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Long T, Abbasi N, Hernandez JE, Li Y, Sayed IM, Ma S, Iemolo A, Yee BA, Yeo GW, Telese F, Ghosh P, Das S, Huang WJM. RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. Gut 2022; 71:1790-1802. [PMID: 34853057 PMCID: PMC9156727 DOI: 10.1136/gutjnl-2021-324984] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/12/2021] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Tuft cells residing in the intestinal epithelium have diverse functions. In the small intestine, they provide protection against inflammation, combat against helminth and protist infections, and serve as entry portals for enteroviruses. In the colon, they had been implicated in tumourigenesis. Commitment of intestinal progenitor cells to the tuft cell lineage requires Rho GTPase Cell Division Cycle 42 (CDC42), a Rho GTPase that acts downstream of the epidermal growth factor receptor and wingless-related integration site signalling cascades, and the master transcription factor POU class 2 homeobox 3 (POU2F3). This study investigates how this pathway is regulated by the DEAD box containing RNA binding protein DDX5 in vivo. DESIGN We assessed the role of DDX5 in tuft cell specification and function in control and epithelial cell-specific Ddx5 knockout mice (DDX5ΔIEC) using transcriptomic approaches. RESULTS DDX5ΔIEC mice harboured a loss of intestinal tuft cell populations, modified microbial repertoire, and altered susceptibilities to ileal inflammation and colonic tumourigenesis. Mechanistically, DDX5 promotes CDC42 protein synthesis through a post-transcriptional mechanism to license tuft cell specification. Importantly, the DDX5-CDC42 axis is parallel but distinct from the known interleukin-13 circuit implicated in tuft cell hyperplasia, and both pathways augment Pou2f3 expression in secretory lineage progenitors. In mature tuft cells, DDX5 not only promotes integrin signalling and microbial responses, it also represses gene programmes involved in membrane transport and lipid metabolism. CONCLUSION RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
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Affiliation(s)
- Tianyun Long
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Nazia Abbasi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Juan E Hernandez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Yuxin Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Attilio Iemolo
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Francesca Telese
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
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Wu X, Wei S, Chen M, Li J, Wei Y, Zhang J, Dong W. P2RY13 Exacerbates Intestinal Inflammation by Damaging the Intestinal Mucosal Barrier via Activating IL-6/STAT3 Pathway. Int J Biol Sci 2022; 18:5056-5069. [PMID: 35982893 PMCID: PMC9379400 DOI: 10.7150/ijbs.74304] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/09/2022] [Indexed: 11/26/2022] Open
Abstract
The pathogenesis of ulcerative colitis (UC) is unclear, while genetic factors have been confirmed to play an important role in its development. P2RY13 is a G protein-coupled receptor (GPCRs), which are involved in the pathogenesis of inflammation and immune disorders. According to GEO database analysis, we first observed that the expression of P2Y13 was increased in UC patients. Therefore, we sought to determine the role of P2Y13 in the development of colitis. Our data showed that P2RY13 was highly expressed in the inflamed intestinal tissues of UC patients. In mice, pharmacological antagonism of P2Y13 can significantly attenuate the intestinal mucosal barrier disruption. In LPS-induced NCM460 cell, knockdown or pharmacological inhibition of P2RY13 increased the expression of intestinal tight junction protein and reduced apoptosis. In addition, we found that the effect of P2Y13 on colitis is related to the activation of the IL-6/STAT3 pathway. Activation of P2Y13 increases IL-6 expression and promotes STAT3 phosphorylation and nuclear transport. Deletion of the STAT3 gene in the intestinal epithelial cells of mice significantly mitigated the exacerbation of colitis due to P2Y13 activation. Thus, P2Y13 can aggravate intestinal mucosal barrier destruction by activating the IL-6/STAT3 pathway. P2Y13 might be a potential drug target for UC.
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Affiliation(s)
- Xiaohan Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, Hubei Province, China
| | - Shuchun Wei
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, Hubei Province, China
| | - Meilin Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, Hubei Province, China
| | - Jinting Li
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, Hubei Province, China
| | - Yuping Wei
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.,Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, Hubei Province, China
| | - Jixiang Zhang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
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53
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Inflammatory auto-immune diseases of the intestine and their management by natural bioactive compounds. Biomed Pharmacother 2022; 151:113158. [PMID: 35644116 DOI: 10.1016/j.biopha.2022.113158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/08/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Autoimmune diseases are caused by the overactivity of the immune system towards self-constituents. Risk factors of autoimmune diseases are multiple and include genetic, epigenetic, environmental, and psychological. Autoimmune chronic inflammatory bowel diseases, including celiac and inflammatory diseases (Crohn's disease and ulcerative colitis), constitute a significant health problem worldwide. Besides the complexity of the symptoms of these diseases, their treatments have only been palliative. Numerous investigations showed that natural phytochemicals could be promising strategies to fight against these autoimmune diseases. In this respect, plant-derived natural compounds such as flavonoids, phenolic acids, and terpenoids exhibited significant effects against three autoimmune diseases affecting the intestine, particularly bowel diseases. This review focuses on the role of natural compounds obtained from medicinal plants in modulating inflammatory auto-immune diseases of the intestine. It covers the most recent literature related to the effect of these natural compounds in the treatment and prevention of auto-immune diseases of the intestine.
