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Deng Y, Yuan X, Lu X, Wu J, Luo C, Zhang T, Liu Q, Tang S, Li Z, Mu X, Hu Y, Du Q, Xu J, Xie R. The Use of Gut Organoids: To Study the Physiology and Disease of the Gut Microbiota. J Cell Mol Med 2025; 29:e70330. [PMID: 39968926 PMCID: PMC11836903 DOI: 10.1111/jcmm.70330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 11/02/2024] [Accepted: 12/16/2024] [Indexed: 02/20/2025] Open
Abstract
The intestinal flora has attracted much attention in recent years. An imbalance in the intestinal flora can cause not only intestinal diseases but also cause a variety of parenteral diseases, such as endocrine diseases, nervous system diseases and cardiovascular diseases. Research on the mechanism of disease is likely to be hampered by sample accessibility, ethical issues, and differences between cellular animal and physiological studies. However, advances in stem cell culture have made it possible to reproduce 3D human tissues in vitro that mimic the cellular, anatomical and functional characteristics of real organs. Recent studies have shown that organoids can be used to simulate the development and disease of the gut and intestinal flora and have a wide range of applications in intestinal flora physiology and disease. Intestinal organoids provide a preeminent in vitro model system for cultivating microbiota that influence GI physiology, as well as for understanding how they encounter intestinal epithelial cells and cause disease. The mechanistic details obtained from such modelling may provide new avenues for the prevention and treatment of many gastrointestinal (GI) disorders. Researchers are now starting to take inspiration from other fields, such as bioengineering, and the rise of interdisciplinary approaches, including organoid chip technology and microfluidics, has greatly accelerated the development of organoids to generate intestinal organoids that are more physiologically relevant and suitable for gut microbiota studies. Here, we describe the development of organoid models of gut biology and the application of organoids to study the pathophysiology of diseases caused by intestinal dysbiosis.
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Affiliation(s)
- Ya Deng
- Department of Endoscopy and Digestive SystemGuizhou Provincial People's HospitalGuiyangGuizhouChina
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Xiaolu Yuan
- The Second Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - XianMin Lu
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Jiangbo Wu
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Chen Luo
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Ting Zhang
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Qi Liu
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Siqi Tang
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Zhuo Li
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Xingyi Mu
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Yanxia Hu
- Zunyi Medical UniversityZunyiGuizhouChina
| | - Qian Du
- Department of Endoscopy and Digestive SystemGuizhou Provincial People's HospitalGuiyangGuizhouChina
| | - Jingyu Xu
- Guizhou Medical UniversityGuiyangGuizhouChina
| | - Rui Xie
- Department of Endoscopy and Digestive SystemGuizhou Provincial People's HospitalGuiyangGuizhouChina
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Xue Q, Pan JP, Qian D, Ji J, Fei LY, Yao S, Tan X, Fan WG. Exploring the Impact of Systemic Inflammatory Regulators on Rosacea Risk: A Bidirectional Mendelian Randomization Analysis. Clin Cosmet Investig Dermatol 2025; 18:191-200. [PMID: 39867972 PMCID: PMC11760274 DOI: 10.2147/ccid.s495773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 01/13/2025] [Indexed: 01/28/2025]
Abstract
Objective Rosacea is a common chronic inflammatory disorder primarily affecting the face. While inflammatory factors are known to play a pivotal role in its pathogenesis, their causal relationship with rosacea remains unclear. This study employed a two-sample bidirectional Mendelian randomization (MR) analysis to investigate the causal links between systemic inflammatory regulators and rosacea. Methods Data on 41 cytokines and growth factors were analyzed from a genome-wide association study (GWAS) meta-analysis involving 8293 individuals and genetic data from the FinnGen database, comprising 1195 rosacea cases and 211,139 controls. The principal inverse variance weighting (IVW) method was used to assess causal relationships, with sensitivity analyses, including heterogeneity and horizontal pleiotropy assessments, conducted to ensure result robustness. Results MR analysis revealed that decreased expression of Stem Cell Factor (SCF), Macrophage Inflammatory Protein-1β (MIP-1β), and Monocyte Chemotactic Protein-1 (MCP-1) was associated with increased rosacea risk (OR = 1.54, 95% CI = 1.05-2.26, p = 0.026). Conversely, elevated expression levels of Stromal Cell-Derived Factor-1α (SDF-1α) and Hepatocyte Growth Factor (HGF) were linked to higher rosacea risk (OR = 1.61, 95% CI = 1.12-2.31, p = 0.009). Reverse MR analyses showed no significant impact of rosacea on systemic inflammatory regulator expression. Conclusion This study identified five inflammatory factors-SCF, SDF-1α, MCP-1, HGF, and MIP-1β-as having causal relationships with rosacea pathogenesis. Further research is required to elucidate their mechanistic roles in disease development.
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Affiliation(s)
- Qiao Xue
- Department of Dermatology, Changshu No. 1 People’s Hospital, Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215500, People’s Republic of China
| | - Jian Peng Pan
- Department of Hand Surgery, Changshu No. 2 People’s Hospital, The Affiliated Changshu Hospital of Nantong University, Changshu, Jiangsu, 215500, People’s Republic of China
| | - Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu No. 1 People’s Hospital, Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215500, People’s Republic of China
| | - Jie Ji
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, People’s Republic of China
| | - Lai Yi Fei
- Department of Dermatology, Changshu No. 1 People’s Hospital, Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215500, People’s Republic of China
| | - Sheng Yao
- Department of Dermatology, Changshu No. 1 People’s Hospital, Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215500, People’s Republic of China
| | - Xing Tan
- Department of Dermatology, Changshu No. 1 People’s Hospital, Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215500, People’s Republic of China
| | - Wen Ge Fan
- Department of Dermatology, Changshu No. 1 People’s Hospital, Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215500, People’s Republic of China
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Nishiyama NC, Silverstein S, Darlington K, Kennedy Ng MM, Clough KM, Bauer M, Beasley C, Bharadwaj A, Ganesan R, Kapadia MR, Lau G, Lian G, Rahbar R, Sadiq TS, Schaner MR, Stem J, Friton J, Faubion WA, Sheikh SZ, Furey TS. eQTL in diseased colon tissue identifies novel target genes associated with IBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618229. [PMID: 39464142 PMCID: PMC11507739 DOI: 10.1101/2024.10.14.618229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.
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Affiliation(s)
- Nina C. Nishiyama
- Curriculum in Bioinformatics and Computational Biology, Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sophie Silverstein
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kimberly Darlington
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meaghan M. Kennedy Ng
- Curriculum in Bioinformatics and Computational Biology, Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katelyn M. Clough
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mikaela Bauer
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Caroline Beasley
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Akshatha Bharadwaj
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rajee Ganesan
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Muneera R. Kapadia
- Department of Surgery, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gwen Lau
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Grace Lian
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Reza Rahbar
- Department of Surgery, REX Healthcare of Wakefield, Raleigh, North Carolina, USA
| | - Timothy S. Sadiq
- Department of Surgery, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew R. Schaner
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan Stem
- Department of Surgery, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - William A. Faubion
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Shehzad Z. Sheikh
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Terrence S. Furey
- Curriculum in Bioinformatics and Computational Biology, Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Tindle C, Fonseca AG, Taheri S, Katkar GD, 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 patients with Crohn's disease reveals molecular subtypes for personalized therapeutics. Cell Rep Med 2024; 5:101748. [PMID: 39332415 PMCID: PMC11513829 DOI: 10.1016/j.xcrm.2024.101748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 07/15/2024] [Accepted: 08/31/2024] [Indexed: 09/29/2024]
Abstract
Crohn's disease (CD) is a complex and heterogeneous condition with no perfect preclinical model or cure. To address this, we explore adult stem cell-derived organoids that retain their tissue identity and disease-driving traits. We prospectively create a biobank of CD patient-derived organoid cultures (PDOs) from colonic biopsies of 53 subjects across all clinical subtypes and healthy subjects. Gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and identified two major molecular subtypes: immune-deficient infectious CD (IDICD) and stress and senescence-induced fibrostenotic CD (S2FCD). Each subtype shows internal consistency in the transcriptome, genome, and phenome. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. Drug screens reverse subtype-specific phenotypes, suggesting phenotyped-genotyped CD PDOs can bridge basic biology and patient trials by enabling preclinical phase "0" human trials for personalized therapeutics.
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Affiliation(s)
- Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Ayden G Fonseca
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Sahar Taheri
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gajanan D Katkar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jasper Lee
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Priti Maity
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stella-Rita Ibeawuchi
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eleadah Vidales
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Rama F Pranadinata
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Mackenzie Fuller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominik L Stec
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Kevin Perry
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Helen N Le
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason Ear
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Soumita Das
- HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA; Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Tocci S, Das S, Sayed IM. An Update on Blastocystis: Possible Mechanisms of Blastocystis-Mediated Colorectal Cancer. Microorganisms 2024; 12:1924. [PMID: 39338600 PMCID: PMC11433781 DOI: 10.3390/microorganisms12091924] [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: 08/28/2024] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Blastocystis is an anaerobic parasite that colonizes the intestinal tract of humans and animals. When it was first discovered, Blastocystis was considered to be a normal flora with beneficial effects on human health, such as maintaining gut hemostasis and improving intestinal barrier integrity. Later, with increasing research on Blastocystis, reports showed that Blastocystis sp. is associated with gastrointestinal disorders, colorectal cancer (CRC), and neurological disorders. The association between Blastocystis sp. and CRC has been confirmed in several countries. Blastocystis sp. can mediate CRC via similar mechanisms to CRC-associated bacteria, including infection-mediated inflammation, increased oxidative stress, induced gut dysbiosis, and damage to intestinal integrity, leading to a leaky gut. IL-8 is the main inflammatory cytokine released from epithelial cells and can promote CRC development. The causal association of Blastocystis sp. with other diseases needs further investigation. In this review, we have provided an update on Blastocystis sp. and summarized the debate about the beneficial and harmful effects of this parasite. We have also highlighted the possible mechanisms of Blastocystis-mediated CRC.
