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Laudadio I, Carissimi C, Scafa N, Bastianelli A, Fulci V, Renzini A, Russo G, Oliva S, Vitali R, Palone F, Cucchiara S, Stronati L. Characterization of patient-derived intestinal organoids for modelling fibrosis in Inflammatory Bowel Disease. Inflamm Res 2024; 73:1359-1370. [PMID: 38842554 PMCID: PMC11282153 DOI: 10.1007/s00011-024-01901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND AND AIMS Intestinal fibrosis is a common complication of Inflammatory Bowel Disease (IBD), namely Crohn's disease (CD) and ulcerative colitis (UC), but the precise mechanism by which it occurs is incompletely understood hampering the development of effective therapeutic strategies. Here, we aimed at inducing and characterizing an inflammation-mediated fibrosis in patient-derived organoids (PDOs) issued from crypts isolated from colonic mucosal biopsies of IBD pediatric patients and age matched-control subjects (CTRLs). METHODS Inflammatory-driven fibrosis was induced by exposing CTRL-, CD- and UC-PDOs to the pro-inflammatory cytokine TNF-α for one day, followed by a co-treatment with TNF-α and TGF-β1 for three days. Fibrotic response was proven by analyzing inflammatory and fibrotic markers by RT-qPCR and immunofluorescence. Transcriptomic changes were assessed by RNA-sequencing. RESULTS Co-treatment with TNF-α and TGF-β1 caused in CTRL- and IBD-PDOs morphological changes towards a mesenchymal-like phenotype and up-regulation of inflammatory, mesenchymal, and fibrotic markers. Transcriptomic profiling highlighted that in all intestinal PDOs, regardless of the disease, the co-exposure to TNF-α and TGF-β1 regulated EMT genes and specifically increased genes involved in positive regulation of cell migration. Finally, we demonstrated that CD-PDOs display a specific response to fibrosis compared to both CTRL- and UC-PDOs, mainly characterized by upregulation of nuclear factors controlling transcription. CONCLUSIONS This study demonstrates that intestinal PDOs may develop an inflammatory-derived fibrosis thus representing a promising tool to study fibrogenesis in IBD. Fibrotic PDOs show increased expression of EMT genes. In particular, fibrotic CD-PDOs display a specific gene expression signature compared to UC and CTRL-PDOs.
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Affiliation(s)
- Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Noemi Scafa
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alex Bastianelli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alessandra Renzini
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Via. A. Scarpa, 16, 00161, Rome, Italy
| | - Giusy Russo
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Salvatore Oliva
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Roberta Vitali
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Francesca Palone
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Salvatore Cucchiara
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
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Zhong T, Cheng X, Gu Q, Fu G, Wang Y, Jiang Y, Xu J, Jiang Z. Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease. Genes Immun 2024; 25:209-218. [PMID: 38789829 PMCID: PMC11178494 DOI: 10.1038/s41435-024-00276-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
The pathogenesis of Crohn's disease (CD) involves abnormal immune cell infiltration and dysregulated immune response. Therefore, thorough research on immune cell abnormalities in CD is crucial for improved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expression Omnibus (GEO) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks evaluated the proportion of immune infiltrating cells, constructed co-expression network and identified key genes, respectively. Based on the dataset (GSE134809), 15 cell clusters were defined and labeled as different cell types. Among the 11 modules, the yellow module had the closest relationship with plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in CD samples was higher than that in control samples. Furthermore, the COL5A2 protein expression remarkably decreased in the group of patients who responded to anti-tumor necrosis factor (TNF) treatments, compared to the non-response group. The comprehensive analyses described here provided novel insight into the landscape of CD-associated immune environment. In addition, COL5A2 were identified as potential diagnostic indicators for CD, as well as promising predictive markers for CD patients.