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54
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Multiomics to elucidate inflammatory bowel disease risk factors and pathways. Nat Rev Gastroenterol Hepatol 2022; 19:399-409. [PMID: 35301463 PMCID: PMC9214275 DOI: 10.1038/s41575-022-00593-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated disease of the intestinal tract, with complex pathophysiology involving genetic, environmental, microbiome, immunological and potentially other factors. Epidemiological data have provided important insights into risk factors associated with IBD, but are limited by confounding, biases and data quality, especially when pertaining to risk factors in early life. Multiomics platforms provide granular high-throughput data on numerous variables simultaneously and can be leveraged to characterize molecular pathways and risk factors for chronic diseases, such as IBD. Herein, we describe omics platforms that can advance our understanding of IBD risk factors and pathways, and available omics data on IBD and other relevant diseases. We highlight knowledge gaps and emphasize the importance of birth, at-risk and pre-diagnostic cohorts, and neonatal blood spots in omics analyses in IBD. Finally, we discuss network analysis, a powerful bioinformatics tool to assemble high-throughput data and derive clinical relevance.
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55
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Lee C, Lin J, Prokop A, Gopalakrishnan V, Hanna RN, Papa E, Freeman A, Patel S, Yu W, Huhn M, Sheikh AS, Tan K, Sellman BR, Cohen T, Mangion J, Khan FM, Gusev Y, Shameer K. StarGazer: A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit. Front Genet 2022; 13:868015. [PMID: 35711912 PMCID: PMC9197487 DOI: 10.3389/fgene.2022.868015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/29/2022] [Indexed: 01/26/2023] Open
Abstract
Target prioritization is essential for drug discovery and repositioning. Applying computational methods to analyze and process multi-omics data to find new drug targets is a practical approach for achieving this. Despite an increasing number of methods for generating datasets such as genomics, phenomics, and proteomics, attempts to integrate and mine such datasets remain limited in scope. Developing hybrid intelligence solutions that combine human intelligence in the scientific domain and disease biology with the ability to mine multiple databases simultaneously may help augment drug target discovery and identify novel drug-indication associations. We believe that integrating different data sources using a singular numerical scoring system in a hybrid intelligent framework could help to bridge these different omics layers and facilitate rapid drug target prioritization for studies in drug discovery, development or repositioning. Herein, we describe our prototype of the StarGazer pipeline which combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits, and is available via https://github.com/AstraZeneca/StarGazer.
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Affiliation(s)
- Chiyun Lee
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Junxia Lin
- Georgetown University, Washington, DC, United States
| | | | | | - Richard N. Hanna
- Early Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Eliseo Papa
- Research Data and Analytics, R&D IT, AstraZeneca, Cambridge, United Kingdom
| | - Adrian Freeman
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Saleha Patel
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Wen Yu
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Monika Huhn
- Biometrics and Information Sciences, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
| | - Abdul-Saboor Sheikh
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Keith Tan
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Bret R. Sellman
- Discovery Microbiome, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Taylor Cohen
- Discovery Microbiome, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Jonathan Mangion
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Faisal M. Khan
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Yuriy Gusev
- Georgetown University, Washington, DC, United States
| | - Khader Shameer
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States,*Correspondence: Khader Shameer,
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Wang W, Liu Z, Yue W, Zhu L, Zhong H, Yang C, He T, Wan P, Geng J. Mucosa-Colonizing Microbiota Correlate With Host Autophagy Signaling in Patients With Inflammatory Bowel Disease. Front Microbiol 2022; 13:875238. [PMID: 35694307 PMCID: PMC9178242 DOI: 10.3389/fmicb.2022.875238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Both bacteria and autophagy are implicated in inflammatory bowel disease (IBD) pathogenesis. However, how bacteria crosstalk with autophagy signaling remains largely known, especially in intestinal mucosa. This study aimed to profile the internal complex autophagy signaling cascade and their external correlation with these bacteria, and consequently provide a systematic and precise target for future IBD diagnosis and therapy. We found the Ulcerative colitis (UC) patients exhibited more severe dysbiosis than the Crohn’s disease (CD) patients, as represented by alpha diversity, community phenotypes, and functional annotation compared with the control population. Meanwhile, CD patients showed greater transcriptional signaling activities of autophagy, endoplasmic reticulum (ER) stress, and bile acid production. Dominant bacteria (e.g., Rhodococcus, Escherichia, Shigella, and Enterococcus) were positively correlated and low-abundance bacteria (e.g., Bacillus, Acidovorax, Acinetobacter, and Stenotrophomonas) were negatively correlated with the autophagy signaling cascade (184 autophagy genes, 52 ER stress genes, and 22 bile acid production genes). Our observations suggested UC patients showed temporary and widespread microbiota turbulence and CD patients showed processive and local autophagy activity during IBD progression. Intestinal mucosa-colonizing bacteria were correlated with the bile/ER stress/autophagy signaling axis in IBD pathogenesis.