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Affiliation(s)
- Stefania Tocci
- Department of Biomedical & Nutritional Sciences, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Soumita Das
- Department of Biomedical & Nutritional Sciences, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Ibrahim M Sayed
- Department of Biomedical & Nutritional Sciences, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
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Cheng M, Xu B, Sun Y, Wang J, Lu Y, Shi C, Pan T, Zhao W, Li X, Song X, Wang J, Wang N, Yang W, Jiang Y, Huang H, Yang G, Zeng Y, Yang D, Wang C, Cao X. ASB3 expression aggravates inflammatory bowel disease by targeting TRAF6 protein stability and affecting the intestinal microbiota. mBio 2024; 15:e0204324. [PMID: 39162488 PMCID: PMC11389410 DOI: 10.1128/mbio.02043-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 07/12/2024] [Indexed: 08/21/2024] Open
Abstract
E3 ubiquitin ligase (E3) plays a vital role in regulating inflammatory responses by mediating ubiquitination. Previous studies have shown that ankyrin repeat and SOCS box-containing protein 3 (ASB3) is involved in immunomodulatory functions associated with cancer. However, the impact of ASB3 on the dynamic interplay of microbiota and inflammatory responses in inflammatory bowel disease (IBD) is unclear. Here, we systematically identify the E3 ligase ASB3 as a facilitative regulator in the development and progression of IBD. We observed that ASB3 exhibited significant upregulation in the lesions of patients with IBD. ASB3-/- mice are resistant to dextran sodium sulfate-induced colitis. IκBα phosphorylation levels and production of proinflammatory factors IL-1β, IL-6, and TNF-α were reduced in the colonic tissues of ASB3-/- mice compared to WT mice. This colitis-resistant phenotype was suppressed after coprophagic microbial transfer and reversed after combined antibiotics removed the gut commensal microbiome. Mechanistically, ASB3 specifically catalyzes K48-linked polyubiquitination of TRAF6 in intestinal epithelial cells. In contrast, in ASB3-deficient organoids, the integrity of the TRAF6 protein is shielded, consequently decelerating the onset of intestinal inflammation. ASB3 is associated with dysregulation of the colitis microbiota and promotes proinflammatory factors' production by disrupting TRAF6 stability. Strategies to limit the protein level of ASB3 in intestinal epithelial cells may help in the treatment of colitis. IMPORTANCE Ubiquitination is a key process that controls protein stability. We determined the ubiquitination of TRAF6 by ASB3 in intestinal epithelial cells during colonic inflammation. Inflammatory bowel disease patients exhibit upregulated ASB3 expression at focal sites, supporting the involvement of degradation of TRAF6, which promotes TLR-Myd88/TRIF-independent NF-κB aberrant activation and intestinal microbiota imbalance. Sustained inflammatory signaling in intestinal epithelial cells and dysregulated protective probiotic immune responses mediated by ASB3 collectively contribute to the exacerbation of inflammatory bowel disease. These findings provide insights into the pathogenesis of inflammatory bowel disease and suggest a novel mechanism by which ASB3 increases the risk of colitis. Our results suggest that future inhibition of ASB3 in intestinal epithelial cells may be a novel clinical strategy.
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Affiliation(s)
- Mingyang Cheng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Bin Xu
- Department of General Surgery, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu Sun
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Junhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yiyuan Lu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunwei Shi
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Tianxu Pan
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wenhui Zhao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaoxu Li
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaomei Song
- Department of Gastroenterology, Chongqing General Hospital, Chongqing, China
| | - Jianzhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Nan Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wentao Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yanlong Jiang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Haibin Huang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guilian Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Dongqin Yang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Chunfeng Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Cao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, China
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7
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Broering MF, Tocci S, Sout NT, Reutelingsperger C, Farsky SHP, Das S, Sayed IM. Development of an Inflamed High Throughput Stem-cell-based Gut Epithelium Model to Assess the Impact of Annexin A1. Stem Cell Rev Rep 2024; 20:1299-1310. [PMID: 38498294 DOI: 10.1007/s12015-024-10708-4] [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] [Accepted: 02/27/2024] [Indexed: 03/20/2024]
Abstract
OBJECTIVE AND DESIGN Annexin A1 (ANXA1) plays a role in maintaining intestinal hemostasis, especially following mucosal inflammation. The published data about ANXA1 was derived from experimental animal models where there is an overlapping between epithelial and immune cells. There is no in vitro gut epithelial model that can assess the direct effect of ANXA1 on the gut epithelium. METHODS We developed high-throughput stem-cell-based murine epithelial cells and bacterial lipopolysaccharides (LPS) were used to induce inflammation. The impact of ANXA1 and its functional part (Ac2-26) was evaluated in the inflamed model. Intestinal integrity was assessed by the transepithelial electrical resistance (TEER), and FITC-Dextran permeability. Epithelial junction proteins were assessed using confocal microscopy and RT-qPCR. Inflammatory cytokines were evaluated by RT-qPCR and ELISA. RESULTS LPS challenge mediated a damage in the epithelial cells as shown by a drop in the TEER and an increase in FITC-dextran permeability; reduced the expression of epithelial junctional proteins (Occludin, ZO-1, and Cadherin) and increased the expression of the gut leaky protein, Claudin - 2. ANXA1 and Ac2-26 treatment reduced the previous damaging effects. In addition, ANXA1 and Ac2-26 inhibited the inflammatory responses mediated by the LPS and increased the transcription of the anti-inflammatory cytokine, IL-10. CONCLUSION ANXA1 and Ac2-26 directly protect the epithelial integrity by affecting the expression of epithelial junction and inflammatory markers. The inflamed gut model is a reliable tool to study intestinal inflammatory diseases, and to evaluate the efficacy of potential anti-inflammatory drugs and the screening of new drugs that could be candidates for inflammatory bowel disease.
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Affiliation(s)
- Milena Fronza Broering
- Department of Biomedical and Nutritional Sciences, University of Massachusetts-Lowell, Lowell, MA, 01854, USA
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, São Paulo, 05508-000, Brazil
| | - Stefania Tocci
- Department of Biomedical and Nutritional Sciences, University of Massachusetts-Lowell, Lowell, MA, 01854, USA
| | - Noah T Sout
- Department of Biomedical and Nutritional Sciences, University of Massachusetts-Lowell, Lowell, MA, 01854, USA
| | - Chris Reutelingsperger
- Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, Maastricht University, Maastricht, 6211 LK, The Netherlands
| | - Sandra H P Farsky
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, São Paulo, 05508-000, Brazil
| | - Soumita Das
- Department of Biomedical and Nutritional Sciences, University of Massachusetts-Lowell, Lowell, MA, 01854, USA.
| | - Ibrahim M Sayed
- Department of Biomedical and Nutritional Sciences, University of Massachusetts-Lowell, Lowell, MA, 01854, USA.
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8
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Xie WY, Ji ZH, Ren WZ, Zhao PS, Wei FH, Hu J, Yuan B, Gao W. Wheat peptide alleviates DSS-induced colitis by activating the Keap1-Nrf2 signaling pathway and maintaining the integrity of the gut barrier. Food Funct 2024; 15:5466-5484. [PMID: 38690672 DOI: 10.1039/d3fo04413k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Inflammatory bowel disease (IBD) is difficult to cure, and formulating a dietary plan is an effective means to prevent and treat this disease. Wheat peptide contains a variety of bioactive peptides with anti-inflammatory and antioxidant functions. The results of this study showed that preventive supplementation with wheat peptide (WP) can significantly alleviate the symptoms of dextran sulfate sodium (DSS)-induced colitis in mice. WP can increase body weight, alleviate colon shortening, and reduce disease activity index (DAI) scores. In addition, WP improved intestinal microbial disorders in mice with colitis. Based on LC-MS, a total of 313 peptides were identified in WP, 4 of which were predicted to be bioactive peptides. The regulatory effects of WP and four bioactive peptides on the Keap1-Nrf2 signaling pathway were verified in Caco-2 cells. In conclusion, this study demonstrated that WP alleviates DSS-induced colitis by helping maintain gut barrier integrity and targeting the Keap1-Nrf2 axis; these results provided a rationale for adding WP to dietary strategies to prevent IBD.
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Affiliation(s)
- Wen-Yin Xie
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Zhong-Hao Ji
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
- Department of Basic Medicine, Changzhi Medical College, Changzhi 046000, Shanxi, China
| | - Wen-Zhi Ren
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Pei-Sen Zhao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Fan-Hao Wei
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - JinPing Hu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Bao Yuan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Wei Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
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9
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Achi SC, McGrosso D, Tocci S, Ibeawuchi SR, Sayed IM, Gonzalez DJ, Das S. Proteome profiling identifies a link between the mitochondrial pathways and host-microbial sensor ELMO1 following Salmonella infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592405. [PMID: 38746404 PMCID: PMC11092768 DOI: 10.1101/2024.05.03.592405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The host EnguLfment and cell MOtility protein 1 (ELMO1) is a cytosolic microbial sensor that facilitates bacterial sensing, internalization, clearance, and inflammatory responses. We have shown previously that ELMO1 binds bacterial effector proteins, including pathogenic effectors from Salmonella and controls host innate immune signaling. To understand the ELMO1-regulated host pathways, we have performed liquid chromatography Multinotch MS3-Tandem Mass Tag (TMT) multiplexed proteomics to determine the global quantification of proteins regulated by ELMO1 in macrophages during Salmonella infection. Comparative proteome analysis of control and ELMO1-depleted murine J774 macrophages after Salmonella infection quantified more than 7000 proteins with a notable enrichment in mitochondrial-related proteins. Gene ontology enrichment analysis revealed 19 upregulated and 11 downregulated proteins exclusive to ELMO1-depleted cells during infection, belonging to mitochondrial functions, metabolism, vesicle transport, and the immune system. By assessing the cellular energetics via Seahorse analysis, we found that Salmonella infection alters mitochondrial metabolism, shifting it from oxidative phosphorylation to glycolysis. Importantly, these metabolic changes are significantly influenced by the depletion of ELMO1. Furthermore, ELMO1 depletion resulted in a decreased ATP rate index following Salmonella infection, indicating its importance in counteracting the effects of Salmonella on immunometabolism. Among the proteins involved in mitochondrial pathways, mitochondrial fission protein DRP1 was significantly upregulated in ELMO1-depleted cells and in ELMO1-KO mice intestine following Salmonella infection. Pharmacological Inhibition of DRP1 revealed the link of the ELMO1-DRP1 pathway in regulating the pro-inflammatory cytokine TNF-α following infection. The role of ELMO1 has been further characterized by a proteome profile of ELMO1-depleted macrophage infected with SifA mutant and showed the involvement of ELMO1-SifA on mitochondrial function, metabolism and host immune/defense responses. Collectively, these findings unveil a novel role for ELMO1 in modulating mitochondrial functions, potentially pivotal in modulating inflammatory responses. Significance Statement Host microbial sensing is critical in infection and inflammation. Among these sensors, ELMO1 has emerged as a key regulator, finely tuning innate immune signaling and discriminating between pathogenic and non-pathogenic bacteria through interactions with microbial effectors like SifA of Salmonella . In this study, we employed Multinotch MS3-Tandem Mass Tag (TMT) multiplexed proteomics to determine the proteome alterations mediated by ELMO1 in macrophages following WT and SifA mutant Salmonella infection. Our findings highlight a substantial enrichment of host proteins associated with metabolic pathways and mitochondrial functions. Notably, we validated the mitochondrial fission protein DRP1 that is upregulated in ELMO1-depleted macrophages and in ELMO1 knockout mice intestine after infection. Furthermore, we demonstrated that Salmonella -induced changes in cellular energetics are influenced by the presence of ELMO1. This work shed light on a possible novel link between mitochondrial dynamics and microbial sensing in modulating immune responses.
