1
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Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nat Cell Biol 2024; 26:250-262. [PMID: 38321203 DOI: 10.1038/s41556-023-01337-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 12/13/2023] [Indexed: 02/08/2024]
Abstract
A key aspect of nutrient absorption is the exquisite division of labour across the length of the small intestine, with individual nutrients taken up at different proximal:distal positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum and ileum. By examining the fine-scale longitudinal transcriptional patterns that span the mouse and human small intestine, we instead identified five domains of nutrient absorption that mount distinct responses to dietary changes, and three regional stem cell populations. Molecular domain identity can be detected with machine learning, which provides a systematic method to computationally identify intestinal domains in mice. We generated a predictive model of transcriptional control of domain identity and validated the roles of Ppar-δ and Cdx1 in patterning lipid metabolism-associated genes. These findings represent a foundational framework for the zonation of absorption across the mammalian small intestine.
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Affiliation(s)
- Rachel K Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Petr Kasparek
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Brisa Palikuqi
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Viragova
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Weichselbaum
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Kara L McKinley
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Asoka Rathnayake
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dedeepya Vaka
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Vinh Nguyen
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Coralie Trentesaux
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Efren Reyes
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander R Gupta
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Chan Zuckerberg BioHub and Center for Cellular Construction 94158, University of California San Francisco, San Francisco, CA, USA
| | - Richard M Locksley
- Department of Medicine and Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - James M Gardner
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA.
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2
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Reyes EA, Castillo-Azofeifa D, Rispal J, Wald T, Zwick RK, Palikuqi B, Mujukian A, Rabizadeh S, Gupta AR, Gardner JM, Boffelli D, Gartner ZJ, Klein OD. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis. J Clin Invest 2023; 133:e163591. [PMID: 37643009 PMCID: PMC10575728 DOI: 10.1172/jci163591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
The gastrointestinal tract relies on the production, maturation, and transit of mucin to protect against pathogens and to lubricate the epithelial lining. Although the molecular and cellular mechanisms that regulate mucin production and movement are beginning to be understood, the upstream epithelial signals that contribute to mucin regulation remain unclear. Here, we report that the inflammatory cytokine tumor necrosis factor (TNF), generated by the epithelium, contributes to mucin homeostasis by regulating both cell differentiation and cystic fibrosis transmembrane conductance regulator (CFTR) activity. We used genetic mouse models and noninflamed samples from patients with inflammatory bowel disease (IBD) undergoing anti-TNF therapy to assess the effect of in vivo perturbation of TNF. We found that inhibition of epithelial TNF promotes the differentiation of secretory progenitor cells into mucus-producing goblet cells. Furthermore, TNF treatment and CFTR inhibition in intestinal organoids demonstrated that TNF promotes ion transport and luminal flow via CFTR. The absence of TNF led to slower gut transit times, which we propose results from increased mucus accumulation coupled with decreased luminal fluid pumping. These findings point to a TNF/CFTR signaling axis in the adult intestine and identify epithelial cell-derived TNF as an upstream regulator of mucin homeostasis.
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Affiliation(s)
- Efren A. Reyes
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
- Department of Pharmaceutical Chemistry and TETRAD Program, UCSF, San Francisco, California, USA
| | - David Castillo-Azofeifa
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
- Department of Regenerative Medicine, Genentech, Inc., South San Francisco, California, USA
| | - Jérémie Rispal
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Tomas Wald
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Rachel K. Zwick
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Brisa Palikuqi
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shervin Rabizadeh
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, Los Angeles, California, USA
| | | | - James M. Gardner
- Department of Surgery, and
- Diabetes Center, UCSF, San Francisco, California, USA
- Chan-Zuckerberg Biohub, San Francisco, California, USA
- The Center for Cellular Construction, San Francisco, California, USA
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, Los Angeles, California, USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry and TETRAD Program, UCSF, San Francisco, California, USA
| | - Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, Los Angeles, California, USA
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3
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Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. bioRxiv 2023:2023.09.20.558726. [PMID: 37790430 PMCID: PMC10542170 DOI: 10.1101/2023.09.20.558726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar-ẟ and Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.