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Affiliation(s)
- Wenxue Wang
- Department of Infectious Disease and Hepatic Disease, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- School of Medicine, Kunming University of Science and Technology, Kunming, China
- Wenxue Wang, ;
| | - Zhongjian Liu
- Institute of Basic and Clinical Medicine, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Wei Yue
- Department of Infectious Disease and Hepatic Disease, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Ling Zhu
- Department of Infectious Disease and Hepatic Disease, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Huijie Zhong
- Department of Infectious Disease and Hepatic Disease, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- School of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Chao Yang
- Department of Gastroenterology, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Tian He
- Department of Gastroenterology, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Ping Wan
- Department of Gastroenterology, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- Ping Wan,
| | - Jiawei Geng
- Department of Infectious Disease and Hepatic Disease, First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- School of Medicine, Kunming University of Science and Technology, Kunming, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- *Correspondence: Jiawei Geng, ;
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57
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Grubišić V, Bali V, Fried DE, Eltzschig HK, Robson SC, Mazei-Robison MS, Gulbransen BD. Enteric glial adenosine 2B receptor signaling mediates persistent epithelial barrier dysfunction following acute DSS colitis. Mucosal Immunol 2022; 15:964-976. [PMID: 35869148 PMCID: PMC9385475 DOI: 10.1038/s41385-022-00550-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023]
Abstract
Intestinal epithelial barrier function is compromised in inflammatory bowel disease and barrier dysfunction contributes to disease progression. Extracellular nucleotides/nucleosides generated in gut inflammation may regulate barrier function through actions on diverse cell types. Enteric glia modulate extracellular purinergic signaling and exert pathophysiological effects on mucosal permeability. These glia may regulate inflammation with paracrine responses, theoretically mediated via adenosine 2B receptor (A2BR) signaling. As the cell-specific roles of A2BRs in models of colitis and barrier dysfunction are unclear, we studied glial A2BRs in acute dextran sodium sulfate (DSS) colitis. We performed and validated conditional ablation of glial A2BRs in Sox10CreERT2+/-;Adora2bf/f mice. Overt intestinal disease activity indices in DSS-colitis were comparable between Sox10CreERT2+/-;Adora2bf/f mice and littermate controls. However, ablating glial A2BRs protected against barrier dysfunction following acute DSS-colitis. These benefits were associated with the normalization of tight junction protein expression and localization including claudin-1, claudin-8, and occludin. Glial A2BR signaling increased levels of proinflammatory mediators in the colon and cell-intrinsic regulation of genes including Csf3, Cxcl1, Cxcl10, and Il6. Our studies show that glial A2BR signaling exacerbates immune responses during DSS-colitis and that this adenosinergic cell-specific mechanism contributes to persistent gut epithelial barrier dysfunction.
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Affiliation(s)
- Vladimir Grubišić
- Department of Physiology and Neuroscience program, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biomedical Sciences and Center for Biomedical Innovation, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY, 11568, USA
| | - Vedrana Bali
- Department of Physiology and Neuroscience program, Michigan State University, East Lansing, MI, 48824, USA
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA
| | - David E Fried
- Department of Physiology and Neuroscience program, Michigan State University, East Lansing, MI, 48824, USA
| | - Holger K Eltzschig
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Simon C Robson
- Division of Gastroenterology, Departments of Medicine and Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Michelle S Mazei-Robison
- Department of Physiology and Neuroscience program, Michigan State University, East Lansing, MI, 48824, USA
| | - Brian D Gulbransen
- Department of Physiology and Neuroscience program, Michigan State University, East Lansing, MI, 48824, USA.
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A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. Nat Commun 2022; 13:2299. [PMID: 35484353 PMCID: PMC9051123 DOI: 10.1038/s41467-022-29998-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
We describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 378 UC patients we map the regulatory effects of the SNPs to a human signalling network containing protein-protein, miRNA-mRNA and transcription factor binding interactions. With unsupervised clustering algorithms we group these patient-specific networks into four distinct clusters driven by PRKCB, HLA, SNAI1/CEBPB/PTPN1 and VEGFA/XPO5/POLH hubs. The pathway analysis identifies calcium homeostasis, wound healing and cell motility as key processes in UC pathogenesis. Using transcriptomic data from an independent patient cohort, with three complementary validation approaches focusing on the SNP-affected genes, the patient specific modules and affected functions, we confirm the regulatory impact of non-coding SNPs. iSNP identified regulatory effects for disease-associated non-coding SNPs, and by predicting the patient-specific pathogenic processes, we propose a systems-level way to stratify patients. Single Nucleotide Polymorphisms (SNPs) affect cellular regulatory networks, and SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Here the authors introduce iSNP, a precision medicine pipeline that combines genomics and network biology approaches to uncover patient specific pathways affected in complex diseases.