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10
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Seidelin JB, Jensen S, Hansen M, de Carvalho Bronze MR, Cuchet-Lourenҫo D, Nejentsev S, LaCasse EC, Nielsen OH. IAPs and RIPK1 mediate LPS-induced cytokine production in healthy subjects and Crohn's disease. Clin Exp Immunol 2024; 215:291-301. [PMID: 37583360 PMCID: PMC10876114 DOI: 10.1093/cei/uxad092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023] Open
Abstract
Innate immune activity fuels intestinal inflammation in Crohn's disease (CD), an inflammatory bowel disease. Identification and targeting of new molecular regulators of the innate activity are warranted to control the disease. Inhibitor of apoptosis proteins (IAPs) regulate both cell survival and inflammatory signaling. We investigated the effects of IAP inhibition by second mitochondria-derived activator of caspases (SMAC) mimetics (SMs) on innate responses and cell death to pathogen-associated molecular patterns in peripheral blood mononuclear cells (PBMCs) and monocytes. IAPs inhibited lipopolysaccharide (LPS)-induced expression of proinflammatory interleukin (IL)-1β, IL-6. Likewise, LPS (but not muramyl dipeptide or Escherichia coli) induced TNF-α was inhibited in CD and control PBMCs. The SM effect was partially reversed by inhibition of receptor-interacting serine/threonine-protein kinase 1 (RIPK1). The effect was mainly cell death independent. Thus, IAP inhibition by SMs leads to reduced production of proinflammatory cytokines and may be considered in the efforts to develop new therapeutic strategies to control CD.
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Affiliation(s)
- Jakob Benedict Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark
| | - Simone Jensen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark
| | - Morten Hansen
- Department of Oncology, Center for Cancer Immune Therapy, Herlev Hospital, University of Copenhagen, Denmark
| | | | | | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Eric Charles LaCasse
- Apoptosis Research Centre, Children’s Hospital of Eastern Ontario Research Institute, Canada
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark
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11
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Sharma A, Achi SC, Ibeawuchi SR, Anandachar MS, Gementera H, Chaudhury U, Usmani F, Vega K, Sayed IM, Das S. The crosstalk between microbial sensors ELMO1 and NOD2 shape intestinal immune responses. Virulence 2023; 14:2171690. [PMID: 36694274 PMCID: PMC9980453 DOI: 10.1080/21505594.2023.2171690] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 01/26/2023] Open
Abstract
Microbial sensors play an essential role in maintaining cellular homoeostasis. Our knowledge is limited on how microbial sensing helps in differential immune response and its link to inflammatory diseases. Recently we have confirmed that ELMO1 (Engulfment and Cell Motility Protein-1) present in cytosol is involved in pathogen sensing, engulfment, and intestinal inflammation. Here, we show that ELMO1 interacts with another sensor, NOD2 (Nucleotide-binding oligomerization domain-containing protein 2), that recognizes bacterial cell wall component muramyl dipeptide (MDP). The polymorphism of NOD2 is linked to Crohn's disease (CD) pathogenesis. Interestingly, we found that overexpression of ELMO1 and mutant NOD2 (L1007fs) were not able to clear the CD-associated adherent invasive E. coli (AIEC-LF82). The functional implications of ELMO1-NOD2 interaction in epithelial cells were evaluated by using enteroid-derived monolayers (EDMs) from ELMO1 and NOD2 KO mice. Subsequently we also assessed the immune response in J774 macrophages depleted of either ELMO1 or NOD2 or both. The infection of murine EDMs with AIEC-LF82 showed higher bacterial load in ELMO1-KO, NOD2 KO EDMs, and ELMO1 KO EDMs treated with NOD2 inhibitors. The murine macrophage cells showed that the downregulation of ELMO1 and NOD2 is associated with impaired bacterial clearance that is linked to reduce pro-inflammatory cytokines and reactive oxygen species. Our results indicated that the crosstalk between microbial sensors in enteric infection and inflammatory diseases impacts the fate of the bacterial load and disease pathogenesis.
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Affiliation(s)
- Aditi Sharma
- Department of Pathology, University of California San Diego; San Diego, California, USA
| | | | - Stella-Rita Ibeawuchi
- Department of Pathology, University of California San Diego; San Diego, California, USA
| | | | - Hobie Gementera
- Department of Pathology, University of California San Diego; San Diego, California, USA
| | - Uddeep Chaudhury
- Department of Pathology, University of California San Diego; San Diego, California, USA
| | - Fatima Usmani
- Department of Pathology, University of California San Diego; San Diego, California, USA
| | - Kevin Vega
- Department of Pathology, University of California San Diego; San Diego, California, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California San Diego; San Diego, California, USA
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Soumita Das
- Department of Pathology, University of California San Diego; San Diego, California, USA
- Department of Biomedical and Nutritional Science, University of Massachusetts-Lowell, Lowell, USA
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12
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Anandachar MS, Roy S, Sinha S, Boadi A, Katkar GD, Ghosh P. Diverse gut pathogens exploit the host engulfment pathway via a conserved mechanism. J Biol Chem 2023; 299:105390. [PMID: 37890785 PMCID: PMC10696401 DOI: 10.1016/j.jbc.2023.105390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/22/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Macrophages clear infections by engulfing and digesting pathogens within phagolysosomes. Pathogens escape this fate by engaging in a molecular arms race; they use WxxxE motif-containing "effector" proteins to subvert the host cells they invade and seek refuge within protective vacuoles. Here, we define the host component of the molecular arms race as an evolutionarily conserved polar "hot spot" on the PH domain of ELMO1 (Engulfment and Cell Motility protein 1), which is targeted by diverse WxxxE effectors. Using homology modeling and site-directed mutagenesis, we show that a lysine triad within the "patch" directly binds all WxxxE effectors tested: SifA (Salmonella), IpgB1 and IpgB2 (Shigella), and Map (enteropathogenic Escherichia coli). Using an integrated SifA-host protein-protein interaction network, in silico network perturbation, and functional studies, we show that the major consequences of preventing SifA-ELMO1 interaction are reduced Rac1 activity and microbial invasion. That multiple effectors of diverse structure, function, and sequence bind the same hot spot on ELMO1 suggests that the WxxxE effector(s)-ELMO1 interface is a convergence point of intrusion detection and/or host vulnerability. We conclude that the interface may represent the fault line in coevolved molecular adaptations between pathogens and the host, and its disruption may serve as a therapeutic strategy.
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Affiliation(s)
- Mahitha Shree Anandachar
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA; Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Suchismita Roy
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA
| | - Saptarshi Sinha
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA
| | - Agyekum Boadi
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA
| | - Gajanan D Katkar
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA; Department of Medicine, University of California San Diego, San Diego, California, USA.
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13
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Schneider K, Arandjelovic S. Apoptotic cell clearance components in inflammatory arthritis. Immunol Rev 2023; 319:142-150. [PMID: 37507355 PMCID: PMC10615714 DOI: 10.1111/imr.13256] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease of the synovial joints that affects ~1% of the human population. Joint swelling and bone erosion, hallmarks of RA, contribute to disability and, sometimes, loss of life. Mechanistically, disease is driven by immune dysregulation characterized by circulating autoantibodies, inflammatory mediators, tissue degradative enzymes, and metabolic dysfunction of resident stromal and recruited immune cells. Cell death by apoptosis has been therapeutically explored in animal models of RA due to the comparisons drawn between synovial hyperplasia and paucity of apoptosis in RA with the malignant transformation of cancer cells. Several efforts to induce cell death have shown benefits in reducing the development and/or severity of the disease. Apoptotic cells are cleared by phagocytes in a process known as efferocytosis, which differs from microbial phagocytosis in its "immuno-silent," or anti-inflammatory, nature. Failures in efferocytosis have been linked to autoimmune disease, whereas administration of apoptotic cells in RA models effectively inhibits inflammatory indices, likely though efferocytosis-mediated resolution-promoting mechanisms. However, the nature of signaling pathways elicited and the molecular identity of clearance mediators in RA are understudied. Furthermore, canonical efferocytosis machinery elements also play important non-canonical functions in homeostasis and pathology. Here, we discuss the roles of efferocytosis machinery components in models of RA and discuss their potential involvement in disease pathophysiology.
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Affiliation(s)
- Kevin Schneider
- University of Virginia, Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, Charlottesville, VA, USA
| | - Sanja Arandjelovic
- University of Virginia, Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, Charlottesville, VA, USA
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14
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Anandachar MS, Roy S, Sinha S, Agyekum B, Ibeawuchi SR, Gementera H, Amamoto A, Katkar GD, Ghosh P. Diverse Gut Pathogens Exploit the Host Engulfment Pathway via a Conserved Mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.09.536168. [PMID: 37066267 PMCID: PMC10104235 DOI: 10.1101/2023.04.09.536168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Macrophages clear infections by engulfing and digesting pathogens within phagolysosomes. Pathogens escape this fate by engaging in a molecular arms race; they use WxxxE motif-containing effector proteins to subvert the host cells they invade and seek refuge within protective vacuoles. Here we define the host component of the molecular arms race as an evolutionarily conserved polar hotspot on the PH-domain of ELMO1 (Engulfment and Cell Motility1), which is targeted by diverse WxxxE-effectors. Using homology modeling and site-directed mutagenesis, we show that a lysine triad within the patch directly binds all WxxxE-effectors tested: SifA (Salmonella), IpgB1 and IpgB2 (Shigella), and Map (enteropathogenic E. coli). Using an integrated SifA-host protein-protein interaction (PPI) network, in-silico network perturbation, and functional studies we show that the major consequences of preventing SifA-ELMO1 interaction are reduced Rac1 activity and microbial invasion. That multiple effectors of diverse structure, function, and sequence bind the same hotpot on ELMO1 suggests that the WxxxE-effector(s)-ELMO1 interface is a convergence point of intrusion detection and/or host vulnerability. We conclude that the interface may represent the fault line in co-evolved molecular adaptations between pathogens and the host and its disruption may serve as a therapeutic strategy.
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15
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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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16
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Achi SC, Karimilangi S, Lie D, Sayed IM, Das S. The WxxxE proteins in microbial pathogenesis. Crit Rev Microbiol 2023; 49:197-213. [PMID: 35287539 PMCID: PMC9737147 DOI: 10.1080/1040841x.2022.2046546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 02/10/2022] [Accepted: 02/19/2022] [Indexed: 12/14/2022]
Abstract
Effector proteins secreted by pathogens modulate various host cellular processes and help in bacterial pathogenesis. Some of these proteins, injected by enteric pathogens via Type Three Secretion System (T3SS) were grouped together based on a conserved signature motif (WxxxE) present in them. The presence of WxxxE motif is not limited to effectors released by enteric pathogens or the T3SS but has been detected in non-enteric pathogens, plant pathogens and in association with Type II and Type IV secretion systems. WxxxE effectors are involved in actin organization, inflammation regulation, vacuole or tubule formation, endolysosomal signalling regulation, tight junction disruption, and apoptosis. The WxxxE sequence has also been identified in TIR [Toll/interleukin-1 (IL-1) receptor] domains of bacteria and host. In the present review, we have focussed on the established and predicted functions of WxxxE effectors secreted by several pathogens, including enteric, non-enteric, and plant pathogens.