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4
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Childs CJ, Holloway EM, Sweet CW, Tsai YH, Wu A, Vallie A, Eiken MK, Capeling MM, Zwick RK, Palikuqi B, Trentesaux C, Wu JH, Pellón-Cardenas O, Zhang CJ, Glass I, Loebel C, Yu Q, Camp JG, Sexton JZ, Klein OD, Verzi MP, Spence JR. EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids. JCI Insight 2023; 8:e165566. [PMID: 36821371 PMCID: PMC10070114 DOI: 10.1172/jci.insight.165566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Epithelial organoids derived from intestinal tissue, called enteroids, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Here, we interrogated the cell signaling environment within the developing human intestine to identify niche cues that may be important for epithelial development and homeostasis. We identified an EGF family member, EPIREGULIN (EREG), which is robustly expressed in the developing human crypt. Enteroids generated from the developing human intestine grown in standard culture conditions, which contain EGF, are dominated by stem and progenitor cells and feature little differentiation and no spatial organization. Our results demonstrate that EREG can replace EGF in vitro, and EREG leads to spatially resolved enteroids that feature budded and proliferative crypt domains and a differentiated villus-like central lumen. Multiomic (transcriptome plus epigenome) profiling of native crypts, EGF-grown enteroids, and EREG-grown enteroids showed that EGF enteroids have an altered chromatin landscape that is dependent on EGF concentration, downregulate the master intestinal transcription factor CDX2, and ectopically express stomach genes, a phenomenon that is reversible. This is in contrast to EREG-grown enteroids, which remain intestine like in culture. Thus, EREG creates a homeostatic intestinal niche in vitro, enabling interrogation of stem cell function, cellular differentiation, and disease modeling.
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Affiliation(s)
- Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Caden W. Sweet
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Yu-Hwai Tsai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Angeline Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Abigail Vallie
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Meghan M. Capeling
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Rachel K. Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Brisa Palikuqi
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Coralie Trentesaux
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Joshua H. Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
| | - Oscar Pellón-Cardenas
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ian Glass
- Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
- Department of Materials Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Qianhui Yu
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - J. Gray Camp
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Jonathan Z. Sexton
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael P. Verzi
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, and
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan Medical School and University of Michigan College of Engineering, Ann Arbor, Michigan, USA
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5
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Sullivan ZA, Khoury-Hanold W, Lim J, Smillie C, Biton M, Reis BS, Zwick RK, Pope SD, Israni-Winger K, Parsa R, Philip NH, Rashed S, Palm N, Wang A, Mucida D, Regev A, Medzhitov R. γδ T cells regulate the intestinal response to nutrient sensing. Science 2021; 371:eaba8310. [PMID: 33737460 DOI: 10.1126/science.aba8310] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 11/02/2020] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
The intestine is a site of direct encounter with the external environment and must consequently balance barrier defense with nutrient uptake. To investigate how nutrient uptake is regulated in the small intestine, we tested the effect of diets with different macronutrient compositions on epithelial gene expression. We found that enzymes and transporters required for carbohydrate digestion and absorption were regulated by carbohydrate availability. The "on-demand" induction of this machinery required γδ T cells, which regulated this program through the suppression of interleukin-22 production by type 3 innate lymphoid cells. Nutrient availability altered the tissue localization and transcriptome of γδ T cells. Additionally, transcriptional responses to diet involved cellular remodeling of the epithelial compartment. Thus, this work identifies a role for γδ T cells in nutrient sensing.