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59
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Construction of disease-specific cytokine profiles by associating disease genes with immune responses. PLoS Comput Biol 2022; 18:e1009497. [PMID: 35404985 PMCID: PMC9022887 DOI: 10.1371/journal.pcbi.1009497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/21/2022] [Accepted: 03/17/2022] [Indexed: 12/29/2022] Open
Abstract
The pathogenesis of many inflammatory diseases is a coordinated process involving metabolic dysfunctions and immune response—usually modulated by the production of cytokines and associated inflammatory molecules. In this work, we seek to understand how genes involved in pathogenesis which are often not associated with the immune system in an obvious way communicate with the immune system. We have embedded a network of human protein-protein interactions (PPI) from the STRING database with 14,707 human genes using feature learning that captures high confidence edges. We have found that our predicted Association Scores derived from the features extracted from STRING’s high confidence edges are useful for predicting novel connections between genes, thus enabling the construction of a full map of predicted associations for all possible pairs between 14,707 human genes. In particular, we analyzed the pattern of associations for 126 cytokines and found that the six patterns of cytokine interaction with human genes are consistent with their functional classifications. To define the disease-specific roles of cytokines we have collected gene sets for 11,944 diseases from DisGeNET. We used these gene sets to predict disease-specific gene associations with cytokines by calculating the normalized average Association Scores between disease-associated gene sets and the 126 cytokines; this creates a unique profile of inflammatory genes (both known and predicted) for each disease. We validated our predicted cytokine associations by comparing them to known associations for 171 diseases. The predicted cytokine profiles correlate (p-value<0.0003) with the known ones in 95 diseases. We further characterized the profiles of each disease by calculating an “Inflammation Score” that summarizes different modes of immune responses. Finally, by analyzing subnetworks formed between disease-specific pathogenesis genes, hormones, receptors, and cytokines, we identified the key genes responsible for interactions between pathogenesis and inflammatory responses. These genes and the corresponding cytokines used by different immune disorders suggest unique targets for drug discovery. The success of anti-TNF treatment in multiple inflammatory diseases suggest that there is a shared cytokine framework that defines highly conserved mechanisms of inflammation. However, clinical trials testing the efficacy of new cytokine inhibitors suggest a more complex set of interacting cytokine mechanisms that are associated with different diseases. In this work, we aim to define the disease-specific role of cytokines that mediate pathogenesis and inflammatory processes, focusing on autoimmune diseases. We hypothesize that specific clinical phenotypes result from the interactions between disease-specific cytokines and disease-related genes (identified through genetics, transcriptomics, and analysis of metabolic dysfunctions), even though they also may share a common cytokine elements and conserved mechanisms of inflammation. We have developed novel network methods that show a robust ability to identify differential associations between characteristic cytokines and genetics factors contributing to pathogenesis. We have validated our methods on 171 well-studied diseases; the predicted associations between cytokines and disease modules correlate with the published data. Our predictions provide the underlying difference of molecular mechanisms that may be responsible for clinical phenotypes.
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60
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Hong SM, Lee AY, Hwang SM, Ha YJ, Kim MJ, Min S, Hwang W, Yoon G, Kwon SM, Woo HG, Kim HH, Jeong WI, Shen HM, Im SH, Lee D, Kim YS. NAMPT mitigates colitis severity by supporting redox-sensitive activation of phagocytosis in inflammatory macrophages. Redox Biol 2022; 50:102237. [PMID: 35063804 PMCID: PMC8784331 DOI: 10.1016/j.redox.2022.102237] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 12/02/2022] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme in the nicotinamide adenine dinucleotide (NAD+) salvage pathway and plays a crucial role in the maintenance of the NAD+ pool during inflammation. Considering that macrophages are essential for tissue homeostasis and inflammation, we sought to examine the functional impact of NAMPT in inflammatory macrophages, particularly in the context of inflammatory bowel disease (IBD). In this study, we show that mice with NAMPT deletion within the myeloid compartment (Namptf/fLysMCre+/-, Nampt mKO) have more pronounced colitis with lower survival rates, as well as numerous uncleared apoptotic corpses within the mucosal layer. Nampt-deficient macrophages exhibit reduced phagocytic activity due to insufficient NAD+ abundance, which is required to produce NADPH for the oxidative burst. Nicotinamide mononucleotide (NMN) treatment rescues NADPH levels in Nampt mKO macrophages and sustains superoxide generation via NADPH oxidase. Consequently, Nampt mKO mice fail to clear dead cells during tissue repair, leading to substantially prolonged chronic colitis. Moreover, systemic administration of NMN, to supply NAD+, effectively suppresses the disease severity of DSS-induced colitis. Collectively, our findings suggest that activation of the NAMPT-dependent NAD+ biosynthetic pathway, via NMN administration, is a potential therapeutic strategy for managing inflammatory diseases.
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Affiliation(s)
- Sun Mi Hong
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - A-Yeon Lee
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Sung-Min Hwang
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Yu-Jin Ha
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Moo-Jin Kim
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Seongki Min
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Won Hwang
- MSBIOTECH. LTD, Chungbuk, 27672, Republic of Korea
| | - Gyesoon Yoon
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - So Mee Kwon
- Department of Physiology, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Hyun Goo Woo
- Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Physiology, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea
| | - Hee-Hoon Kim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Won-Il Jeong
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Han-Ming Shen
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea; ImmunoBiome, Bio Open Innovation Center, Pohang, 37673, Republic of Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea.
| | - You-Sun Kim
- Department of Biochemistry, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea; Department of Biomedical Sciences, Graduate School of Ajou University, 164 Worldcup-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16499, Republic of Korea.