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Affiliation(s)
- Tingting Zhong
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianru Gu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujie Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Xu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Flood P, Hanrahan N, Nally K, Melgar S. Human intestinal organoids: Modeling gastrointestinal physiology and immunopathology - current applications and limitations. Eur J Immunol 2024; 54:e2250248. [PMID: 37957831 DOI: 10.1002/eji.202250248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023]
Abstract
Human intestinal organoids are an ideal model system for studying gastrointestinal physiology and immunopathology. Altered physiology and mucosal immune response are hallmarks of numerous intestinal functional and inflammatory diseases, including inflammatory bowel disease (IBD), coeliac disease, irritable bowel syndrome (IBS), and obesity. These conditions impact the normal epithelial functions of the intestine, such as absorption, barrier function, secretion, and host-microbiome communication. They are accompanied by characteristic intestinal symptoms and have significant societal, economic, and healthcare burdens. To develop new treatment options, cutting-edge research is required to investigate their etiology and pathology. Human intestinal organoids derived from patient tissue recapitulate the key physiological and immunopathological aspects of these conditions, providing a promising platform for elucidating disease mechanisms. This review will summarize recent reports on patient-derived human small intestinal and colonic organoids and highlight how these models have been used to study intestinal epithelial functions in the context of inflammation, altered physiology, and immune response. Furthermore, it will elaborate on the various organoid systems in use and the techniques/assays currently available to study epithelial functions. Finally, it will conclude by discussing the limitations and future perspectives of organoid technology.
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Affiliation(s)
- Peter Flood
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Naomi Hanrahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, School of Medicine, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
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Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
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Rutherford D, Ho GT. Therapeutic Potential of Human Intestinal Organoids in Tissue Repair Approaches in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2023; 29:1488-1498. [PMID: 37094358 PMCID: PMC10472753 DOI: 10.1093/ibd/izad044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 04/26/2023]
Abstract
Inflammatory bowel diseases (IBDs) are chronic immune-mediated conditions characterized by significant gut tissue damage due to uncontrolled inflammation. Anti-inflammatory treatments have improved, but there are no current prorepair approaches. Organoids have developed into a powerful experimental platform to study mechanisms of human diseases. Here, we specifically focus on its role as a direct tissue repair modality in IBD. We discuss the scientific rationale for this, recent parallel advances in scientific technologies (CRISPR [clustered regularly interspaced short palindromic repeats]/Cas9 and metabolic programming), and in addition, the clinical IBD context in which this therapeutic approach is tractable. Finally, we review the translational roadmap for the application of organoids and the need for this as a novel direction in IBD.
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Affiliation(s)
- Duncan Rutherford
- Gut Research Unit, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Gwo-Tzer Ho
- Gut Research Unit, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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Szabó L, Seubert AC, Kretzschmar K. Modelling adult stem cells and their niche in health and disease with epithelial organoids. Semin Cell Dev Biol 2023; 144:20-30. [PMID: 36127261 DOI: 10.1016/j.semcdb.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Adult stem cells are responsible for homoeostasis and regeneration of epithelial tissues. Stem cell function is regulated by both cell autonomous mechanisms as well as the niche. Deregulated stem cell function contributes to diseases such as cancer. Epithelial organoid cultures generated from tissue-resident adult stem cells have allowed unprecedented insights into the biology of epithelial tissues. The subsequent adaptation of organoid technology enabled the modelling of the communication of stem cells with their cellular and non-cellular niche as well as diseases. Starting from its first model described in 2009, the murine small intestinal organoid, we discuss here how epithelial organoid cultures have been become a prime in vitro research tool for cell and developmental biology, bioengineering, and biomedicine in the last decade.
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Affiliation(s)
- Lili Szabó
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Anna C Seubert
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Kai Kretzschmar
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany.
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Karakasheva TA, Zhou Y, Xie HM, Soto GE, Johnson TD, Stoltz MA, Roach DM, Nema N, Umeweni CN, Naughton K, Dolinsky L, Pippin JA, Wells AD, Grant SF, Ghanem L, Terry N, Muir AB, Hamilton KE. Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures. GASTRO HEP ADVANCES 2023; 2:830-842. [PMID: 37736163 PMCID: PMC10512767 DOI: 10.1016/j.gastha.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/12/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND AND AIMS A key histopathological feature of inflammatory bowel disease is damage to the mucosa, including breakdown of the epithelial barrier. Human enteroids and colonoids are a critical bench-to-bedside tool for studying the epithelium in inflammatory bowel disease. The goal of the current study was to define transcriptional differences in healthy versus diseased subjects that are sustained in enteroids and colonoids, including from disease-spared tissue. METHODS Biopsies and matching enteroid or colonoid cultures from pediatric patients with ileal Crohn disease (N = 6) and control subjects (N = 17) were subjected to RNA sequencing followed by bioinformatic and machine learning analyses. Late passage enteroids were exposed to cytokines to assess durable transcriptional differences. RESULTS We observed substantial overlap of pathways upregulated in Crohn disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. KEGG pathways for cytokine-cytokine receptor interaction, chemokine signaling, protein export, and Toll-like receptor signaling were upregulated in both ileal and rectal biopsies, as well as enteroids and colonoids. In vitro cytokine exposure reactivated genes previously increased in biopsies. Machine learning predicted biopsy location (100% accuracy) and donor disease status (83% accuracy). A random forest classifier generated using ileal enteroids identified rectal colonoids from ileal Crohn disease subjects with 80% accuracy. CONCLUSION We confirmed transcriptional profiles of Crohn disease biopsies are expressed in enteroids and colonoids. Furthermore, transcriptomic data from disease-spared rectal tissue can identify patients with ileal Crohn disease. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.
