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Aquino LVCD, Olindo SL, Silva YLFE, Oliveira LRMD, Moura YBF, Rodrigues ALR, Praxedes ÉA, Oliveira MFD, Silva AR, Pereira AF. Cryopreservation and passaging optimization for Galea spixii (Wagler, 1831) adult skin fibroblast lines: A step forward in species management and genetic studies. Acta Histochem 2024; 126:152185. [PMID: 39059228 DOI: 10.1016/j.acthis.2024.152185] [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: 03/22/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND In vitro culture of fibroblasts is a technique based on cell isolation, physiological characterization, and cryopreservation. This technique has not been described for Galea spixii, therefore, it can be used to learn about its cellular biology and genetic diversity. OBJECTIVE We established fibroblast lines of six G. spixii individuals from several passages (second, fifth, eighth, and tenth) and cryopreserved them. METHODS Fibroblasts recovered from skin biopsies were identified based on morphology, immunocytochemistry, and karyotyping. The cells were analyzed for morphology, ultrastructure, viability, proliferation, metabolism, oxidative stress, bioenergetic potential, and apoptosis before and after cryopreservation. RESULTS After the eighth passage, the fibroblasts showed morphological and karyotypic changes, although their viability, metabolism, and proliferation did not change. An increase in oxidative stress and bioenergetic potential from the fifth to the eighth passages were also observed. Post cryopreservation, cell damage with respect to the ultrastructure, viability, proliferative rate, apoptotic levels, oxidative stress, and bioenergetic potential were verified. CONCLUSION Fibroblasts up to the tenth passage could be cultured in vitro. However, cells at the fifth passage were of better quality to be used for reproductive techniques. Additionally, optimization of the cryopreservation protocol is essential to improve the physiological parameters of these cells.
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Affiliation(s)
| | - Samara Lima Olindo
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, RN, Brazil.
| | | | | | | | | | - Érika Almeida Praxedes
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, RN, Brazil. erikaalmeida-@hotmail.com
| | - Moacir Franco de Oliveira
- Laboratory of Applied Animal Morphophysiology, Federal Rural University of Semi-Arid, Mossoró, RN, Brazil.
| | - Alexandre Rodrigues Silva
- Laboratory of Animal Germplasma Conservation, Federal Rural University of Semi-Arid, Mossoró, RN, Brazil.
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Honan AM, Jacobsen GE, Drum H, Vazquez EN, Quintero MA, Deshpande AR, Sussman DA, Kerman DH, Damas OM, Proksell S, Van der Jeught K, Abreu MT, Chen Z. Stromal-Like Cells Are Found in Peripheral Blood of Patients With Inflammatory Bowel Disease and Correlate With Immune Activation State. Clin Transl Gastroenterol 2024; 15:e1. [PMID: 38829958 DOI: 10.14309/ctg.0000000000000721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
INTRODUCTION Recent studies have identified a critical role of stromal-immune cell interactions in immunity and immune tolerance. Transcriptomic profiling has implicated stromal cells in immune-mediated disorders including the 2 common forms of inflammatory bowel disease (IBD), Crohn's disease (CD), and ulcerative colitis (UC). Stromal-immune interactions may edify inflammatory state and the development of IBD-related complications such as fibrosis, yet the lack of protein markers has hampered studying stromal-immune perturbation. METHODS In this study, we designed a 40-color spectral flow cytometry assay to characterize hematopoietic and nonhematopoietic cells in intestinal biopsies and matched blood samples from patients with CD or UC. RESULTS We identified circulating stromal-like cells that are significantly more abundant in IBD blood samples than in healthy controls. Those cells expressed podoplanin (PDPN), a commonly used marker for fibroblasts, and they were associated with activated and memory T and B cells and altered natural killer cell, monocyte, and macrophage populations. PDPN + cells in the blood correlated with PDPN + cells in the colon. Principal component analysis distinctly separated healthy blood samples from IBD blood samples, with stromal-like cells and B-cell subtypes dominating the IBD signature; Pearson correlation detected an association between PDPN + stromal-like cells and B-cell populations in IBD blood and gut biopsies. DISCUSSION These observations suggest that PDPN + cells in the blood may serve as a biomarker of IBD. Understanding the relationship between stromal cells and immune cells in the intestine and the blood may provide a window into disease pathogenesis and insight into therapeutic targets for IBD.