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Affiliation(s)
| | - Sareh Karimilangi
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Dominique Lie
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Ibrahim M. Sayed
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
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17
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Cordero RY, Cordero JB, Stiemke AB, Datta LW, Buyske S, Kugathasan S, McGovern DPB, Brant SR, Simpson CL. Trans-ancestry, Bayesian meta-analysis discovers 20 novel risk loci for inflammatory bowel disease in an African American, East Asian and European cohort. Hum Mol Genet 2023; 32:873-882. [PMID: 36308435 PMCID: PMC9941836 DOI: 10.1093/hmg/ddac269] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated chronic intestinal disorder with major phenotypes: ulcerative colitis (UC) and Crohn's disease (CD). Multiple studies have identified over 240 IBD susceptibility loci. However, most studies have centered on European (EUR) and East Asian (EAS) populations. The prevalence of IBD in non-EUR, including African Americans (AAs), has risen in recent years. Here we present the first attempt to identify loci in AAs using a trans-ancestry Bayesian approach (MANTRA) accounting for heterogeneity between diverse ancestries while allowing for the similarity between closely related populations. We meta-analyzed genome-wide association studies (GWAS) and Immunochip data from a 2015 EUR meta-analysis of 38 155 IBD cases and 48 485 controls and EAS Immunochip study of 2824 IBD cases and 3719 controls, and our recent AA IBD GWAS of 2345 cases and 5002 controls. Across the major IBD phenotypes, we found significant evidence for 92% of 205 loci lead SNPs from the 2015 meta-analysis, but also for three IBD loci only established in latter studies. We detected 20 novel loci, all containing immunity-related genes or genes with other evidence for IBD or immune-mediated disease relevance: PLEKHG5;TNFSFR25 (encoding death receptor 3, receptor for TNFSF15 gene product TL1A), XKR6, ELMO1, BC021024;PI4KB;PSMD4 and APLP1 for IBD; AUTS2, XKR6, OSER1, TET2;AK094561, BCAP29 and APLP1 for CD; and GABBR1;MOG, DQ570892, SPDEF;ILRUN, SMARCE1;CCR7;KRT222;KRT24;KRT25, ANKS1A;TCP11, IL7, LRRC18;WDFY4, XKR6 and TNFSF4 for UC. Our study highlights the value of combining low-powered genomic studies from understudied populations of diverse ancestral backgrounds together with a high-powered study to enable novel locus discovery, including potentially important therapeutic IBD gene targets.
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Affiliation(s)
- Roberto Y Cordero
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jennifer B Cordero
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew B Stiemke
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ 08854, USA
| | - Subra Kugathasan
- Department of Pediatrics and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
- Rutgers Crohn’s and Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Human Genetics Institute of New Jersey and Department of Genetics, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Claire L Simpson
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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18
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Ivanova M, Bottiglieri L, Sajjadi E, Venetis K, Fusco N. Malignancies in Patients with Celiac Disease: Diagnostic Challenges and Molecular Advances. Genes (Basel) 2023; 14:376. [PMID: 36833303 PMCID: PMC9956047 DOI: 10.3390/genes14020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Celiac disease (CD) is a multiorgan autoimmune disorder of the chronic intestinal disease group characterized by duodenal inflammation in genetically predisposed individuals, precipitated by gluten ingestion. The pathogenesis of celiac disease is now widely studied, overcoming the limits of the purely autoimmune concept and explaining its hereditability. The genomic profiling of this condition has led to the discovery of numerous genes involved in interleukin signaling and immune-related pathways. The spectrum of disease manifestations is not limited to the gastrointestinal tract, and a significant number of studies have considered the possible association between CD and neoplasms. Patients with CD are found to be at increased risk of developing malignancies, with a particular predisposition of certain types of intestinal cancer, lymphomas, and oropharyngeal cancers. This can be partially explained by common cancer hallmarks present in these patients. The study of gut microbiota, microRNAs, and DNA methylation is evolving to find the any possible missing links between CD and cancer incidence in these patients. However, the literature is extremely mixed and, therefore, our understanding of the biological interplay between CD and cancer remains limited, with significant implications in terms of clinical management and screening protocols. In this review article, we seek to provide a comprehensive overview of the genomics, epigenomics, and transcriptomics data on CD and its relation to the most frequent types of neoplasms that may occur in these patients.
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Affiliation(s)
- Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Luca Bottiglieri
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
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19
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Sayed IM, Chakraborty A, Das S. Assays with Patient-Derived Organoids to Evaluate the Impact of Microbial Infection on Base Excision Repair (BER) Enzymes. Methods Mol Biol 2023; 2701:157-172. [PMID: 37574481 DOI: 10.1007/978-1-0716-3373-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Microbes play an important role in regulating cellular responses and the induction of chronic diseases. Infection and chronic inflammation can cause DNA damage, and the accumulation of mutations leads to cancer development. The well-known examples of cancer-associated microbes are Helicobacter pylori in gastric cancer and Fusobacterium nucleatum (Fn), Bacteroides fragilis, and E.coli NC101 in colorectal cancer (CRC). These carcinopathogens modify the expressions of the base excision repair enzymes and cause DNA damage. This chapter will show how Fn can initiate CRC through the downregulation of a critical enzyme of the base excision repair (BER) pathway that subsequently causes accumulation of DNA damage. We used the stem cell-based organoid model and enteroid-derived monolayer (EDM) from the murine and human colon to assess the impact of infection on the expression of BER enzymes on the transcriptional and translational levels and to develop other functional assays. For example, we used this EDM model to assess the inflammatory response, DNA damage response, and physiological responses, where we correlated the level of these parameters to BER enzyme levels.
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Affiliation(s)
- Ibrahim M Sayed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Asyut, Egypt
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Soumita Das
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA.
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20
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M'Koma AE. Inflammatory Bowel Disease: Clinical Diagnosis and Pharmaceutical Management. MEDICAL RESEARCH ARCHIVES 2023; 11:10.18103/mra.v11i1.3135. [PMID: 37089816 PMCID: PMC10118064 DOI: 10.18103/mra.v11i1.3135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease has an enormous impact on public health, medical systems, economies, and social conditions. Biologic therapy has ameliorated the treatment and clinical course of patients with inflammatory bowel disease. The efficacy and safety profiles of currently available therapies are still less that optimal in numerous ways, highlighting the requirement for new therapeutic targets. A bunch of new drug studies are underway in inflammatory bowel disease with promising results. This is an outlined guideline of clinical diagnosis and pharmaceutical therapy of inflammatory bowel disease. Outline delineates the overall recommendations on the modern principles of desirable practice to bolster the adoption of best implementations and exploration as well as inflammatory bowel disease patient, gastroenterologist, and other healthcare provider education. Inflammatory bowel disease encompasses Crohn's disease and ulcerative colitis, the two unsolved medical inflammatory bowel disease-subtypes condition with no drug for cure. The signs and symptoms on first presentation relate to the anatomical localization and severity of the disease and less with the resulting diagnosis that can clinically and histologically be non-definitive to interpret and establish criteria, specifically in colonic inflammatory bowel disease when the establishment is inconclusive is classified as indeterminate colitis. Conservative pharmaceuticals and accessible avenues do not depend on the disease phenotype. The first line management is to manage symptoms and stabilize active disease; at the same time maintenance therapy is indicated. Nutrition and diet do not play a primary therapeutic role but is warranted as supportive care. There is need of special guideline that explore solution of groundwork gap in terms of access limitations to inflammatory bowel disease care, particularly in developing countries and the irregular representation of socioeconomic stratification with a strategic plan, for the unanswered questions and perspective for the future, especially during the surfaced global COVID-19 pandemic caused by coronavirus SARS-CoV2 impacting on both the patient's psychological functioning and endoscopy services. Establishment of a global registry system and accumulated experiences have led to consensus for inflammatory bowel disease management under the COVID-19 pandemic. Painstakingly, the pandemic has influenced medical care systems for these patients. I briefly herein viewpoint summarize among other updates the telemedicine roles during the pandemic and how operationally inflammatory bowel disease centers managed patients and ensured quality of care. In conclusion: inflammatory bowel disease has become a global emergent disease. Serious medical errors are public health problem observed in developing nations i.e., to distinguish inflammatory bowel disease and infectious and parasitic diseases. Refractory inflammatory bowel disease is a still significant challenge in the management of patients with Crohn's disease and ulcerative colitis. There are gaps in knowledge and future research directions on the recent newly registered pharmaceuticals. The main clinical outcomes for inflammatory bowel disease were maintained during the COVID-19 pandemic period.
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Affiliation(s)
- Amosy Ephreim M'Koma
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States
- Division of General Surgery, Section of Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
- Affiliated Scientist Investigator, The American Society of Colon, and Rectal Surgeons (ASCRS), Arlington Heights, IL 60005, Unite States
- The American Gastroenterological Association (AGA), Bethesda, MD 20814, United States
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21
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Wen B, Li S, Ruan L, Yang Y, Chen Z, Zhang B, Yang X, Jie H, Li S, Zeng Z, Liu S. Engulfment and cell motility protein 1 fosters reprogramming of tumor-associated macrophages in colorectal cancer. Cancer Sci 2022; 114:410-422. [PMID: 36310143 PMCID: PMC9899619 DOI: 10.1111/cas.15628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/26/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Abstract
Functional reprogramming of tumor-associated macrophages (TAMs) is crucial to their potent tumor-supportive capacity. However, the molecular mechanism behind the reprogramming process remains poorly understood. Here, we identify engulfment and cell motility protein 1 (ELMO1) as a crucial player for TAM reprogramming in colorectal cancer (CRC). The expression of ELMO1 in stromal but not epithelial tumor cells was positively associated with advanced clinical stage and poor disease-free survival in CRC. An increase in ELMO1 expression was specifically found in TAMs, but not in other multiple nonmalignant stromal cells. Gain- and loss-of-function assays indicated ELMO1 reprogrammed macrophages to a TAM-like phenotype through Rac1 activation. In turn, ELMO1-reprogrammed macrophages were shown to not only facilitate the malignant behaviors of CRC cells but exhibited potent phagocytosis of tumor cells. Taken together, our work underscores the importance of ELMO1 in determining functional reprogramming of TAMs and could provide new insights on potential therapeutic strategies against CRC.