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Affiliation(s)
- Zuri A Sullivan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Jaechul Lim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Chris Smillie
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Rachel K Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Scott D Pope
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, New Haven, CT, USA
| | - Kavita Israni-Winger
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Naomi H Philip
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Saleh Rashed
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Noah Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Division of Rheumatology, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Ruslan Medzhitov
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, New Haven, CT, USA
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6
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Zwick RK, Ohlstein B, Klein OD. Intestinal renewal across the animal kingdom: comparing stem cell activity in mouse and Drosophila. Am J Physiol Gastrointest Liver Physiol 2019; 316:G313-G322. [PMID: 30543448 PMCID: PMC6415738 DOI: 10.1152/ajpgi.00353.2018] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The gastrointestinal (GI) tract renews frequently to sustain nutrient digestion and absorption in the face of consistent tissue stress. In many species, proliferative intestinal stem cells (ISCs) are responsible for the repair of the damage arising from chemical and mechanical aspects of food breakdown and exposure to pathogens. As the cellular source of all mature cell types of the intestinal epithelium throughout adulthood, ISCs hold tremendous therapeutic potential for understanding and treating GI disease in humans. This review focuses on recent advances in our understanding of ISC identity, behavior, and regulation during homeostasis and injury-induced repair, as revealed by two major animal models used to study regeneration of the small intestine: Drosophila melanogaster and Mus musculus. We emphasize recent findings from Drosophila that are likely to translate to the mammalian GI system, as well as challenging topics in mouse ISC biology that may be ideally suited for investigation in flies. For context, we begin by reviewing major physiological similarities and distinctions between the Drosophila midgut and mouse small intestine.
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Affiliation(s)
- Rachel K. Zwick
- 1Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, California
| | - Benjamin Ohlstein
- 2Department of Genetics and Development, Columbia University Medical Center, New York, New York
| | - Ophir D. Klein
- 1Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, California,3Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, California
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7
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Shook BA, Wasko RR, Rivera Gonzalez GC, Salazar-Gatzimas E, López-Giráldez F, Dash BC, Muñoz-Rojas AR, Aultman KD, Zwick RK, Lei V, Arbiser JL, Miller-Jensen K, Clark DA, Hsia HC, Horsley V. Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair. Science 2018; 362:362/6417/eaar2971. [PMID: 30467144 PMCID: PMC6684198 DOI: 10.1126/science.aar2971] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 07/20/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022]
Abstract
During tissue repair, myofibroblasts produce extracellular matrix (ECM) molecules for tissue resilience and strength. Altered ECM deposition can lead to tissue dysfunction and disease. Identification of distinct myofibroblast subsets is necessary to develop treatments for these disorders. We analyzed profibrotic cells during mouse skin wound healing, fibrosis, and aging and identified distinct subpopulations of myofibroblasts, including adipocyte precursors (APs). Multiple mouse models and transplantation assays demonstrate that proliferation of APs but not other myofibroblasts is activated by CD301b-expressing macrophages through insulin-like growth factor 1 and platelet-derived growth factor C. With age, wound bed APs and differential gene expression between myofibroblast subsets are reduced. Our findings identify multiple fibrotic cell populations and suggest that the environment dictates functional myofibroblast heterogeneity, which is driven by fibroblast-immune interactions after wounding.
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Affiliation(s)
- Brett A. Shook
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA,Corresponding Author. (B.A.S.); (V.H.)