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Affiliation(s)
- Amanda M Honan
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Gillian E Jacobsen
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
- Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Hannah Drum
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Emily N Vazquez
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Maria A Quintero
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
| | - Amar R Deshpande
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
| | - Daniel A Sussman
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - David H Kerman
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
| | - Oriana M Damas
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
| | - Siobhan Proksell
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
| | - Kevin Van der Jeught
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Maria T Abreu
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
- Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami-Miller School of Medicine, Miami, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Zhibin Chen
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
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Gill HK, Yin S, Nerurkar NL, Lawlor JC, Lee C, Huycke TR, Mahadevan L, Tabin CJ. Hox gene activity directs physical forces to differentially shape chick small and large intestinal epithelia. Dev Cell 2024:S1534-5807(24)00449-0. [PMID: 39116876 DOI: 10.1016/j.devcel.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 04/15/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024]
Abstract
Hox transcription factors play crucial roles in organizing developmental patterning across metazoa, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of intestinal subregions early in embryogenesis, which ultimately leads to their specialization in both form and function. Although the midgut forms villi, the hindgut develops sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements of the embryonic chick intestine and mathematical modeling, we demonstrate that the posterior Hox gene HOXD13 regulates biophysical phenomena that shape the hindgut lumen. We further show that HOXD13 acts through the transforming growth factor β (TGF-β) pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme-together, these features lead to hindgut-specific surface buckling. TGF-β, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional identity that direct posterior intestinal morphogenesis.
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Affiliation(s)
- Hasreet K Gill
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sifan Yin
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Nandan L Nerurkar
- The Fu Foundation School of Engineering and Applied Science, Columbia University, New York, NY 10027, USA
| | - John C Lawlor
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - ChangHee Lee
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tyler R Huycke
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - L Mahadevan
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Clifford J Tabin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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Younesi FS, Miller AE, Barker TH, Rossi FMV, Hinz B. Fibroblast and myofibroblast activation in normal tissue repair and fibrosis. Nat Rev Mol Cell Biol 2024; 25:617-638. [PMID: 38589640 DOI: 10.1038/s41580-024-00716-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
The term 'fibroblast' often serves as a catch-all for a diverse array of mesenchymal cells, including perivascular cells, stromal progenitor cells and bona fide fibroblasts. Although phenotypically similar, these subpopulations are functionally distinct, maintaining tissue integrity and serving as local progenitor reservoirs. In response to tissue injury, these cells undergo a dynamic fibroblast-myofibroblast transition, marked by extracellular matrix secretion and contraction of actomyosin-based stress fibres. Importantly, whereas transient activation into myofibroblasts aids in tissue repair, persistent activation triggers pathological fibrosis. In this Review, we discuss the roles of mechanical cues, such as tissue stiffness and strain, alongside cell signalling pathways and extracellular matrix ligands in modulating myofibroblast activation and survival. We also highlight the role of epigenetic modifications and myofibroblast memory in physiological and pathological processes. Finally, we discuss potential strategies for therapeutically interfering with these factors and the associated signal transduction pathways to improve the outcome of dysregulated healing.
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Affiliation(s)
- Fereshteh Sadat Younesi
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew E Miller
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, VA, USA
| | - Thomas H Barker
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, VA, USA
| | - Fabio M V Rossi
- School of Biomedical Engineering and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Boris Hinz
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario, Canada.
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.
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5
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Harnik Y, Yakubovsky O, Hoefflin R, Novoselsky R, Bahar Halpern K, Barkai T, Korem Kohanim Y, Egozi A, Golani O, Addadi Y, Kedmi M, Keidar Haran T, Levin Y, Savidor A, Keren-Shaul H, Mayer C, Pencovich N, Pery R, Shouval DS, Tirosh I, Nachmany I, Itzkovitz S. A spatial expression atlas of the adult human proximal small intestine. Nature 2024; 632:1101-1109. [PMID: 39112711 DOI: 10.1038/s41586-024-07793-3] [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: 10/11/2023] [Accepted: 07/05/2024] [Indexed: 08/17/2024]
Abstract
The mouse small intestine shows profound variability in gene expression along the crypt-villus axis1,2. Whether similar spatial heterogeneity exists in the adult human gut remains unclear. Here we use spatial transcriptomics, spatial proteomics and single-molecule fluorescence in situ hybridization to reconstruct a comprehensive spatial expression atlas of the adult human proximal small intestine. We describe zonated expression and cell type representation for epithelial, mesenchymal and immune cell types. We find that migrating enterocytes switch from lipid droplet assembly and iron uptake at the villus bottom to chylomicron biosynthesis and iron release at the tip. Villus tip cells are pro-immunogenic, recruiting γδ T cells and macrophages to the tip, in contrast to their immunosuppressive roles in mouse. We also show that the human small intestine contains abundant serrated and branched villi that are enriched at the tops of circular folds. Our study presents a detailed resource for understanding the biology of the adult human small intestine.