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Affiliation(s)
- Tatiana A. Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hongbo M. Xie
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gloria E. Soto
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Tiana D. Johnson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Madison A. Stoltz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Daana M. Roach
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Noor Nema
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chizoba N. Umeweni
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kaitlyn Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lauren Dolinsky
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - James A. Pippin
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Struan F.A. Grant
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Diabetes and Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Louis Ghanem
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Immunology, Translational Sciences and Medicine, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Natalie Terry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Immunology, Clinical Development, Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Amanda B. Muir
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Tindle C, Katkar GD, Fonseca AG, Taheri S, Lee J, Maity P, Sayed IM, Ibeawuchi SR, Vidales E, Pranadinata RF, Fuller M, Stec DL, Anandachar MS, Perry K, Le HN, Ear J, Boland BS, Sandborn WJ, Sahoo D, Das S, Ghosh P. A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532245. [PMID: 36993763 PMCID: PMC10054961 DOI: 10.1101/2023.03.11.532245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Crohn's disease (CD) is a complex, clinically heterogeneous disease of multifactorial origin; there is no perfect pre-clinical model, little insight into the basis for such heterogeneity, and still no cure. To address these unmet needs, we sought to explore the translational potential of adult stem cell-derived organoids that not only retain their tissue identity, but also their genetic and epigenetic disease-driving traits. We prospectively created a biobank of CD patient-derived organoid cultures (PDOs) using biopsied tissues from colons of 34 consecutive subjects representing all clinical subtypes (Montreal Classification B1-B3 and perianal disease). PDOs were generated also from healthy subjects. Comparative gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and revealed that despite the clinical heterogeneity there are two major molecular subtypes: immune-deficient infectious-CD [IDICD] and stress and senescence-induced fibrostenotic-CD [S2FCD]. The transcriptome, genome and phenome show a surprising degree of internal consistency within each molecular subtype. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. These insights enabled drug screens that reversed subtype-specific phenotypes, e.g., impaired microbial clearance in IDICD was reversed using agonists for nuclear receptors, and senescence in S2FCD was rectified using senotherapeutics, but not vice versa . Phenotyped-genotyped CD-PDOs may fill the gap between basic biology and patient trials by enabling pre-clinical Phase '0' human trials for personalized therapeutics. GRAPHIC ABSTRACT In Brief This work creates a prospectively biobanked phenotyped-genotyped Crohn's disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTS Prospectively biobanked CD-organoids recapitulate the disease epithelium in patientsThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypesOne subtype shows impaired microbial clearance, another increased cellular senescencePhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics.
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Morelli M, Kurek D, Ng CP, Queiroz K. Gut-on-a-Chip Models: Current and Future Perspectives for Host-Microbial Interactions Research. Biomedicines 2023; 11:biomedicines11020619. [PMID: 36831155 PMCID: PMC9953162 DOI: 10.3390/biomedicines11020619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The intestine contains the largest microbial community in the human body, the gut microbiome. Increasing evidence suggests that it plays a crucial role in maintaining overall health. However, while many studies have found a correlation between certain diseases and changes in the microbiome, the impact of different microbial compositions on the gut and the mechanisms by which they contribute to disease are not well understood. Traditional pre-clinical models, such as cell culture or animal models, are limited in their ability to mimic the complexity of human physiology. New mechanistic models, such as organ-on-a-chip, are being developed to address this issue. These models provide a more accurate representation of human physiology and could help bridge the gap between clinical and pre-clinical studies. Gut-on-chip models allow researchers to better understand the underlying mechanisms of disease and the effect of different microbial compositions on the gut. They can help to move the field from correlation to causation and accelerate the development of new treatments for diseases associated with changes in the gut microbiome. This review will discuss current and future perspectives of gut-on-chip models to study host-microbial interactions.