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61
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Zhao Y, Chen L, Chen L, Huang J, Chen S, Yu Z. Exploration of the Potential Relationship Between Gut Microbiota Remodeling Under the Influence of High-Protein Diet and Crohn's Disease. Front Microbiol 2022; 13:831176. [PMID: 35308389 PMCID: PMC8927681 DOI: 10.3389/fmicb.2022.831176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022] Open
Abstract
Diet and gut microbiota are both important factors in the pathogenesis of Crohn’s disease, and changes in diet can lead to alteration in gut microbiome. However, there is still insufficient exploration on interaction within the gut microbiota under high-protein diet (HPD) intervention. We analyzed the gut microbial network and marker taxa from patients with Crohn’s disease in public database (GMrepo, https://gmrepo.humangut.info) combined with investigation of the changes of composition and function of intestinal microbiome in mice fed on HPD by metagenomic sequencing. The results showed that there was an indirect negative correlation between Escherichia coli and Lachnospiraceae in patients with Crohn’s disease, and Escherichia coli was a marker for both Crohn’s disease and HPD intervention. Besides, enriched HH_1414 (one of the orthologs in eggNOG) related to tryptophan metabolism was from Helicobacter, whereas reduced orthologs (OGs) mainly contributed by Lachnospiraceae after HPD intervention. Our research indicates that some compositional changes in gut microbiota after HPD intervention are consistent with those in patients with Crohn’s disease, providing insights into potential impact of altered gut microbes under HPD on Crohn’s disease.
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Affiliation(s)
- Yiming Zhao
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Lulu Chen
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Liyu Chen
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Shuijiao Chen
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
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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: 3.0] [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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63
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Takeshima Y, Iwasaki Y, Nakano M, Narushima Y, Ota M, Nagafuchi Y, Sumitomo S, Okamura T, Elkon K, Ishigaki K, Suzuki A, Kochi Y, Yamamoto K, Fujio K. Immune cell multiomics analysis reveals contribution of oxidative phosphorylation to B-cell functions and organ damage of lupus. Ann Rheum Dis 2022; 81:845-853. [PMID: 35236659 DOI: 10.1136/annrheumdis-2021-221464] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/09/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease. While the long-term prognosis has greatly improved, better long-term survival is still necessary. The type I interferon (IFN) signature, a prominent feature of SLE, is not an ideal therapeutic target or outcome predictor. To explore immunological pathways in SLE more precisely, we performed transcriptomic, epigenomic and genomic analyses using 19 immune cell subsets from peripheral blood. METHODS We sorted 19 immune cell subsets and identified the mRNA expression profiles and genetic polymorphisms in 107 patients with SLE and 92 healthy controls. Combined differentially expressed genes and expression quantitative trait loci analysis was conducted to find key driver genes in SLE pathogenesis. RESULTS We found transcriptomic, epigenetic and genetic importance of oxidative phosphorylation (OXPHOS)/mitochondrial dysfunction in SLE memory B cells. Particularly, we identified an OXPHOS-regulating gene, PRDX6 (peroxiredoxin 6), as a key driver in SLE B cells. Prdx6-deficient B cells showed upregulated mitochondrial respiration as well as antibody production. We revealed OXPHOS signature was associated with type I IFN signalling-related genes (ISRGs) signature in SLE memory B cells. Furthermore, the gene sets related to innate immune signalling among ISRGs presented correlation with OXPHOS and these two signatures showed associations with SLE organ damage as well as specific clinical phenotypes. CONCLUSION This work elucidated the potential prognostic marker for SLE. Since OXPHOS consists of the electron transport chain, a functional unit in mitochondria, these findings suggest the importance of mitochondrial dysfunction as a key immunological pathway involved in SLE.
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Affiliation(s)
- Yusuke Takeshima
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan .,Department of Palliative Medicine, Saitama Medical University, Saitama, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan
| | - Yuta Narushima
- Research Division, Chugai Pharmaceutical Co Ltd, Kamakura, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Keith Elkon
- Division of Rheumatology, University of Washington, Seattle, Washington, USA
| | - Kazuyoshi Ishigaki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan.,Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan
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Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
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65
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Brandão LAC, de Moura RR, Marzano AV, Moltrasio C, Tricarico PM, Crovella S. Variant Enrichment Analysis to Explore Pathways Functionality in Complex Autoinflammatory Skin Disorders through Whole Exome Sequencing Analysis. Int J Mol Sci 2022; 23:2278. [PMID: 35216413 PMCID: PMC8877088 DOI: 10.3390/ijms23042278] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
The challenge of unravelling the molecular basis of multifactorial disorders nowadays cannot rely just on association studies searching for potential causative variants shared by groups of patients and not present in healthy individuals; indeed, association studies have as a main limitation the lack of information on the interactions between the disease-causing variants. Thus, new genomic analysis tools focusing on disrupted pathways rather than associated gene variants are required to better understand the complexity of a disease. Therefore, we developed the Variant Enrichment Analysis (VEA) workflow, a tool applicable for whole exome sequencing data, able to find differences between the numbers of genetic variants in a given pathway in comparison with a reference dataset. In this study, we applied VEA to discover novel pathways altered in patients with complex autoinflammatory skin disorders, namely PASH (n = 9), 3 of whom are overlapping with SAPHO) and PAPASH (n = 3). With this approach we have been able to identify pathways related to neutrophil and endothelial cells homeostasis/activations, as disrupted in our patients. We hypothesized that unregulated neutrophil transendothelial migration could elicit increased neutrophil infiltration and tissue damage. Based on our findings, VEA, in our experimental dataset, allowed us to predict novel pathways impaired in subjects with autoinflammatory skin disorders.