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Affiliation(s)
- Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oran Yakubovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Roy Novoselsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Barkai
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Sheba Medical Center, Ramat Gan, Israel
| | - Yael Korem Kohanim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Keidar Haran
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Niv Pencovich
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Pery
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror S Shouval
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Nachmany
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Aquino LVC, Rodrigues LLV, Olindo SL, Silva YLF, Oliveira LRM, Moura YBF, Pereira AF. L-Proline as a Cryoprotective Agent for the Preservation of Galea Spixii Skin Fibroblasts. Biopreserv Biobank 2024. [PMID: 38985578 DOI: 10.1089/bio.2024.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Abstract
Somatic cell biobanking is a promising strategy for developing reproductive techniques. Although cryopreservation, a technique used for creating biobanks, has been performed on Galea spixii, structural and physiological damage to its cells highlight the need to optimize the cryoprotective solution being used. Therefore, the osmoprotective activity of 5 mM L-proline was evaluated as an alternative cryoprotectant for G. spixii fibroblast conservation. The concentration was defined based on previous studies conducted on mammalian cells. Cells derived from the skin of six individuals were cultured until the fifth passage were cryopreserved under the following treatments: (i) control (non-cryopreserved); (ii) a solution with 10% dimethyl sulfoxide (Me2SO), 10% fetal bovine serum (FBS), and 0.2 M sucrose; (iii) a solution with 10% Me2SO, 10% FBS, and 5 mM L-proline; and (iv) a solution with 10% Me2SO, 10% FBS, 0.2 M sucrose, and 5 mM L-proline. Tests were conducted to analyze cell morphology, viability, metabolism, proliferation, and apoptosis; reactive oxygen species (ROS) levels; and mitochondrial membrane activity (ΔΨm). A reduction in the number of viable cells (72.3% ± 1.2%) was observed in the sucrose-containing group compared to the control (86.7% ± 2.0%) and L-proline (88.4% ± 1.8% and 87.8% ± 2.1%) groups. After apoptotic analysis, a reduction in the number of viable cells was observed in the group with sucrose alone (74.6% ± 4.1%) compared to the control group (88.2% ± 1.1%). The ROS levels (1.03 ± 0.5 and 1.07 ± 0.5, respectively) and ΔΨm values (0.99 ± 0.42 and 1.22 ± 0.73, respectively) observed in the groups with L-proline were similar to that observed in the control group (1.00 ± 0.5 and 1.00 ± 0.4, respectively). Moreover, no difference was observed between groups for cell morphology, metabolism, or proliferation. Thus, L-proline is a cryoprotectant agent that can be used during G. spixii fibroblast cryopreservation, alone or with sucrose. In addition, we developed an adequate biobank for G. spixii, whereby stored cells could be used for reproductive techniques.