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Lechuga S, Braga-Neto MB, Naydenov NG, Rieder F, Ivanov AI. Understanding disruption of the gut barrier during inflammation: Should we abandon traditional epithelial cell lines and switch to intestinal organoids? Front Immunol 2023; 14:1108289. [PMID: 36875103 PMCID: PMC9983034 DOI: 10.3389/fimmu.2023.1108289] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
Disruption of the intestinal epithelial barrier is a hallmark of mucosal inflammation. It increases exposure of the immune system to luminal microbes, triggering a perpetuating inflammatory response. For several decades, the inflammatory stimuli-induced breakdown of the human gut barrier was studied in vitro by using colon cancer derived epithelial cell lines. While providing a wealth of important data, these cell lines do not completely mimic the morphology and function of normal human intestinal epithelial cells (IEC) due to cancer-related chromosomal abnormalities and oncogenic mutations. The development of human intestinal organoids provided a physiologically-relevant experimental platform to study homeostatic regulation and disease-dependent dysfunctions of the intestinal epithelial barrier. There is need to align and integrate the emerging data obtained with intestinal organoids and classical studies that utilized colon cancer cell lines. This review discusses the utilization of human intestinal organoids to dissect the roles and mechanisms of gut barrier disruption during mucosal inflammation. We summarize available data generated with two major types of organoids derived from either intestinal crypts or induced pluripotent stem cells and compare them to the results of earlier studies with conventional cell lines. We identify research areas where the complementary use of colon cancer-derived cell lines and organoids advance our understanding of epithelial barrier dysfunctions in the inflamed gut and identify unique questions that could be addressed only by using the intestinal organoid platforms.
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Affiliation(s)
- Susana Lechuga
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Manuel B. Braga-Neto
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Nayden G. Naydenov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Andrei I. Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
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Maddipatla SC, Kolachala VL, Venkateswaran S, Dodd AF, Pelia RS, Geem D, Yin H, Sun Y, Xu C, Mo A, Kosters A, Yang J, Matthews JD, Ghosn E, Kugathasan S, Qiu P. Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn's Disease. Inflamm Bowel Dis 2023; 29:274-285. [PMID: 36206201 PMCID: PMC9890215 DOI: 10.1093/ibd/izac201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Crohn's disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn's. METHODS Ileal biopsies were obtained from (1) control subjects (n = 6), (2) treatment-naïve patients (n = 7), and (3) established (n = 14) Crohn's patients along with remission (n = 3) and refractory (n = 11) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139 906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type. RESULTS We identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-naïve, and established groups, with the significant changes in the epithelial subtypes of the treatment-naïve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn's phenotypes, indicating changes in cellular activity. CONCLUSIONS Our study identified cellular and transcriptional signatures associated with treatment-naïve Crohn's disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.
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Affiliation(s)
- Sushma Chowdary Maddipatla
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasantha L Kolachala
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Anne F Dodd
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Ranjit Singh Pelia
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Duke Geem
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Hong Yin
- Department of Pathology, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Yutong Sun
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Congmin Xu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Angela Mo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Astrid Kosters
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Junkai Yang
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jason D Matthews
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Eliver Ghosn
- Emory Vaccine Center, Lowance Center for Human Immunology, Departments of Medicine and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University School of Medicine, Atlanta, GA, USAand
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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12
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Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models. Sci Rep 2023; 13:203. [PMID: 36604447 PMCID: PMC9814625 DOI: 10.1038/s41598-022-26816-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. A clear gap in our existing CD diagnostics and current disease management approaches is the lack of highly specific biomarkers that can be used to streamline or personalize disease management. Comprehensive profiling of metabolites holds promise; however, these high-dimensional profiles need to be reduced to have relevance in the context of CD. Machine learning approaches are optimally suited to bridge this gap in knowledge by contextualizing the metabolic alterations in CD using genome-scale metabolic network reconstructions. Our work presents a framework for studying altered metabolic reactions between patients with CD and controls using publicly available transcriptomic data and existing gene-driven metabolic network reconstructions. Additionally, we apply the same methods to patient-derived ileal enteroids to explore the utility of using this experimental in vitro platform for studying CD. Furthermore, we have piloted an untargeted metabolomics approach as a proof-of-concept validation strategy in human ileal mucosal tissue. These findings suggest that in silico metabolic modeling can potentially identify pathways of clinical relevance in CD, paving the way for the future discovery of novel diagnostic biomarkers and therapeutic targets.