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Affiliation(s)
- Bo Wen
- Department of Gastrointestinal SurgeryCentral Hospital of ShaoyangShaoyangChina
| | - Sheng Li
- Department of Gastrointestinal SurgeryCentral Hospital of ShaoyangShaoyangChina
| | - Lei Ruan
- Department of Colorectal Surgery and Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Yanping Yang
- Department of PathologyCentral Hospital of ShaoyangShaoyangChina
| | - Zilin Chen
- Department of Medical OncologyCentral Hospital of ShaoyangShaoyangChina
| | - Bin Zhang
- Department of Gastrointestinal SurgeryCentral Hospital of ShaoyangShaoyangChina
| | - Xin Yang
- Department of Colorectal Surgery and Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Haiqing Jie
- Department of Colorectal Surgery and Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Shujuan Li
- Department of PharmacyThe Third Affiliated Hospital of Zhengzhou UniversityZhengzhou, HenanChina
| | - Ziwei Zeng
- Department of Colorectal Surgery and Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,University Clinic MannheimMedical Faculty Mannheim, University of HeidelbergMannheimGermany
| | - Sisi Liu
- Department of PathologyCentral Hospital of ShaoyangShaoyangChina
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22
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Sharma A, Achi SC, Ibeawuchi S, Anandachar MS, Gementera H, Chaudhury U, Usmani F, Vega K, Sayed IM, Das S. The crosstalk between microbial sensors ELMO1 and NOD2 shape intestinal immune responses.. [DOI: 10.1101/2022.07.09.499433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
ABSTRACTMicrobial sensors play an essential role in maintaining cellular homeostasis. Our knowledge is limited on how microbial sensing helps in differential immune response and its link to inflammatory diseases. Recently, we have shown that cytosolic sensor ELMO1 (Engulfment and Cell Motility Protein-1) binds to effectors from pathogenic bacteria and controls intestinal inflammation. Here, we show that ELMO1 interacts with another sensor, NOD2 (Nucleotide-binding oligomerization domain-containing protein 2), that recognizes bacterial cell wall component muramyl dipeptide (MDP). The polymorphism of NOD2 is linked to Crohn’s disease (CD) pathogenesis. Interestingly, we found that overexpression of ELMO1 and mutant NOD2 (L1007fs) were not able to clear the CD-associated adherent invasive E. coli (AIEC-LF82). To understand the interplay of microbial sensing of ELMO1-NOD2 in epithelial cells and macrophages, we used enteroid-derived monolayers (EDMs) from ELMO1 and NOD2 KO mice and ELMO1 and NOD2-depleted murine macrophage cell lines. The infection of murine EDMs with AIEC-LF82 showed higher bacterial load in ELMO1-KO, NOD2 KO EDMs, and ELMO1 KO EDMs treated with NOD2 inhibitors. The murine macrophage cells showed that the downregulation of ELMO1 and NOD2 is associated with impaired bacterial clearance that is linked to reduced pro-inflammatory cytokines and reactive oxygen species. Our results indicated that the crosstalk between microbial sensors in enteric infection and inflammatory diseases impacts the fate of the bacterial load and disease pathogenesis.
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23
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Boger M, Bennewitz K, Wohlfart DP, Hausser I, Sticht C, Poschet G, Kroll J. Comparative Morphological, Metabolic and Transcriptome Analyses in elmo1−/−, elmo2−/−, and elmo3−/− Zebrafish Mutants Identified a Functional Non-Redundancy of the Elmo Proteins. Front Cell Dev Biol 2022; 10:918529. [PMID: 35874819 PMCID: PMC9304559 DOI: 10.3389/fcell.2022.918529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
The ELMO protein family consists of the homologues ELMO1, ELMO2 and ELMO3. Several studies have shown that the individual ELMO proteins are involved in a variety of cellular and developmental processes. However, it has poorly been understood whether the Elmo proteins show similar functions and act redundantly. To address this question, elmo1−/−, elmo2−/− and elmo3−/− zebrafish were generated and a comprehensive comparison of the phenotypic changes in organ morphology, transcriptome and metabolome was performed in these mutants. The results showed decreased fasting and increased postprandial blood glucose levels in adult elmo1−/−, as well as a decreased vascular formation in the adult retina in elmo1−/−, but an increased vascular formation in the adult elmo3−/− retina. The phenotypical comparison provided few similarities, as increased Bowman space areas in adult elmo1−/− and elmo2−/− kidneys, an increased hyaloid vessel diameter in elmo1−/− and elmo3−/− and a transcriptional downregulation of the vascular development in elmo1−/−, elmo2−/−, and elmo3−/− zebrafish larvae. Besides this, elmo1−/−, elmo2−/−, and elmo3−/− zebrafish exhibited several distinct changes in the vascular and glomerular structure and in the metabolome and the transcriptome. Especially, elmo3−/− zebrafish showed extensive differences in the larval transcriptome and an impaired survivability. Together, the data demonstrated that the three zebrafish Elmo proteins regulate not only similar but also divergent biological processes and mechanisms and show a low functional redundancy.
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Affiliation(s)
- Mike Boger
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katrin Bennewitz
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Philipp Wohlfart
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ingrid Hausser
- Institute of Pathology IPH, EM Lab, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jens Kroll
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- *Correspondence: Jens Kroll,
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24
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Lucafò M, Muzzo A, Marcuzzi M, Giorio L, Decorti G, Stocco G. Patient-derived organoids for therapy personalization in inflammatory bowel diseases. World J Gastroenterol 2022; 28:2636-2653. [PMID: 35979165 PMCID: PMC9260862 DOI: 10.3748/wjg.v28.i24.2636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders of the intestinal tract that have emerged as a growing problem in industrialized countries. Knowledge of IBD pathogenesis is still incomplete, and the most widely-accepted interpretation considers genetic factors, environmental stimuli, uncontrolled immune responses and altered intestinal microbiota composition as determinants of IBD, leading to dysfunction of the intestinal epithelial functions. In vitro models commonly used to study the intestinal barrier do not fully reflect the proper intestinal architecture. An important innovation is represented by organoids, 3D in vitro cell structures derived from stem cells that can self-organize into functional organ-specific structures. Organoids may be generated from induced pluripotent stem cells or adult intestinal stem cells of IBD patients and therefore retain their genetic and transcriptomic profile. These models are powerful pharmacological tools to better understand IBD pathogenesis, to study the mechanisms of action on the epithelial barrier of drugs already used in the treatment of IBD, and to evaluate novel target-directed molecules which could improve therapeutic strategies. The aim of this review is to illustrate the potential use of organoids for therapy personalization by focusing on the most significant advances in IBD research achieved through the use of adult stem cells-derived intestinal organoids.
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Affiliation(s)
- Marianna Lucafò
- Advanced Translational Diagnostics Laboratory, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, Trieste 34137, Italy
| | - Antonella Muzzo
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste 34127, Italy
| | - Martina Marcuzzi
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Lorenzo Giorio
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Giuliana Decorti
- Advanced Translational Diagnostics Laboratory, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, Trieste 34137, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste 34127, Italy
| | - Gabriele Stocco
- Advanced Translational Diagnostics Laboratory, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, Trieste 34137, Italy
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
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25
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Tocci S, Ibeawuchi SR, Das S, Sayed IM. Role of ELMO1 in inflammation and cancer-clinical implications. Cell Oncol (Dordr) 2022; 45:505-525. [PMID: 35668246 DOI: 10.1007/s13402-022-00680-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Engulfment and cell motility protein 1 (ELMO1) is a key protein for innate immunity since it is required for the clearance of apoptotic cells and pathogenic bacteria as well as for the control of inflammatory responses. ELMO1, through binding with Dock180 and activation of the Rac1 signaling pathway, plays a significant role in cellular shaping and motility. Rac-mediated actin cytoskeletal rearrangement is essential for bacterial phagocytosis, but also plays a crucial role in processes such as cancer cell invasion and metastasis. While the role of ELMO1 in bacterial infection and inflammatory responses is well established, its implication in cancer is not widely explored yet. Molecular changes or epigenetic alterations such as DNA methylation, which ultimately leads to alterations in gene expression and deregulation of cellular signaling, has been reported for ELMO1 in different cancer types. CONCLUSIONS In this review, we provide an updated and comprehensive summary of the roles of ELMO1 in infection, inflammatory diseases and cancer. We highlight the possible mechanisms regulated by ELMO1 that are relevant for cancer development and progression and provide insight into the possible use of ELMO1 as a diagnostic biomarker and therapeutic target.
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Affiliation(s)
- Stefania Tocci
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
| | - Ibrahim M Sayed
- Department of Pathology, University of California San Diego, La Jolla, CA, USA. .,Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt.
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M’Koma AE. Inflammatory Bowel Disease: Clinical Diagnosis and Surgical Treatment-Overview. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:567. [PMID: 35629984 PMCID: PMC9144337 DOI: 10.3390/medicina58050567] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022]
Abstract
This article is an overview of guidelines for the clinical diagnosis and surgical treatment of predominantly colonic inflammatory bowel diseases (IBD). This overview describes the systematically and comprehensively multidisciplinary recommendations based on the updated principles of evidence-based literature to promote the adoption of best surgical practices and research as well as patient and specialized healthcare provider education. Colonic IBD represents idiopathic, chronic, inflammatory disorders encompassing Crohn's colitis (CC) and ulcerative colitis (UC), the two unsolved medical subtypes of this condition, which present similarity in their clinical and histopathological characteristics. The standard state-of-the-art classification diagnostic steps are disease evaluation and assessment according to the Montreal classification to enable explicit communication with professionals. The signs and symptoms on first presentation are mainly connected with the anatomical localization and severity of the disease and less with the resulting diagnosis "CC" or "UC". This can clinically and histologically be non-definitive to interpret to establish criteria and is classified as indeterminate colitis (IC). Conservative surgical intervention varies depending on the disease phenotype and accessible avenues. The World Gastroenterology Organizations has, for this reason, recommended guidelines for clinical diagnosis and management. Surgical intervention is indicated when conservative treatment is ineffective (refractory), during intractable gastrointestinal hemorrhage, in obstructive gastrointestinal luminal stenosis (due to fibrotic scar tissue), or in the case of abscesses, peritonitis, or complicated fistula formation. The risk of colitis-associated colorectal cancer is realizable in IBD patients before and after restorative proctocolectomy with ileal pouch-anal anastomosis. Therefore, endoscopic surveillance strategies, aimed at the early detection of dysplasia, are recommended. During the COVID-19 pandemic, IBD patients continued to be admitted for IBD-related surgical interventions. Virtual and phone call follow-ups reinforcing the continuity of care are recommended. There is a need for special guidelines that explore solutions to the groundwork gap in terms of access limitations to IBD care in developing countries, and the irregular representation of socioeconomic stratification needs a strategic plan for how to address this serious emerging challenge in the global pandemic.
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Affiliation(s)
- Amosy Ephreim M’Koma
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, TN 37208-3500, USA; or ; Tel.: +1-615-327-6796; Fax: +1-615-327-6440
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, TN 37208-3599, USA
- Division of General Surgery, Section of Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232-0260, USA
- The American Society of Colon and Rectal Surgeons (ASCRS), 2549 Waukegan Road, #210, Bannockburn, IL 600015, USA
- The American Gastroenterological Association (AGA), Bethesda, MD 20814, USA
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27
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Katkar GD, Sayed IM, Anandachar MS, Castillo V, Vidales E, Toobian D, Usmani F, Sawires JR, Leriche G, Yang J, Sandborn WJ, Das S, Sahoo D, Ghosh P. Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. Commun Biol 2022; 5:231. [PMID: 35288651 PMCID: PMC8921270 DOI: 10.1038/s42003-022-03168-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
A computational platform, Boolean network explorer (BoNE), has recently been developed to infuse AI-enhanced precision into drug discovery; it enables invariant Boolean Implication Networks of disease maps for prioritizing high-value targets. Here we used BoNE to query an Inflammatory Bowel Disease (IBD)-map and prioritize a therapeutic strategy that involves dual agonism of two nuclear receptors, PPARα/γ. Balanced agonism of PPARα/γ was predicted to modulate macrophage processes, ameliorate colitis, 'reset' the gene expression network from disease to health. Predictions were validated using a balanced and potent PPARα/γ-dual-agonist (PAR5359) in Citrobacter rodentium- and DSS-induced murine colitis models. Using inhibitors and agonists, we show that balanced-dual agonism promotes bacterial clearance efficiently than individual agonists, both in vivo and in vitro. PPARα is required and sufficient to induce the pro-inflammatory cytokines and cellular ROS, which are essential for bacterial clearance and immunity, whereas PPARγ-agonism blunts these responses, delays microbial clearance; balanced dual agonism achieved controlled inflammation while protecting the gut barrier and 'reversal' of the transcriptomic network. Furthermore, dual agonism reversed the defective bacterial clearance observed in PBMCs derived from IBD patients. These findings not only deliver a macrophage modulator for use as barrier-protective therapy in IBD, but also highlight the potential of BoNE to rationalize combination therapy.