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Affiliation(s)
- Leonardo V C Aquino
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
| | - Luanna L V Rodrigues
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
| | - Samara L Olindo
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
| | - Yara L F Silva
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
| | - Lhara R M Oliveira
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
| | - Yasmin B F Moura
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
| | - Alexsandra F Pereira
- Laboratory of Animal Biotechnology, Federal Rural University of Semi-Arid, Mossoró, Brazil
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Seidelin JB, Bronze M, Poulsen A, Attauabi M, Woetmann A, Mead BE, Karp JM, Riis LB, Bjerrum JT. Non-TGFβ profibrotic signaling in ulcerative colitis after in vivo experimental intestinal injury in humans. Am J Physiol Gastrointest Liver Physiol 2024; 327:G70-G79. [PMID: 38713614 DOI: 10.1152/ajpgi.00074.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/09/2024]
Abstract
Although impaired regeneration is important in many gastrointestinal diseases including ulcerative colitis (UC), the dynamics of mucosal regeneration in humans are poorly investigated. We have developed a model to study these processes in vivo in humans. Epithelial restitution (ER) and extracellular matrix (ECM) regulation after an experimental injury of the sigmoid colonic mucosa was assessed by repeated high-resolution endoscopic imaging, histological assessment, RNA sequencing, deconvolution analysis, and 16S rDNA sequencing of the injury niche microbiome of 19 patients with UC in remission and 20 control subjects. Human ER had a 48-h lag before induction of regenerative epithelial cells [wound-associated epithelial (WAE) and transit amplifying (TA) cells] along with the increase of fibroblast-derived stem cell growth factor gremlin 1 mRNA (GREM1). However, UC deconvolution data showed rapid induction of inflammatory fibroblasts and upregulation of major structural ECM collagen mRNAs along with tissue inhibitor of metalloproteinase 1 (TIMP1), suggesting increased profibrotic ECM deposition. No change was seen in transforming growth factor β (TGFβ) mRNA, whereas the profibrotic cytokines interleukin 13 (IL13) and IL11 were upregulated in UC, suggesting that human postinjury responses could be TGFβ-independent. In conclusion, we found distinct regulatory layers of regeneration in the normal human colon and a potential targetable profibrotic dysregulation in UC that could lead to long-term end-organ failure, i.e., intestinal damage.NEW & NOTEWORTHY The study reveals the regulatory dynamics of epithelial regeneration and extracellular matrix remodeling after experimental injury of the human colon in vivo and shows that human intestinal regeneration is different from data obtained from animals. A lag phase in epithelial restitution is associated with induction of stromal cell-derived epithelial growth factors. Postinjury regeneration is transforming growth factor β-independent, and we find a profibrotic response in patients with ulcerative colitis despite being in remission.
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Affiliation(s)
- Jakob B Seidelin
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mariana Bronze
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Anja Poulsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mohamed Attauabi
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E Mead
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Department of Chemistry; Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, United States
| | - Jeffrey M Karp
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Department of Anesthesiology, Perioperative and Pain Medicine,Brigham and Women's Hospital, Cambridge, Massachusetts, United States
| | - Lene B Riis
- Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jacob T Bjerrum
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
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Downie JM, Musich RJ, Geraghty CM, Caraballo A, He S, Khawaled S, Lachut K, Long T, Zhou JY, Yilmaz OH, Stappenbeck T, Chan AT, Drew DA. Optimizing single-cell RNA sequencing methods for human colon biopsies: droplet-based vs. picowell-based platforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600526. [PMID: 38979379 PMCID: PMC11230261 DOI: 10.1101/2024.06.24.600526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background & Aims Single-cell RNA sequencing (scRNA) has empowered many insights into gastrointestinal microenvironments. However, profiling human biopsies using droplet-based scRNA (D-scRNA) is challenging since it requires immediate processing to minimize epithelial cell damage. In contrast, picowell-based (P-scRNA) platforms permit short-term frozen storage before sequencing. We compared P- and D-scRNA platforms on cells derived from human colon biopsies. Methods Endoscopic rectosigmoid mucosal biopsies were obtained from two adults and conducted D-scRNA (10X Chromium) and P-scRNA (Honeycomb HIVE) in parallel using an individual's pool of single cells (> 10,000 cells/participant). Three experiments were performed to evaluate 1) P-scRNA with cells under specific storage conditions (immediately processed [fresh], vs. frozen at -20C vs. -80C [2 weeks]); 2) fresh P-scRNA versus fresh D-scRNA; and 3) P-scRNA stored at -80C with fresh D-scRNA. Results Significant recovery of loaded cells was achieved for fresh (80.9%) and -80C (48.5%) P-scRNA and D-scRNA (76.6%), but not -20C P-scRNA (3.7%). However, D-scRNA captures more typeable cells among recovered cells (71.5% vs. 15.8% Fresh and 18.4% -80C P-scRNA), and these cells exhibit higher gene coverage at the expense of higher mitochondrial read fractions across most cell types. Cells profiled using D-scRNA demonstrated more consistent gene expression profiles among the same cell type than those profiled using P-scRNA. Significant intra-cell-type differences were observed in profiled gene classes across platforms. Conclusions Our results highlight non-overlapping advantages of P-scRNA and D-scRNA and underscore the need for innovation to enable high-fidelity capture of colonic epithelial cells. The platform-specific variation highlights the challenges of maintaining rigor and reproducibility across studies that use different platforms.