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Affiliation(s)
- Lucas André Cavalcanti Brandão
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Ronald Rodrigues de Moura
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Angelo Valerio Marzano
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.V.M.); (C.M.)
- Department of Physiopathology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy
| | - Chiara Moltrasio
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.V.M.); (C.M.)
- Department of Medical Surgical and Health Sciences, University of Trieste, 34137 Trieste, Italy
| | - Paola Maura Tricarico
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, University of Qatar, Doha 2713, Qatar;
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Andreuzzi E, Fejza A, Polano M, Poletto E, Camicia L, Carobolante G, Tarticchio G, Todaro F, Di Carlo E, Scarpa M, Scarpa M, Paulitti A, Capuano A, Canzonieri V, Maiero S, Fornasarig M, Cannizzaro R, Doliana R, Colombatti A, Spessotto P, Mongiat M. Colorectal cancer development is affected by the ECM molecule EMILIN-2 hinging on macrophage polarization via the TLR-4/MyD88 pathway. J Exp Clin Cancer Res 2022; 41:60. [PMID: 35148799 PMCID: PMC8840294 DOI: 10.1186/s13046-022-02271-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/22/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Colorectal cancer is one of the most frequent and deadly tumors. Among the key regulators of CRC growth and progression, the microenvironment has emerged as a crucial player and as a possible route for the development of new therapeutic opportunities. More specifically, the extracellular matrix acts directly on cancer cells and indirectly affecting the behavior of stromal and inflammatory cells, as well as the bioavailability of growth factors. Among the ECM molecules, EMILIN-2 is frequently down-regulated by methylation in CRC and the purpose of this study was to verify the impact of EMILIN-2 loss in CRC development and its possible value as a prognostic biomarker. METHODS The AOM/DSS CRC protocol was applied to Emilin-2 null and wild type mice. Tumor development was monitored by endoscopy, the molecular analyses performed by IHC, IF and WB and the immune subpopulations characterized by flow cytometry. Ex vivo cultures of monocyte/macrophages from the murine models were used to verify the molecular pathways. Publicly available datasets were exploited to determine the CRC patients' expression profile; Spearman's correlation analyses and Cox regression were applied to evaluate the association with the inflammatory response; the clinical outcome was predicted by Kaplan-Meier survival curves. Pearson correlation analyses were also applied to a cohort of patients enrolled in our Institute. RESULTS In preclinical settings, loss of EMILIN-2 associated with an increased number of tumor lesions upon AOM/DSS treatment. In addition, in the early stages of the disease, the Emilin-2 knockout mice displayed a myeloid-derived suppressor cells-rich infiltrate. Instead, in the late stages, lack of EMILIN-2 associated with a decreased number of M1 macrophages, resulting in a higher percentage of the tumor-promoting M2 macrophages. Mechanistically, EMILIN-2 triggered the activation of the Toll-like Receptor 4/MyD88/NF-κB pathway, instrumental for the polarization of macrophages towards the M1 phenotype. Accordingly, dataset and immunofluorescence analyses indicated that low EMILIN-2 expression levels correlated with an increased M2/M1 ratio and with poor CRC patients' prognosis. CONCLUSIONS These novel results indicate that EMILIN-2 is a key regulator of the tumor-associated inflammatory environment and may represent a promising prognostic biomarker for CRC patients.
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Affiliation(s)
- Eva Andreuzzi
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy.
| | - Albina Fejza
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Evelina Poletto
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Lucrezia Camicia
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Greta Carobolante
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Giulia Tarticchio
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Federico Todaro
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Emma Di Carlo
- Department of Medicine and Sciences of Aging, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Melania Scarpa
- Ricerca Traslazionale Avanzata, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | - Marco Scarpa
- Clinica Chirurgica I- Azienda Ospedaliera di Padova, Padua, Italy
| | - Alice Paulitti
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Alessandra Capuano
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Stefania Maiero
- Division of Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Mara Fornasarig
- Division of Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Renato Cannizzaro
- Division of Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Roberto Doliana
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Alfonso Colombatti
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Paola Spessotto
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Maurizio Mongiat
- Department of Research and Diagnosis, Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy.