| | - Renee R. Wasko
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | | | | | | | - Biraja C. Dash
- Department of Surgery (Plastic), Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Krystal D. Aultman
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Rachel K. Zwick
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Vivian Lei
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Jack L. Arbiser
- Department of Dermatology, Atlanta Veterans Administration Health Center, Emory University, Atlanta, GA 30322, USA
| | - Kathryn Miller-Jensen
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA,Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Damon A. Clark
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06511, USA
| | - Henry C. Hsia
- Department of Surgery (Plastic), Yale School of Medicine, New Haven, CT 06510, USA
| | - Valerie Horsley
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA. .,Department of Dermatology, Yale University, New Haven, CT 06511, USA
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8
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Zwick RK, Rudolph MC, Shook BA, Holtrup B, Roth E, Lei V, Van Keymeulen A, Seewaldt V, Kwei S, Wysolmerski J, Rodeheffer MS, Horsley V. Adipocyte hypertrophy and lipid dynamics underlie mammary gland remodeling after lactation. Nat Commun 2018; 9:3592. [PMID: 30181538 PMCID: PMC6123393 DOI: 10.1038/s41467-018-05911-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/30/2018] [Indexed: 12/23/2022] Open
Abstract
Adipocytes undergo pronounced changes in size and behavior to support diverse tissue functions, but the mechanisms that control these changes are not well understood. Mammary gland-associated white adipose tissue (mgWAT) regresses in support of milk fat production during lactation and expands during the subsequent involution of milk-producing epithelial cells, providing one of the most marked physiological examples of adipose growth. We examined cellular mechanisms and functional implications of adipocyte and lipid dynamics in the mouse mammary gland (MG). Using in vivo analysis of adipocyte precursors and genetic tracing of mature adipocytes, we find mature adipocyte hypertrophy to be a primary mechanism of mgWAT expansion during involution. Lipid tracking and lipidomics demonstrate that adipocytes fill with epithelial-derived milk lipid. Furthermore, ablation of mgWAT during involution reveals an essential role for adipocytes in milk trafficking from, and proper restructuring of, the mammary epithelium. This work advances our understanding of MG remodeling and tissue-specific roles for adipocytes.
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Affiliation(s)
- Rachel K Zwick
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA
| | - Michael C Rudolph
- Division of Endocrinology, Metabolism, and Diabetes, University of Colorado, Mail Stop F-8305; RC1 North, 12800 E. 19th Avenue P18-5107, Aurora, CO, 80045, USA
| | - Brett A Shook
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA
| | - Brandon Holtrup
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA
| | - Eve Roth
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA
| | - Vivian Lei
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA
| | - Alexandra Van Keymeulen
- WELBIO, Interdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles (ULB), 808, route de Lennik, BatC, C6-130, 1070, Brussels, Belgium
| | - Victoria Seewaldt
- Department of Population Sciences and Bekman Institute, City of Hope, 1500 East Duarte Rd., Duarte, CA, 91010, USA
| | - Stephanie Kwei
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University, 333 Ceder St., New Haven, CT, 06510, USA
| | - John Wysolmerski
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University, 333 Ceder St., New Haven, CT, 06510, USA
| | - Matthew S Rodeheffer
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University, 333 Ceder St., New Haven, CT, 06510, USA
| | - Valerie Horsley
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect St., New Haven, CT, 06520, USA.
- Department of Dermatology, Yale University, 333 Ceder St., New Haven, CT, 06510, USA.
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9
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Abstract
Adipose tissue depots can exist in close association with other organs, where they assume diverse, often non-traditional functions. In stem cell-rich skin, bone marrow, and mammary glands, adipocytes signal to and modulate organ regeneration and remodeling. Skin adipocytes and their progenitors signal to hair follicles, promoting epithelial stem cell quiescence and activation, respectively. Hair follicles signal back to adipocyte progenitors, inducing their expansion and regeneration, as in skin scars. In mammary glands and heart, adipocytes supply lipids to neighboring cells for nutritional and metabolic functions, respectively. Adipose depots adjacent to skeletal structures function to absorb mechanical shock. Adipose tissue near the surface of skin and intestine senses and responds to bacterial invasion, contributing to the body's innate immune barrier. As the recognition of diverse adipose depot functions increases, novel therapeutic approaches centered on tissue-specific adipocytes are likely to emerge for a range of cancers and regenerative, infectious, and autoimmune disorders.