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9
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Mimpen JY, Ramos-Mucci L, Paul C, Kurjan A, Hulley PA, Ikwuanusi CT, Cohen CJ, Gwilym SE, Baldwin MJ, Cribbs AP, Snelling SJB. Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon. FASEB J 2024; 38:e23629. [PMID: 38742770 DOI: 10.1096/fj.202300601rrr] [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: 03/29/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
The molecular and cellular basis of health in human tendons remains poorly understood. Among human tendons, hamstring tendon has markedly low pathology and can provide a prototypic healthy tendon reference. The aim of this study was to determine the transcriptomes and location of all cell types in healthy hamstring tendon. Using single nucleus RNA sequencing, we profiled the transcriptomes of 10 533 nuclei from four healthy donors and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and identified cell types previously unreported in tendons, including different skeletal muscle cell types, satellite cells, adipocytes, and undefined nervous system cells. The location of these cell types within tendon was defined using spatial transcriptomics and imaging, and potential transcriptional networks and cell-cell interactions were analyzed. We demonstrate that fibroblasts have the highest number of potential cell-cell interactions in our dataset, are present throughout the tendon, and play an important role in the production and organization of extracellular matrix, thus confirming their role as key regulators of hamstring tendon homeostasis. Overall, our findings underscore the complexity of the cellular networks that underpin healthy human tendon function and the central role of fibroblasts as key regulators of hamstring tendon tissue homeostasis.
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Affiliation(s)
- Jolet Y Mimpen
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lorenzo Ramos-Mucci
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Claudia Paul
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alina Kurjan
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Philippa A Hulley
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Carla J Cohen
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom of Great Britain and Northern Ireland
| | - Stephen E Gwilym
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathew J Baldwin
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sarah J B Snelling
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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10
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Dong Y, Johnson BA, Ruan L, Zeineldin M, Bi T, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, Smith B, Zhao N, Searson P, Watanabe S, Donowitz M, Larman TC, Li R. Disruption of epithelium integrity by inflammation-associated fibroblasts through prostaglandin signaling. SCIENCE ADVANCES 2024; 10:eadj7666. [PMID: 38569041 PMCID: PMC10990275 DOI: 10.1126/sciadv.adj7666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Inflammation-associated fibroblasts (IAFs) are associated with progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial cells is unknown. Here, we developed an in vitro model whereby human colon fibroblasts are induced by specific cytokines and recapitulate key features of IAFs in vivo. When cocultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid expansion and barrier disruption due to swelling and rupture of individual epithelial cells. Colonoids cocultured with IAFs also show increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated by a paracrine pathway involving prostaglandin E2 and its receptor EP4, leading to protein kinase A -dependent activation of the cystic fibrosis transmembrane conductance regulator. EP4-specific chemical inhibitors effectively prevented IAF-induced colonoid swelling and restored normal proliferation and genome stability. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a therapeutic avenue to mitigate inflammation-associated epithelial injury.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Blake A. Johnson
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Linhao Ruan
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tianhao Bi
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Albert Z. Liu
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ian Chiu
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Barbara Smith
- Microscope Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Peter Searson
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tatianna C. Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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11
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Ventrello SW, McMurry NR, Edwards NM, Bain LJ. Chronic arsenic exposure affects stromal cells and signaling in the small intestine in a sex-specific manner. Toxicol Sci 2024; 198:303-315. [PMID: 38310360 DOI: 10.1093/toxsci/kfae016] [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: 02/05/2024] Open
Abstract
Arsenic is a toxicant that is ingested through drinking water and food, exposing nearly 140 million people to levels above the 10 ppb guideline concentration. Studies have shown that arsenic affects intestinal stem cells (ISCs), but the mechanisms by which arsenic alters the formation of adult cells in the small intestine are not well understood. Signals derived from intestinal stromal cells initiate and maintain differentiation. The goal of this study is to evaluate arsenic's effect on intestinal stromal cells, including PdgfrαLo trophocytes, located proximal to the ISCs, and PdgfrαHi telocytes, located proximal to the transit-amplifying region and up the villi. Adult Sox9tm2Crm-EGFP mice were exposed to 0, 33, and 100 ppb sodium arsenite in their drinking water for 13 weeks, and sections of duodenum were examined. Flow cytometry indicated that arsenic exposure dose-responsively reduced Sox9+ epithelial cells and trended toward increased Pdgfrα+ cells. The trophocyte marker, CD81, was reduced by 10-fold and 9.0-fold in the 100 ppb exposure group in male and female mice, respectively. Additionally, a significant 2.2- to 3.1-fold increase in PdgfrαLo expression was found in male mice in trophocytes and Igfbp5+ cells. PdgfrαHi protein expression, a telocyte marker, was more prevalent along the villus/crypt structure in females, whereas Gli1 expression (telocytes) was reduced in male mice exposed to arsenic. Principle coordinate analysis confirmed the sex-dependent response to arsenic exposure, with an increase in trophocyte and decrease in telocyte marker expression observed in male mice. These results imply that arsenic alters intestinal mesenchymal cells in a sex-dependent manner.
