal pathogen attack, and facilitates daily nutrient absorption and immune balance. Inflammatory bowel disease (IBD) is characterized by chronic relapsing inflammation of the entire digestive tract. Impaired mucosal healing is a prominent biological feature of IBD. Intestinal self-renewal is primarily dependent on functional intestinal stem cells (ISCs), especially Lgr5+ crypt base columnar (CBC) cells and transient-amplifying (TA) cells in the crypt base. However, intestinal wound healing is a complicated process that is often associated with epithelial cells, and mesenchymal and immune cells in the mucosal microenvironment. Upon intestinal injury, nonproliferative cells rapidly migrate towards the wound bed to reseal the damaged epithelium, which is followed by cell proliferation and differentiation. YAP is generally localized in the nucleus of Lgr5+ CBC cells, where it transcriptionally regulates the expression of the ISC marker Lgr5 and plays an important role in intestinal self-renewal. YAP/TAZ are the primary mechanical sensors of the cellular microenvironment. Their functions include expanding progenitor and stem cell populations, reprogramming differentiated cells into a primitive state, and mediating the regenerative function of reserve stem cells. Thus, YAP/TAZ play extremely crucial roles in epithelial repair after damage. This review provides an overview of the Hippo–YAP/TAZ signaling pathway and the processes of intestinal self-renewal and regeneration. In particular, we summarize the roles of YAP/TAZ in the phases of intestinal self-renewal and regeneration to suggest a potential strategy for IBD treatment.
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Affiliation(s)
- Feihong Deng
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Center of Digestive Disease, Central South University, Changsha, China
- *Correspondence: Feihong Deng, ; Xuehong Wang,
| | - Zengrong Wu
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Center of Digestive Disease, Central South University, Changsha, China
| | - Fei Zou
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Center of Digestive Disease, Central South University, Changsha, China
| | - Su Wang
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Center of Digestive Disease, Central South University, Changsha, China
| | - Xuehong Wang
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Center of Digestive Disease, Central South University, Changsha, China
- *Correspondence: Feihong Deng, ; Xuehong Wang,
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Chen L, Meng Q, Li S, Jiang Y, Zhang C, Tang S, Zhong R, Tang X, Zhang S, Feng X, Zhao Y, Zhang H. Multi-Omics Uncover Neonatal Cecal Cell Development Potentials. Front Cell Dev Biol 2022; 10:840298. [PMID: 35912104 PMCID: PMC9334561 DOI: 10.3389/fcell.2022.840298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
Although, the cecum plays vital roles in absorption of water, electrolytes, and other small molecules, and harbors trillions of commensal bacteria to shape large intestine immune functions, it is unknown the cecum development potentials at single cell level during the very crucial neonatal developmental period. Using singe cell RNA-seq and proteomics, we have characterized six major types of cecal cells: undifferentiated cells; immune cells (Ims); cecumocytes (CCs); goblet, Paneth like cells (PLCs), and enteroendocrine cells (EECs) with specific markers. CCs mature with a gradual decrease in proportion of cells; however, Ims develop with a continuing increase in proportion of cells. Meanwhile, goblet and EEC cells reduced in proportion of cells from do to d14 or d21; PLCs increased in proportion of cells from d0 to d7 then decreased at d14 and d21. The cells exhibit specific development and maturation trends controlled by transcriptional factors, ligand-receptor pairs, and other factors. As piglets grow, cecal content and mucosal microbial diversity increases dramatically with population of beneficial microbiota, such as lactobacillus. Moreover, cecal mucosal-associated and cecal content microbiota are positively correlated and both show significant correlation with different types of cecal cells and plasma metabolites. This is the first presentation of neonatal cecal cell development and maturation naturally at single cell level with transcript, protein, microbiota and metabolism perspectives. Furthermore, this study provides an important tool for the determination of novel interventions in cecal drug delivery and metabolism studies.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shen Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Jiang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanlong Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, NY, United States
| | - Xiaohui Feng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yong Zhao, ; Hongfu Zhang,
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yong Zhao, ; Hongfu Zhang,
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