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Affiliation(s)
- Gajanan D Katkar
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California San Diego, San Diego, USA.,Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Vanessa Castillo
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, USA
| | - Eleadah Vidales
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, USA
| | - Daniel Toobian
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, USA
| | - Fatima Usmani
- Department of Pathology, University of California San Diego, San Diego, USA
| | - Joseph R Sawires
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, USA
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, USA
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, USA
| | - William J Sandborn
- Department of Medicine, University of California San Diego, San Diego, USA.
| | - Soumita Das
- Department of Pathology, University of California San Diego, San Diego, USA.
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacob's School of Engineering, University of California San Diego, San Diego, USA. .,Department of Pediatrics, University of California San Diego, San Diego, USA. .,Rebecca and John Moore Comprehensive Cancer Center, University of California San Diego, San Diego, USA.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, USA. .,Department of Medicine, University of California San Diego, San Diego, USA. .,Rebecca and John Moore Comprehensive Cancer Center, University of California San Diego, San Diego, USA. .,Veterans Affairs Medical Center, La Jolla, San Diego, USA.
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Quach A, Jayaratne RR, Lee BJ, Ibeawuchi SR, Lim E, Das S, Barrett KE. Diarrheal pathogenesis in Salmonella infection may result from an imbalance in intestinal epithelial differentiation through reduced Notch signaling. J Physiol 2022; 600:1851-1865. [PMID: 35100665 DOI: 10.1113/jp282585] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/20/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Salmonella is a leading foodborne pathogen known to cause high chloride content diarrhea. Salmonella infection of murine enteroid-derived monolayers decreased DRA expression. Salmonella infection resulted in upregulation of the secretory epithelial marker ATOH1, the goblet cell marker Muc2, and the enteroendocrine cell marker ChgA. Downregulation of DRA may result from infection-induced Notch inhibition, as reflected by decreased expression of Notch intracellular domain and Hes1, as well as from decreased HNF1α signaling. The imbalance in intestinal epithelial differentiation favoring secretory over absorptive cell types is a possible mechanism by which Salmonella elicits diarrhea and may be relevant therapeutically. ABSTRACT Infections with non-typhoidal Salmonella spp. represent the most burdensome foodborne illnesses worldwide, yet despite their prevalence, the mechanism through which Salmonella elicits diarrhea is not entirely known. Intestinal ion transporters play important roles in fluid and electrolyte homeostasis in the intestine. We have previously shown that infection with Salmonella caused decreased colonic expression of the chloride/bicarbonate exchanger SLC26A3 (Down-Regulated in Adenoma; DRA) in a mouse model. In this study, we focused on the mechanism of DRA downregulation during Salmonella infection, by using murine epithelial enteroid-derived monolayers (EDM). The decrease in DRA expression caused by infection was recapitulated in EDM and accompanied by increased expression of ATOH1, the goblet cell marker Muc2, and the enteroendocrine cell marker ChgA. This suggested biased epithelial differentiation towards the secretory, rather than absorptive phenotype. In addition, the downstream Notch effector, Notch Intracellular Domain (NICD) and Hes1 were decreased following Salmonella infection. The relevance of Notch signaling was further investigated using a γ-secretase inhibitor, which recapitulated the downregulation in Hes1 and DRA as well as upregulation in ATOH1 and Muc2 seen following infection. Our findings suggest that Salmonella infection may result in a shift from absorptive to secretory cell types through Notch inhibition, which explains why there is a decreased capacity for absorption and ultimately the accumulation of diarrheal fluid. Our work also shows the value of EDM as a model to investigate mechanisms that might be targeted for therapy of diarrhea caused by Salmonella infection. Abstract figure legend Upon infection of the intestinal epithelium with Salmonella, diarrhea may be explained by an imbalance of intestinal epithelial differentiation. Downregulation of cell-fate commitment to the absorptive lineage, as reflected by decreased Hes1 and DRA, was observed. Conversely, upregulation of epithelial differentiation into secretory cell types was observed, as reflected by increased ATOH1, Muc2, and ChgA. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew Quach
- Division of Gastroenterology, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Rashini R Jayaratne
- Division of Gastroenterology, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Beom Jae Lee
- Division of Gastroenterology, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA.,Department of Gastroenterology, Korea University Guro Hospital, Seoul, 08308, Republic of Korea
| | - Stella-Rita Ibeawuchi
- Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Eileen Lim
- Division of Gastroenterology, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Kim E Barrett
- Division of Gastroenterology, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA.,Current affiliation: UC Davis School of Medicine, Education Building, 4610 X Street, Sacramento, CA, 95817, USA
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Sayed IM, Ibeawuchi SR, Lie D, Anandachar MS, Pranadinata R, Raffatellu M, Das S. The interaction of enteric bacterial effectors with the host engulfment pathway control innate immune responses. Gut Microbes 2022; 13:1991776. [PMID: 34719317 PMCID: PMC8565811 DOI: 10.1080/19490976.2021.1991776] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Host engulfment protein ELMO1 generates intestinal inflammation following internalization of enteric bacteria. In Shigella, bacterial effector IpgB1 interacts with ELMO1 and promotes bacterial invasion. IpgB1 belongs to the WxxxE effector family, a motif found in several effectors of enteric pathogens. Here, we have studied the role of WxxxE effectors, with emphasis on Salmonella SifA and whether it interacts with ELMO1 to regulate inflammation. In-silico-analysis of WxxxE effectors was performed using BLAST search and Clustal W program. The interaction of ELMO1 with SifA was assessed by GST pulldown assay and co-immunoprecipitation. ELMO1 knockout mice, and ELMO1-depleted murine macrophage J774 cell lines were challenged with WT and SifA mutant Salmonella. Bacterial effectors containing the WxxxE motif were transfected in WT and ELMO1-depleted J774 cells to assess the inflammatory cytokines. ELMO1 generates differential pro-inflammatory cytokines between pathogenic and nonpathogenic bacteria. WxxxE motif is present in pathogens and in the TIR domain of host proteins. The C-terminal part of ELMO1 interacts with SifA where WxxxE motif is important for interaction. ELMO1-SifA interaction affects bacterial colonization, dissemination, and inflammatory cytokines in vivo. Moreover, ELMO1-SifA interaction increases TNF-α and IL-6 production from the macrophage cell line and is associated with enhanced Rac1 activity. ELMO1 also interacts with WxxxE effectors IpgB1, IpgB2, and Map and induces inflammation after challenge with microbes or microbial ligands. ELMO1 generates a differential response through interaction with the WxxxE motif, which is absent in commensals. ELMO1-WxxxE interaction plays a role in bacterial pathogenesis and induction of inflammatory response.
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Affiliation(s)
- Ibrahim M Sayed
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Dominique Lie
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Rama Pranadinata
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Manuela Raffatellu
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, LA Jolla, CA, USA,Center for Mucosal Immunology, Chiba University-UC San Diego, La Jolla, CAUSA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA, USA,CONTACT Soumita Das Department of Pathology, University of California, San Diego, 9500 Gilman Drive, Mc 0644, George Palade Laboratory, Office Rm 256, San Diego, Ca, 92093-0644, USA
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Singh S, Anshita D, Ravichandiran V. MCP-1: Function, regulation, and involvement in disease. Int Immunopharmacol 2021; 101:107598. [PMID: 34233864 PMCID: PMC8135227 DOI: 10.1016/j.intimp.2021.107598] [Citation(s) in RCA: 431] [Impact Index Per Article: 107.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/25/2021] [Accepted: 03/17/2021] [Indexed: 02/08/2023]
Abstract
MCP-1 (Monocyte chemoattractant protein-1), also known as Chemokine (CC-motif) ligand 2 (CCL2), is from family of CC chemokines. It has a vital role in the process of inflammation, where it attracts or enhances the expression of other inflammatory factors/cells. It leads to the advancement of many disorders by this main mechanism of migration and infiltration of inflammatory cells like monocytes/macrophages and other cytokines at the site of inflammation. MCP-1 has been inculpated in the pathogenesis of numerous disease conditions either directly or indirectly like novel corona virus, cancers, neuroinflammatory diseases, rheumatoid arthritis, cardiovascular diseases. The elevated MCP-1 level has been observed in COVID-19 patients and proven to be a biomarker associated with the extremity of disease along with IP-10. This review will focus on involvement and role of MCP-1 in various pathological conditions.
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Affiliation(s)
- Sanjiv Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Export Promotion Industrial Park (EPIP), Zandaha Road, Hajipur, Bihar, India.
| | - D Anshita
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Export Promotion Industrial Park (EPIP), Zandaha Road, Hajipur, Bihar, India
| | - V Ravichandiran
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Export Promotion Industrial Park (EPIP), Zandaha Road, Hajipur, Bihar, India
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Sayed IM, Tindle C, Fonseca AG, Ghosh P, Das S. Functional assays with human patient-derived enteroid monolayers to assess the human gut barrier. STAR Protoc 2021; 2:100680. [PMID: 34337445 PMCID: PMC8313751 DOI: 10.1016/j.xpro.2021.100680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Here, we describe the use of polarized patient enteroid-derived monolayers (EDMs) to assess the impact of e-cigarettes on the human gut barrier. These EDMs can be adapted to culture in a 96-well plate for high-throughput screening. We model the effect of e-cigarettes by combining pathogens, enteroids, and e-cigarette vapor-infused media and assess gut barrier integrity, bacterial internalization, and inflammatory response of the gut epithelium. This protocol can be used to assess the effects of e-cigarette components on gut functions. For complete details on the use and execution of this protocol, please refer to Sharma et al. (2021).
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Affiliation(s)
- Ibrahim M. Sayed
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
- HUMANOID CoRE, University of California, San Diego, CA 92093, USA
| | - Ayden G. Fonseca
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
- HUMANOID CoRE, University of California, San Diego, CA 92093, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
- HUMANOID CoRE, University of California, San Diego, CA 92093, USA
- Department of Medicine, University of California, San Diego, CA 92093, USA
- Moore’s Comprehensive Cancer Center, University of California, San Diego, CA 92093, USA
- Veterans Affairs Medical Center, VA San Diego Healthcare System, La Jolla, San Diego, CA 92093, USA
| | - Soumita Das
- Department of Pathology, University of California, San Diego, CA 92093, USA
- HUMANOID CoRE, University of California, San Diego, CA 92093, USA
- Moore’s Comprehensive Cancer Center, University of California, San Diego, CA 92093, USA
- Veterans Affairs Medical Center, VA San Diego Healthcare System, La Jolla, San Diego, CA 92093, USA
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Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar GD, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S. Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. eLife 2021; 10:e66417. [PMID: 34463615 PMCID: PMC8463074 DOI: 10.7554/elife.66417] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. Methods We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Results Infected ALO monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Conclusions Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines. Funding This work was supported by the National Institutes for Health (NIH) grants 1R01DK107585-01A1, 3R01DK107585-05S1 (to SD); R01-AI141630, CA100768 and CA160911 (to PG) and R01-AI 155696 (to PG, DS and SD); R00-CA151673 and R01-GM138385 (to DS), R01- HL32225 (to PT), UCOP-R00RG2642 (to SD and PG), UCOP-R01RG3780 (to P.G. and D.S) and a pilot award from the Sanford Stem Cell Clinical Center at UC San Diego Health (P.G, S.D, D.S). GDK was supported through The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. L.C.A's salary was supported in part by the VA San Diego Healthcare System. This manuscript includes data generated at the UC San Diego Institute of Genomic Medicine (IGC) using an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (#S10 OD026929).