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Affiliation(s)
- Scott W Ventrello
- Department of Biological Sciences, Clemson University, Clemson, South Carolina 29634, USA
| | - Nicholas R McMurry
- Department of Biological Sciences, Clemson University, Clemson, South Carolina 29634, USA
| | - Nicholas M Edwards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina 29634, USA
| | - Lisa J Bain
- Department of Biological Sciences, Clemson University, Clemson, South Carolina 29634, USA
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12
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Bernier-Latmani J, González-Loyola A, Petrova TV. Mechanisms and functions of intestinal vascular specialization. J Exp Med 2024; 221:e20222008. [PMID: 38051275 PMCID: PMC10697212 DOI: 10.1084/jem.20222008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
The intestinal vasculature has been studied for the last 100 years, and its essential role in absorbing and distributing ingested nutrients is well known. Recently, fascinating new insights into the organization, molecular mechanisms, and functions of intestinal vessels have emerged. These include maintenance of intestinal epithelial cell function, coping with microbiota-induced inflammatory pressure, recruiting gut-specific immune cells, and crosstalk with other organs. Intestinal function is also regulated at the systemic and cellular levels, such that the postprandial hyperemic response can direct up to 30% of systemic blood to gut vessels, while micron-sized endothelial cell fenestrations are necessary for nutrient uptake. In this review, we will highlight past discoveries made about intestinal vasculature in the context of new findings of molecular mechanisms underpinning gut function. Such comprehensive understanding of the system will pave the way to breakthroughs in nutrient uptake optimization, drug delivery efficiency, and treatment of human diseases.
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Affiliation(s)
- Jeremiah Bernier-Latmani
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
| | | | - Tatiana V. Petrova
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
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13
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Dong Y, Johnson BA, Ruan L, Zeineldin M, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, Smith B, Zhao N, Searson P, Watanabe S, Donowitz M, Larman TC, Li R. Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling: IAFs disrupt colon epithelium via PGE2-EP4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560060. [PMID: 37808771 PMCID: PMC10557697 DOI: 10.1101/2023.09.28.560060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Inflammation-associated fibroblasts (IAFs) are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. In this study, we developed an in vitro model whereby human colon fibroblasts are induced to become IAFs by specific cytokines and recapitulate key features of IAFs in vivo. When co-cultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid swelling and barrier disruption due to swelling and rupture of individual epithelial cells. Epithelial cells co-cultured with IAFs also exhibit increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated through a paracrine pathway involving prostaglandin E2 (PGE2) and the PGE2 receptor EP4, leading to PKA-dependent activation of the CFTR chloride channel. Importantly, EP4-specific chemical inhibitors effectively prevented colonoid swelling and restored normal proliferation and genome stability of IAF-exposed epithelial cells. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a potential treatment to mitigate inflammation-associated epithelial injury.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Blake A. Johnson
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Linhao Ruan
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Albert Z. Liu
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Ian Chiu
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore
| | - Barbara Smith
- Microscope Facility, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University; Baltimore, Maryland, 21218, U.S.A
| | - Peter Searson
- Institute for Nanobiotechnology, Johns Hopkins University; Baltimore, Maryland, 21218, U.S.A
- Department of Materials Science and Engineering, Johns Hopkins University; Baltimore, MD, 21218, U.S.A
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
- Department of Physiology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Tatianna C. Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Rong Li
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore
- Department of Biological Sciences, National University of Singapore; Singapore
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