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13
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Dotti I, Mayorgas A, Salas A. Generation of human colon organoids from healthy and inflammatory bowel disease mucosa. PLoS One 2022; 17:e0276195. [PMID: 36301950 PMCID: PMC9612551 DOI: 10.1371/journal.pone.0276195] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/01/2022] [Indexed: 11/05/2022] Open
Abstract
Ulcerative colitis and Crohn's disease are chronic inflammatory bowel diseases (IBD) of unknown cause characterized by a relapsing-remitting behavior. Growing evidence supports the idea that the epithelial barrier plays a central role in the pathogenesis of IBD as well as in its evolution over time, thus representing a potential target for novel therapeutic options. In the last decade, the introduction of 3D epithelial cultures from ex vivo-expanded intestinal adult stem cells (ASCs) has impacted our ability to study the function of the epithelium in several gastrointestinal disorders, including IBD. Here, we describe in detail a reproducible protocol to generate Matrigel-embedded epithelial organoids from ASCs of non-IBD and IBD donors using small colonic biopsies, including steps for its optimization. A slightly modified version of this protocol is also provided in case surgical samples are used. With this method, epithelial organoids can be expanded over several passages, thereby generating a large quantity of viable cells that can be used in multiple downstream analyses including genetic, transcriptional, proteomic and/or functional studies. In addition, 3D cultures generated using our protocol are suitable for the establishment of 2D cultures, which can model relevant cell-to-cell interactions that occur in IBD mucosa.
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Affiliation(s)
- Isabella Dotti
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
- * E-mail:
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14
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Sahoo DK, Borcherding DC, Chandra L, Jergens AE, Atherly T, Bourgois-Mochel A, Ellinwood NM, Snella E, Severin AJ, Martin M, Allenspach K, Mochel JP. Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor. Cancers (Basel) 2022; 14:3525. [PMID: 35884586 PMCID: PMC9322748 DOI: 10.3390/cancers14143525] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Lipopolysaccharide (LPS) is associated with chronic intestinal inflammation and promotes intestinal cancer progression in the gut. While the interplay between LPS and intestinal immune cells has been well-characterized, little is known about LPS and the intestinal epithelium interactions. In this study, we explored the differential effects of LPS on proliferation and the transcriptome in 3D enteroids/colonoids obtained from dogs with naturally occurring gastrointestinal (GI) diseases including inflammatory bowel disease (IBD) and intestinal mast cell tumor. The study objective was to analyze the LPS-induced modulation of signaling pathways involving the intestinal epithelia and contributing to colorectal cancer development in the context of an inflammatory (IBD) or a tumor microenvironment. While LPS incubation resulted in a pro-cancer gene expression pattern and stimulated proliferation of IBD enteroids and colonoids, downregulation of several cancer-associated genes such as Gpatch4, SLC7A1, ATP13A2, and TEX45 was also observed in tumor enteroids. Genes participating in porphyrin metabolism (CP), nucleocytoplasmic transport (EEF1A1), arachidonic acid, and glutathione metabolism (GPX1) exhibited a similar pattern of altered expression between IBD enteroids and IBD colonoids following LPS stimulation. In contrast, genes involved in anion transport, transcription and translation, apoptotic processes, and regulation of adaptive immune responses showed the opposite expression patterns between IBD enteroids and colonoids following LPS treatment. In brief, the crosstalk between LPS/TLR4 signal transduction pathway and several metabolic pathways such as primary bile acid biosynthesis and secretion, peroxisome, renin-angiotensin system, glutathione metabolism, and arachidonic acid pathways may be important in driving chronic intestinal inflammation and intestinal carcinogenesis.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
- SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Dana C. Borcherding
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Lawrance Chandra
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Todd Atherly
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Agnes Bourgois-Mochel
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - N. Matthew Ellinwood
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (N.M.E.); (E.S.)
| | - Elizabeth Snella
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (N.M.E.); (E.S.)
| | - Andrew J. Severin
- Office of Biotechnology’s Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA;
| | | | - Karin Allenspach
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Jonathan P. Mochel
- SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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15
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Cottle C, Anbazhagan M, Lipat A, Patel M, Porter A, Hogan K, Rajan D, Matthews J, Kugathasan S, Chinnadurai R. Complexity of Secretory Chemokines in Human Intestinal Organoid Cultures Ex Vivo. GASTRO HEP ADVANCES 2022; 1:457-460. [PMID: 35634262 PMCID: PMC9141070 DOI: 10.1016/j.gastha.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 12/27/2022]
Affiliation(s)
- C. Cottle
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
| | - M. Anbazhagan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - A. Lipat
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
| | - M. Patel
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
| | - A.P. Porter
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
| | - K. Hogan
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
| | - D. Rajan
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
| | - J.D. Matthews
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - S. Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - R. Chinnadurai
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia
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