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Affiliation(s)
- Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
| | - MacKenzie Fuller
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
| | - Ayden Fonseca
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
| | - Sahar Taheri
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San DiegoSan DiegoUnited States
| | | | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research InstituteLa JollaUnited States
| | - Gajanan Dattatray Katkar
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
| | - Amanraj Claire
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
| | - Vanessa Castillo
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
| | - Moises Hernandez
- Division of Cardiothoracic Surgery, University of California San DiegoSan DiegoUnited States
| | - Hana Russo
- Department of Pathology, University of California San DiegoSan DiegoUnited States
| | - Jason Duran
- Division of Cardiology, Department of Internal Medicine, UC San Diego Medical CenterSan DiegoUnited States
| | - Laura E Crotty Alexander
- Pulmonary Critical Care Section, Veterans Affairs (VA) San Diego Healthcare SystemLa JollaUnited States
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San DiegoLa Jolla, CAUnited States
| | - Ann Tipps
- Department of Pathology, University of California San DiegoSan DiegoUnited States
| | - Grace Lin
- Department of Pathology, University of California San DiegoSan DiegoUnited States
| | | | - Ranajoy Chattopadhyay
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
- Cell Applications Inc.La Jolla, CAUnited States
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research InstituteLa JollaUnited States
- Division of Infectious Diseases, Department of Medicine, University of California, San DiegoLa JollaUnited States
- Department of Immunology and Microbiology, The Scripps Research InstituteLa JollaUnited States
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San DiegoSan DiegoUnited States
- Department of Pediatrics, University of California, San DiegoLa Jolla, CAUnited States
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San DiegoSan DiegoUnited States
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
- Department of Medicine, University of California, San DiegoLa Jolla, CAUnited States
| | - Soumita Das
- HUMANOID CoRE, University of California San DiegoSan DiegoUnited States
- Department of Pathology, University of California San DiegoSan DiegoUnited States
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Sayed IM, Ramadan HKA, El-Mokhtar MA, Abdel-Wahid L. Microbiome and gastrointestinal malignancies. CURRENT OPINION IN PHYSIOLOGY 2021. [DOI: 10.1016/j.cophys.2021.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chen F, Liu Q, Xiong Y, Xu L. Current Strategies and Potential Prospects of Nanomedicine-Mediated Therapy in Inflammatory Bowel Disease. Int J Nanomedicine 2021; 16:4225-4237. [PMID: 34188471 PMCID: PMC8236271 DOI: 10.2147/ijn.s310952] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD) such as Crohn's disease and ulcerative colitis are highly debilitating. IBDs are associated with the imbalance of inflammatory mediators within the inflamed bowel. Conventional drugs for IBD treatment include anti-inflammatory medications and immune suppressants. However, they suffer from a lack of bioavailability and high dose-induced systemic side effects. Nanoparticle (NP)-derived therapy improves therapeutic efficacy and increases targeting specificity. Recent studies have shown that nanomedicines, based on bowel disease's pathophysiology, are a fast-growing field. NPs can prolong the circulation period and reduce side effects by improving drug encapsulation and targeted delivery. Here, this review summarizes various IBD therapies with a focus on NP-derived applications, whereas their challenges and future perspectives have also been discussed.
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Affiliation(s)
- Fengqian Chen
- Translational Research Program, Department of Anesthesiology and Center for Shock Trauma Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Qi Liu
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Yang Xiong
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, People’s Republic of China
| | - Li Xu
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, 310006, People’s Republic of China
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Kim Y, Quach A, Das S, Barrett KE. Potentiation of calcium-activated chloride secretion and barrier dysfunction may underlie EGF receptor tyrosine kinase inhibitor-induced diarrhea. Physiol Rep 2021; 8:e14490. [PMID: 32652816 PMCID: PMC7354088 DOI: 10.14814/phy2.14490] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/23/2020] [Indexed: 12/13/2022] Open
Abstract
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFr TKIs) are first‐line therapies for various cancers, and cause dose‐limiting severe diarrhea in many patients. We hypothesized that diarrhea caused by EGFr TKIs might reflect actions on epithelial transport, barrier function, or both, which we tested using cell cultures including murine and human enteroid‐derived monolayers (EDMs), analyzed using electrophysiological and other relevant methods. EGFr TKIs (such as afatinib, erlotinib, and osimertinib) reversed the acute inhibitory effect of EGF on chloride secretion induced by carbachol (CCh) across T84 human colonic epithelial cells, which correlated with the diarrhea‐inducing effect of each agent clinically. EGFr TKIs also reduced transepithelial electrical resistance (TEER), whereas co‐treatment with CCh delayed the decrease in TEER compared with that of cells co‐treated with EGF. Furthermore, afatinib and erlotinib prevented EGF‐ or CCh‐induced EGFr phosphorylation. EGFr TKIs also suppressed phosphorylation of extracellular signal‐regulated kinase (Erk)1/2 in response to EGF, whereas they had weaker effects on CCh‐induced Erk1/2 phosphorylation. In human EDMs, EGF potentiated ion transport induced by CCh, whereas afatinib reversed this effect. The ability of EGFr TKIs to reverse the effects of EGF on calcium‐dependent chloride secretion could contribute to the diarrheal side effects of these agents, and their disruption of epithelial barrier dysfunction is likely also pathophysiologically significant. CCh‐activated Erk1/2 phosphorylation was relatively insensitive to EGFr TKIs and delayed the deleterious effects of EGFr TKIs on barrier function. These findings confirm and extend those of other authors, and may be relevant to designing strategies to overcome the diarrheal side effects of EGFr TKIs.
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Affiliation(s)
- Younjoo Kim
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Gastroenterology, Department of Internal Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Andrew Quach
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Kim E Barrett
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Ollivier A, Mahe MM, Guasch G. Modeling Gastrointestinal Diseases Using Organoids to Understand Healing and Regenerative Processes. Cells 2021; 10:cells10061331. [PMID: 34072095 PMCID: PMC8230068 DOI: 10.3390/cells10061331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/14/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022] Open
Abstract
The gastrointestinal tract is a continuous series of organs from the mouth to the esophagus, stomach, intestine and anus that allows digestion to occur. These organs are frequently associated with chronic stress and injury during life, subjecting these tissues to frequent regeneration and to the risk of developing disease-associated cancers. The possibility of generating human 3D culture systems, named organoids, that resemble histologically and functionally specific organs, has opened up potential applications in the analysis of the cellular and molecular mechanisms involved in epithelial wound healing and regenerative therapy. Here, we review how during normal development homeostasis takes place, and the role of the microenvironmental niche cells in the intestinal stem cell crypt as an example. Then, we introduce the notion of a perturbed niche during disease conditions affecting the esophageal–stomach junction and the colon, and describe the potential applications of organoid models in the analysis of human gastrointestinal disease mechanisms. Finally, we highlight the perspectives of organoid-based regenerative therapy to improve the repair of the epithelial barrier.
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Affiliation(s)
- Alexane Ollivier
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, CEDEX 09, 13273 Marseille, France;
| | - Maxime M. Mahe
- Cincinnati Children’s Hospital Medical Center, Department of Pediatric General and Thoracic Surgery, Cincinnati, OH 45229, USA;
- University of Cincinnati, Department of Pediatrics, Cincinnati, OH 45220, USA
- UMR Inserm 1235-TENS, INSERM, Université de Nantes, Institut des Maladies de l’Appareil Digestif–CHU de Nantes, 1 Rue Gaston Veil, CEDEX 1, 44035 Nantes, France
| | - Géraldine Guasch
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, CEDEX 09, 13273 Marseille, France;
- Correspondence:
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Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar G, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S. Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.17.344002. [PMID: 33106807 PMCID: PMC7587781 DOI: 10.1101/2020.10.17.344002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19 which can be immediately utilized to investigate COVID-19 pathogenesis, and vet new therapies and vaccines.
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Mayorgas A, Dotti I, Martínez-Picola M, Esteller M, Bonet-Rossinyol Q, Ricart E, Salas A, Martínez-Medina M. A Novel Strategy to Study the Invasive Capability of Adherent-Invasive Escherichia coli by Using Human Primary Organoid-Derived Epithelial Monolayers. Front Immunol 2021; 12:646906. [PMID: 33854511 PMCID: PMC8039293 DOI: 10.3389/fimmu.2021.646906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Over the last decades, Adherent-Invasive Escherichia coli (AIEC) has been linked to the pathogenesis of Crohn’s Disease. AIEC’s characteristics, as well as its interaction with the gut immune system and its role in intestinal epithelial barrier dysfunction, have been extensively studied. Nevertheless, the currently available techniques to investigate the cross-talk between this pathogen and intestinal epithelial cells (IECs) are based on the infection of immortalized cell lines. Despite their many advantages, cell lines cannot reproduce the conditions in tissues, nor do they reflect interindividual variability or gut location-specific traits. In that sense, the use of human primary cultures, either healthy or diseased, offers a system that can overcome all of these limitations. Here, we developed a new infection model by using freshly isolated human IECs. For the first time, we generated and infected monolayer cultures derived from human colonic organoids to study the mechanisms and effects of AIEC adherence and invasion on primary human epithelial cells. To establish the optimal conditions for AIEC invasion studies in human primary organoid-derived epithelial monolayers, we designed an infection-kinetics study to assess the infection dynamics at different time points, as well as with two multiplicities of infection (MOI). Overall, this method provides a model for the study of host response to AIEC infections, as well as for the understanding of the molecular mechanisms involved in adhesion, invasion and intracellular replication. Therefore, it represents a promising tool for elucidating the cross-talk between AIEC and the intestinal epithelium in healthy and diseased tissues.
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Affiliation(s)
- Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Isabella Dotti
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Marta Martínez-Picola
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Miriam Esteller
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Queralt Bonet-Rossinyol
- Laboratory of Molecular Microbiology, Department of Biology, Universitat de Girona, Girona, Spain
| | - Elena Ricart
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
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Sayed IM, El-Hafeez AAA, Maity PP, Das S, Ghosh P. Modeling colorectal cancers using multidimensional organoids. Adv Cancer Res 2021; 151:345-383. [PMID: 34148617 PMCID: PMC8221168 DOI: 10.1016/bs.acr.2021.02.005] [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: 10/21/2022]
Abstract
Organoids have revolutionized cancer research as highly adaptable models that enable an array of experimental techniques to interrogate tissue morphology and function. Because they preserve the genetic, phenotypic, and behavioral traits of their source tissue, organoids have gained traction as the most relevant models for drug discovery, tracking therapeutic response and for personalized medicine. As organoids are indisputably becoming a mainstay of cancer research, this review specifically addresses how colon-derived organoids can be perfected as multidimensional, scalable, reproducible models of healthy, pre-neoplastic and neoplastic conditions of the colon and for use in high-throughput "Phase-0" human clinical trials-in-a-dish.