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Pinton P. Computational models in inflammatory bowel disease. Clin Transl Sci 2022; 15:824-830. [PMID: 35122401 PMCID: PMC9010263 DOI: 10.1111/cts.13228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/28/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and relapsing disease with multiple underlying influences and notable heterogeneity among its clinical and response-to-treatment phenotypes. There is no cure for IBD, and none of the currently available therapies have demonstrated clinical efficacies beyond 40%-60%. Data collected about its omics, pathogenesis, and treatment strategies have grown exponentially with time making IBD a prime candidate for artificial intelligence (AI) mediated discovery support. AI can be leveraged to further understand or identify IBD features to improve clinical outcomes. Various treatment candidates are currently under evaluation in clinical trials, offering further approaches and opportunities for increasing the efficacies of treatments. However, currently, therapeutic plans are largely determined using clinical features due to the lack of specific biomarkers, and it has become necessary to step into precision medicine to predict therapeutic responses to guarantee optimal treatment efficacy. This is accompanied by the application of AI and the development of multiscale hybrid models combining mechanistic approaches and machine learning. These models ultimately lead to the creation of digital twins of given patients delivering on the promise of precision dosing and tailored treatment. Interleukin-6 (IL-6) is a prominent cytokine in cell-to-cell communication in the inflammatory responses' regulation. Dysregulated IL-6-induced signaling leads to severe immunological or proliferative pathologies, such as IBD and colon cancer. This mini-review explores multiscale models with the aim of predicting the response to therapy in IBD. Modeling IL-6 biology and generating digital twins enhance the credibility of their prediction.
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Lou Y, Song M, Han M, Zhong J, Tian X, Ren Y, Song Y, Duan L, Zhao P, Song X, Zhang W, Chen YH, Wang H. Tumor necrosis factor-α-induced protein 8-like 2 Fosters Tumor-Associated Microbiota to Promote the Development of Colorectal Cancer. Cancer Immunol Res 2022; 10:354-367. [PMID: 35101901 DOI: 10.1158/2326-6066.cir-21-0666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/29/2021] [Accepted: 01/28/2022] [Indexed: 12/24/2022]
Abstract
Although increasing evidence links the gut microbiota with the development of colorectal cancer, the molecular mechanisms for microbiota regulation of tumorigenesis are not fully understood. Here, we found that a member of the TNF-α-induced protein 8 (TNFAIP8) family called TIPE2 (TNFAIP8-like 2) was significantly upregulated in murine intestinal tumors and in human colorectal cancer (CRC), and colorectal cancer with high expression of Tipe2 mRNA associated with reduced survival time of patients. Consistent with these findings, TIPE2 deficiency significantly inhibited the development of CRC in mice treated with azoxymethane/dextran sodium sulfate and in Apcmin/+ mice. TIPE2 deficiency attenuated the severity of colitis by successfully resolving and restricting colonic inflammation and protected colonic myeloid cells from death during colitis. Transplantation of TIPE2-deficient bone marrow into WT mice successfully dampened the latter's tumorigenic phenotype, indicating a hematopoietic-specific role for TIPE2. Mechanistically, restricting the expansion of Enterobacteriaceae/E. coli decreased intestinal inflammation and reduced the incidence of colonic tumors. Collectively, these data suggest that hematopoietic TIPE2 regulates intestinal anti-tumor immunity by regulation of gut microbiota. TIPE2 may represent a new therapeutic target for treating CRC.
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Affiliation(s)
- Yunwei Lou
- School of Laboratory Medicine, Xinxiang Medical University
| | - Miaomiao Song
- School of Laboratory Medicine, Xinxiang Medical University
| | - Meijuan Han
- School of Laboratory Medicine, Xinxiang Medical University
| | - Jiateng Zhong
- School of Basic Medical Sciences, Xinxiang Medical University
| | - Xueqin Tian
- School of Laboratory Medicine, Xinxiang Medical University
| | - Yahan Ren
- School of Laboratory Medicine, Xinxiang Medical University
| | - Yaru Song
- The Affiliated Renmin Hospital of Xinxiang Medical University
| | - Liangwei Duan
- School of Laboratory Medicine, Xinxiang Medical University
| | - Peiqing Zhao
- Center of Translational Medicine, Zibo Central Hospital Affiliated to Shandong University
| | | | - Wen Zhang
- School of Laboratory Medicine, Xinxiang Medical University
| | - Youhai H Chen
- Center for Cancer Immunology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
| | - Hui Wang
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine.