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Affiliation(s)
- Rachel K Zwick
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Christian F Guerrero-Juarez
- Department of Developmental and Cell Biology, University of California, Irvine, 845 Health Sciences Road, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Valerie Horsley
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA; Department of Dermatology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, 845 Health Sciences Road, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
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Shaykhiev R, Wang R, Zwick RK, Hackett NR, Leung R, Moore MAS, Sima CS, Chao IW, Downey RJ, Strulovici-Barel Y, Salit J, Crystal RG. Airway basal cells of healthy smokers express an embryonic stem cell signature relevant to lung cancer. Stem Cells 2014; 31:1992-2002. [PMID: 23857717 DOI: 10.1002/stem.1459] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/09/2013] [Accepted: 04/27/2013] [Indexed: 12/30/2022]
Abstract
Activation of the human embryonic stem cell (hESC) signature genes has been observed in various epithelial cancers. In this study, we found that the hESC signature is selectively induced in the airway basal stem/progenitor cell population of healthy smokers (BC-S), with a pattern similar to that activated in all major types of human lung cancer. We further identified a subset of 6 BC-S hESC genes, whose coherent overexpression in lung adenocarcinoma (AdCa) was associated with reduced lung function, poorer differentiation grade, more advanced tumor stage, remarkably shorter survival, and higher frequency of TP53 mutations. BC-S shared with hESC and a considerable subset of lung carcinomas a common TP53 inactivation molecular pattern which strongly correlated with the BC-S hESC gene expression. These data provide transcriptome-based evidence that smoking-induced reprogramming of airway BC toward the hESC-like phenotype might represent a common early molecular event in the development of aggressive lung carcinomas in humans.
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Affiliation(s)
- Renat Shaykhiev
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York
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11
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Zwick RK, Schmidt BA. Pushing the boundaries: the development of super-resolution microscopy at yale and beyond: an interview with Derek Toomre, PhD. Yale J Biol Med 2014; 87:55-62. [PMID: 24600336 PMCID: PMC3941448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rachel K. Zwick
- To whom all correspondence should be addressed: Rachel Zwick, Yale University, Department of Molecular, Cellular, and Developmental Biology, Kline Biology Tower, 219 Prospect St., New Haven, CT 06520; Tele: 203-432-3482;
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12
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Zwick RK, Schmidt BA. When Anton van Leeuwenhoek looked through his early microscopes in the 1600s, he realized that the world was teeming with microbial organisms. Introduction. Yale J Biol Med 2014; 87:1. [PMID: 24741749 PMCID: PMC3941459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rachel K. Zwick
- To whom all correspondence should be addressed: Rachel Zwick, Yale University, Department of Molecular, Cellular, and Developmental Biology, Kline Biology Tower, 219 Prospect St., New Haven, CT 06520; Tele: 203-432-3482;
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13
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Didon L, Zwick RK, Chao IW, Walters MS, Wang R, Hackett NR, Crystal RG. RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium. Respir Res 2013; 14:70. [PMID: 23822649 PMCID: PMC3710277 DOI: 10.1186/1465-9921-14-70] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/10/2013] [Indexed: 11/30/2022] Open
Abstract
Background Ciliated cells play a central role in cleansing the airways of inhaled contaminants. They are derived from basal cells that include the airway stem/progenitor cells. In animal models, the transcription factor FOXJ1 has been shown to induce differentiation to the ciliated cell lineage, and the RFX transcription factor-family has been shown to be necessary for, but not sufficient to induce, correct cilia development. Methods To test the hypothesis that FOXJ1 and RFX3 cooperatively induce expression of ciliated genes in the differentiation process of basal progenitor cells toward a ciliated cell linage in the human airway epithelium, primary human airway basal cells were assessed under conditions of in vitro differentiation induced by plasmid-mediated gene transfer of FOXJ1 and/or RFX3. TaqMan PCR was used to quantify mRNA levels of basal, secretory, and cilia-associated genes. Results Basal cells, when cultured in air-liquid interface, differentiated into a ciliated epithelium, expressing FOXJ1 and RFX3. Transfection of FOXJ1 into resting basal cells activated promoters and induced expression of ciliated cell genes as well as both FOXJ1 and RFX3, but not basal cell genes. Transfection of RFX3 induced expression of RFX3 but not FOXJ1, nor the expression of cilia-related genes. The combination of FOXJ1 + RFX3 enhanced ciliated gene promoter activity and mRNA expression beyond that due to FOXJ1 alone. Corroborating immunoprecipitation studies demonstrated an interaction between FOXJ1 and RFX3. Conclusion FOXJ1 is an important regulator of cilia gene expression during ciliated cell differentiation, with RFX3 as a transcriptional co-activator to FOXJ1, helping to induce the expression of cilia genes in the process of ciliated cell differentiation of basal/progenitor cells.