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Affiliation(s)
- Ibrahim M Sayed
- Department of Pathology, University of California, San Diego, CA, United States
| | - Amer Ali Abd El-Hafeez
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, United States
| | - Priti P Maity
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, United States
| | - Soumita Das
- Department of Pathology, University of California, San Diego, CA, United States; Rebecca and John Moore Comprehensive Cancer Center, University of California, San Diego, CA, United States; HUMANOID Center of Research Excellence (CoRE), University of California, San Diego, CA, United States.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, United States; Rebecca and John Moore Comprehensive Cancer Center, University of California, San Diego, CA, United States; Department of Medicine, University of California, San Diego, CA, United States; Veterans Affairs Medical Center, San Diego, CA, United States; HUMANOID Center of Research Excellence (CoRE), University of California, San Diego, CA, United States.
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40
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Sharma A, Lee J, Fonseca AG, Moshensky A, Kothari T, Sayed IM, Ibeawuchi SR, Pranadinata RF, Ear J, Sahoo D, Crotty-Alexander LE, Ghosh P, Das S. E-cigarettes compromise the gut barrier and trigger inflammation. iScience 2021. [PMID: 33537654 DOI: 10.1101/2020.07.29.227348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
E-cigarette usage continues to rise, yet the safety of e-cigarette aerosols is questioned. Using murine models of acute and chronic e-cigarette aerosol inhalation, murine colon transcriptomics, and murine and human gut-derived organoids in co-culture models, we assessed the effects of e-cigarette use on the gut barrier. Histologic and transcriptome analyses revealed that chronic, but not acute, nicotine-free e-cigarette use increased inflammation and reduced expression of tight junction (TJ) markers. Exposure of murine and human enteroid-derived monolayers (EDMs) to nicotine-free e-cigarette aerosols alone or in co-culture with bacteria also causes barrier disruption, downregulation of TJ protein, and enhanced inflammation in response to infection. These data highlight the harmful effects of "non-nicotine" component of e-cigarettes on the gut barrier. Considering the importance of an intact gut barrier for host fitness and the impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to both medicine and public health.
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Affiliation(s)
- Aditi Sharma
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Jasper Lee
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Ayden G Fonseca
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
| | - Alex Moshensky
- Department of Medicine, University of California, San Diego, CA 92093, USA
| | - Taha Kothari
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | | | - Rama F Pranadinata
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
| | - Jason Ear
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
- Department of Medicine, University of California, San Diego, CA 92093, USA
| | - Debashis Sahoo
- Department of Pediatrics, University of California, San Diego, CA 92093, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, CA 92093, USA
- Rebecca and John Moore Comprehensive Cancer Center, University of California, San Diego, CA 92093, USA
| | - Laura E Crotty-Alexander
- Department of Medicine, University of California, San Diego, CA 92093, USA
- Veterans Affairs Medical Center, VA San Diego Healthcare System, La Jolla, San Diego, CA 92093, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
- Department of Medicine, University of California, San Diego, CA 92093, USA
- Rebecca and John Moore Comprehensive Cancer Center, University of California, San Diego, CA 92093, USA
- Veterans Affairs Medical Center, VA San Diego Healthcare System, La Jolla, San Diego, CA 92093, USA
| | - Soumita Das
- Department of Pathology, University of California, San Diego, CA 92093, USA
- Rebecca and John Moore Comprehensive Cancer Center, University of California, San Diego, CA 92093, USA
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Li J, Xu X, Tiwari M, Chen Y, Fuller M, Bansal V, Tamayo P, Das S, Ghosh P, Sen GL. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation. Nat Commun 2021; 12:784. [PMID: 33542242 PMCID: PMC7862286 DOI: 10.1038/s41467-021-21067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
In adult tissue, stem and progenitor cells must tightly regulate the balance between proliferation and differentiation to sustain homeostasis. How this exquisite balance is achieved is an area of active investigation. Here, we show that epidermal genes, including ~30% of induced differentiation genes already contain stalled Pol II at the promoters in epidermal stem and progenitor cells which is then released into productive transcription elongation upon differentiation. Central to this process are SPT6 and PAF1 which are necessary for the elongation of these differentiation genes. Upon SPT6 or PAF1 depletion there is a loss of human skin differentiation and stratification. Unexpectedly, loss of SPT6 also causes the spontaneous transdifferentiation of epidermal cells into an intestinal-like phenotype due to the stalled transcription of the master regulator of epidermal fate P63. Our findings suggest that control of transcription elongation through SPT6 plays a prominent role in adult somatic tissue differentiation and the inhibition of alternative cell fate choices.
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Affiliation(s)
- Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Xiaojun Xu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Mackenzie Fuller
- Departments of Medicine and Cellular and Molecular Medicine, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
- Department of Pathology, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - Varun Bansal
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Pablo Tamayo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Division of Medical Genetics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Soumita Das
- Department of Pathology, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.
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Sayed IM, Chakraborty A, Abd El-Hafeez AA, Sharma A, Sahan AZ, Huang WJM, Sahoo D, Ghosh P, Hazra TK, Das S. The DNA Glycosylase NEIL2 Suppresses Fusobacterium-Infection-Induced Inflammation and DNA Damage in Colonic Epithelial Cells. Cells 2020; 9:E1980. [PMID: 32872214 PMCID: PMC7565382 DOI: 10.3390/cells9091980] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer, while the majority (80-85%) of CRCs are sporadic and are microsatellite stable (MSS), and approximately 15-20% of them display microsatellite instability (MSI). Infection and chronic inflammation are known to induce DNA damage in host tissues and can lead to oncogenic transformation of cells, but the role of DNA repair proteins in microbe-associated CRCs remains unknown. Using CRC-associated microbes such as Fusobacterium nucleatum (Fn) in a coculture with murine and human enteroid-derived monolayers (EDMs), here, we show that, among all the key DNA repair proteins, NEIL2, an oxidized base-specific DNA glycosylase, is significantly downregulated after Fn infection. Fn infection of NEIL2-null mouse-derived EDMs showed a significantly higher level of DNA damage, including double-strand breaks and inflammatory cytokines. Several CRC-associated microbes, but not the commensal bacteria, induced the accumulation of DNA damage in EDMs derived from a murine CRC model, and Fn had the most pronounced effect. An analysis of publicly available transcriptomic datasets showed that the downregulation of NEIL2 is often encountered in MSS compared to MSI CRCs. We conclude that the CRC-associated microbe Fn induced the downregulation of NEIL2 and consequent accumulation of DNA damage and played critical roles in the progression of CRCs.
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Affiliation(s)
- Ibrahim M. Sayed
- Department of Pathology, University of California, San Diego, CA 92093, USA; (I.M.S.); (A.S.); (A.Z.S.)
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX-77555, USA; (A.C.); (T.K.H.)
| | - Amer Ali Abd El-Hafeez
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA.; (A.A.A.E.-H.); (W.J.M.H.); (P.G.)
| | - Aditi Sharma
- Department of Pathology, University of California, San Diego, CA 92093, USA; (I.M.S.); (A.S.); (A.Z.S.)
| | - Ayse Z. Sahan
- Department of Pathology, University of California, San Diego, CA 92093, USA; (I.M.S.); (A.S.); (A.Z.S.)
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA.; (A.A.A.E.-H.); (W.J.M.H.); (P.G.)
| | - Debashis Sahoo
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
- Department of Computer Science and Engineering, Jacob’s School of Engineering, La Jolla, CA 92093, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA.; (A.A.A.E.-H.); (W.J.M.H.); (P.G.)
- Department of Medicine, University of California, San Diego, CA 92093, USA
- Moores Cancer Center, University of California, San Diego, CA 92093, USA
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX-77555, USA; (A.C.); (T.K.H.)
| | - Soumita Das
- Department of Pathology, University of California, San Diego, CA 92093, USA; (I.M.S.); (A.S.); (A.Z.S.)
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43
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El-Mokhtar MA, Seddik MI, Osman A, Adel S, Abdel Aziz EM, Mandour SA, Mohammed N, Zarzour MA, Abdel-Wahid L, Radwan E, Sayed IM. Hepatitis E Virus Mediates Renal Injury via the Interaction between the Immune Cells and Renal Epithelium. Vaccines (Basel) 2020; 8:E454. [PMID: 32824088 PMCID: PMC7564770 DOI: 10.3390/vaccines8030454] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Renal disorders are associated with Hepatitis E virus (HEV) infection. Progression to end-stage renal disease and acute kidney injury are complications associated with HEV infection. The mechanisms by which HEV mediates the glomerular diseases remain unclear. CD10+/CD13+ primary proximal tubular (PT) epithelial cells, isolated from healthy donors, were infected with HEV. Inflammatory markers and kidney injury markers were assessed in the presence or absence of peripheral blood mononuclear cells (PBMCs) isolated from the same donors. HEV replicated efficiently in the PT cells as shown by the increase in HEV load over time and the expression of capsid Ag. In the absence of PBMCs, HEV was not nephrotoxic, with no direct effect on the transcription of chemokines (Cxcl-9, Cxcl-10, and Cxcl-11) nor the kidney injury markers (kidney injury molecule 1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), and interleukin 18 (lL-18)). While higher inflammatory responses, upregulation of chemokines and kidney injury markers expression, and signs of nephrotoxicity were recorded in HEV-infected PT cells cocultured with PBMCs. Interestingly, a significantly higher level of IFN-γ was released in the PBMCs-PT coculture compared to PT alone during HEV infection. In conclusion: The crosstalk between immune cells and renal epithelium and the signal axes IFN-γ/chemokines and IL-18 could be the immune-mediated mechanisms of HEV-induced renal disorder.
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Affiliation(s)
- Mohamed A. El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Mohamed Ismail Seddik
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt; (M.I.S.); (A.O.)
| | - Asmaa Osman
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt; (M.I.S.); (A.O.)
| | - Sara Adel
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71515, Egypt;
| | - Essam M. Abdel Aziz
- Department of Internal Medicine, Nephrology Division, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Sahar A. Mandour
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia 66111, Egypt;
| | - Nasreldin Mohammed
- Department of Urology and Renal Transplantation Centre, Faculty of Medicine, Assiut University Hospital, Assiut 71515, Egypt; (N.M.); (M.A.Z.)
| | - Mohamed A. Zarzour
- Department of Urology and Renal Transplantation Centre, Faculty of Medicine, Assiut University Hospital, Assiut 71515, Egypt; (N.M.); (M.A.Z.)
| | - Lobna Abdel-Wahid
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Eman Radwan
- Department of Medical Biochemistry, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Ibrahim M. Sayed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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