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Affiliation(s)
- Lukas Didon
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USA
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14
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Hackett NR, Shaykhiev R, Walters MS, Wang R, Zwick RK, Ferris B, Witover B, Salit J, Crystal RG. The human airway epithelial basal cell transcriptome. PLoS One 2011; 6:e18378. [PMID: 21572528 PMCID: PMC3087716 DOI: 10.1371/journal.pone.0018378] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 03/05/2011] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population. METHODOLOGY/PRINCIPAL FINDINGS Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the "human airway basal cell signature" as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels. CONCLUSION/SIGNIFICANCE The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium.
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Affiliation(s)
- Neil R. Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Renat Shaykhiev
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Matthew S. Walters
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Rui Wang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Rachel K. Zwick
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Barbara Ferris
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Bradley Witover
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
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15
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Fukui T, Shaykhiev R, Wang R, Zwick RK, Hackett NR, Downey RJ, Crystal RG. Abstract 4721: Airway basal cell signature predicts aggressive phenotype of human lung adenocarcinoma. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Molecular changes in the airway epithelium are central to the pathogenesis of lung cancer. Human airway epithelium is composed of 4 major cell types including ciliated, columnar, secretory and basal cells (BC), with the BC representing the stem/progenitor population. Although BC have been considered as putative tumor-initiating cells of squamous cell lung carcinoma, there is little evidence with regard to the contribution of BC to human lung adenocarcinoma (ADC). Given that a subset of smokers develop ADC and smoking increases BC proliferation, we hypothesized that BC-associated molecular features are enriched in ADC smokers contributing to a distinct, more aggressive clinical phenotype. BC were purified from the freshly isolated airway epithelium of healthy individuals by a cell culture-based method. Genome-wide gene expression analyses of BC (n=4 nonsmokers; n=4 smokers) compared with the intact large airway epithelium (LAE; n=21 nonsmokers; n=31 smokers) were performed separately for nonsmokers and smokers using HG-U133 Plus 2.0 array to identify the normal and smoking-associated BC signatures, respectively, based on the following criteria: (1) P call of “Present” in ≥50% of BC samples; (2) p<0.01 with Benjamini-Hochberg correction; and (3) >5-fold higher expression level in BC vs complete airway epithelium. ADC samples (n=167) were derived from patients undergoing lung resection. ADC genes related to smoking status were identified by genome-wide comparison of ADC smokers (ADC-S; n=131) and ADC nonsmokers (ADC-NS; n=36). Multivariate survival analysis was performed using Cox proportional hazards model. The BC signature included 1,623 and 2,408 probe sets in healthy nonsmokers and smokers, respectively. Among the ADC-S up-regulated genes, 44% (46 of 105) overlapped with BC signature genes, including 32 smoking-associated BC signature genes compared to 25 BC signature genes among 614 ADC-NS up-regulated genes (4%). ADC patients with high expression of the ADC-S up-regulated BC signature (n=97) exhibited a distinct clinical phenotype with a poorer tumor differentiation grade (p<0.001), lower frequency of prognostically favorable bronchoalveolar carcinoma features (p<0.02), shorter survival (p<0.002) and higher frequency of TP53 mutations (p<0.002) compared to ADC patients with low expression of the BC signature genes (n=70). Human airway BC signature is enriched in ADC in association with smoking status and aggressive clinical phenotype consistent with the hypothesis that airway BC represent a putative cell-of-origin and hence, a therapeutic target for a subset of aggressive lung ADC associated with smoking.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4721. doi:10.1158/1538-7445.AM2011-4721
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Affiliation(s)
| | | | - Rui Wang
- 1Weill Cornell Medical College, New York, NY
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