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Ungar B, Yavzori M, Fudim E, Picard O, Kopylov U, Eliakim R, Shouval D, Levin Y, Savidor A, Ben-Moshe S, Manco R, Dan S, Egozi A, Bahar Halpern K, Mayer C, Barshack I, Ben-Horin S, Itzkovitz S. Host transcriptome signatures in human faecal-washes predict histological remission in patients with IBD. Gut 2022; 71:gutjnl-2021-325516. [PMID: 35046090 DOI: 10.1136/gutjnl-2021-325516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/08/2021] [Indexed: 12/08/2022]
Abstract
BACKGROUND Colonoscopy is the gold standard for evaluation of inflammation in inflammatory bowel diseases (IBDs), yet entails cumbersome preparations and risks of injury. Existing non-invasive prognostic tools are limited in their diagnostic power. Moreover, transcriptomics of colonic biopsies have been inconclusive in their association with clinical features. AIMS To assess the utility of host transcriptomics of faecal wash samples of patients with IBD compared with controls. METHODS In this prospective cohort study, we obtained biopsies and faecal-wash samples from patients with IBD and controls undergoing lower endoscopy. We performed RNAseq of biopsies and matching faecal-washes, and associated them with endoscopic and histological inflammation status. We also performed faecal mass-spectrometry proteomics on a subset of samples. We inferred cell compositions using computational deconvolution and used classification algorithms to identify informative genes. RESULTS We analysed biopsies and faecal washes from 39 patients (20 IBD, 19 controls). Host faecal-transcriptome carried information that was distinct from biopsy RNAseq and faecal proteomics. Transcriptomics of faecal washes, yet not of biopsies, from patients with histological inflammation were significantly correlated to one another (p=5.3×10-12). Faecal-transcriptome had significantly higher statistical power in identifying histological inflammation compared with transctiptome of intestinal biopsies (150 genes with area under the curve >0.9 in faecal samples vs 10 genes in biopsy RNAseq). These results were replicated in a validation cohort of 22 patients (10 IBD, 12 controls). Faecal samples were enriched in inflammatory monocytes, regulatory T cells, natural killer-cells and innate lymphoid cells. CONCLUSIONS Faecal wash host transcriptome is a statistically powerful biomarker reflecting histological inflammation. Furthermore, it opens the way to identifying important correlates and therapeutic targets that may be obscured using biopsy transcriptomics.
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Affiliation(s)
- Bella Ungar
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Yavzori
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Ella Fudim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Orit Picard
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Rami Eliakim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, & Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rita Manco
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Stav Dan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shomron Ben-Horin
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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70
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Electroacupuncture Attenuated Anxiety and Depression-Like Behavior via Inhibition of Hippocampal Inflammatory Response and Metabolic Disorders in TNBS-Induced IBD Rats. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8295580. [PMID: 35087621 PMCID: PMC8789424 DOI: 10.1155/2022/8295580] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023]
Abstract
This study was designed to explore the potential mechanisms of electroacupuncture (EA) in treating inflammatory bowel disease- (IBD-) related anxiety and mood disorders. A colitis model was induced in rats with 2, 4, 6-trinitrohydrosulfonic acid (TNBS), followed by ST36 and SP6 targeted therapy by EA or sham EA treatment. The elevated plus maze (EPM) and open-field test (OFT) were performed to assess the state of anxiety and depression-like behavior. Tests were carried out by 16S rDNA amplification sequence, 1H nuclear magnetic resonance (1H NMR) spectroscopy, immunofluorescence staining, and enzyme-linked immunosorbent assay (ELISA). The analyses detailed metabolic alterations and the Toll-like receptor 4 (TLR4) signaling pathway/NOD-like receptor protein 3 (NLRP3) inflammasome in rats' hippocampal region. Furthermore, the activity of the hypothalamic-pituitary adrenal (HPA) axis and gut microbiome was assessed. As a result of treatment, EA significantly improved in the behavioral tests and altered the composition of the gut microbiome through a significant increase in the density of short chain fatty acids (SCFAs) producers mainly including Ruminococcaceae, Phascolarctobacterium, and Akkermansiaceae. EA upregulated the metabolites of the hippocampus mainly containing l-glutamine and gamma-aminobutyric acid (GABA), as well as ZO-1 expression. Whereas the treatment blocked the TLR4/nuclear factor- kappa B (NF-κB) signaling pathways and NLRP3 inflammasomes, along with downregulating the interleukin- (IL-) 1β level. The hyperactivity of the HPA axis was also diminished. In conclusion, EA at ST36 and SP6 attenuated anxiety and depression-like behavior in colitis model rats through their effects on the gut microbiome by modulating the hippocampal inflammatory response and metabolic disorders, as well as the HPA axis. This study provides evidence for clinical application of EA to serve as an adjunctive treatment for IBD-related anxiety and depression.
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71
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Lozano AX, Chaudhuri AA, Nene A, Bacchiocchi A, Earland N, Vesely MD, Usmani A, Turner BE, Steen CB, Luca BA, Badri T, Gulati GS, Vahid MR, Khameneh F, Harris PK, Chen DY, Dhodapkar K, Sznol M, Halaban R, Newman AM. T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:353-362. [PMID: 35027754 DOI: 10.1038/s41591-021-01623-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
Severe immune-related adverse events (irAEs) occur in up to 60% of patients with melanoma treated with immune checkpoint inhibitors (ICIs). However, it is unknown whether a common baseline immunological state precedes irAE development. Here we applied mass cytometry by time of flight, single-cell RNA sequencing, single-cell V(D)J sequencing, bulk RNA sequencing and bulk T cell receptor (TCR) sequencing to study peripheral blood samples from patients with melanoma treated with anti-PD-1 monotherapy or anti-PD-1 and anti-CTLA-4 combination ICIs. By analyzing 93 pre- and early on-ICI blood samples and 3 patient cohorts (n = 27, 26 and 18), we found that 2 pretreatment factors in circulation-activated CD4 memory T cell abundance and TCR diversity-are associated with severe irAE development regardless of organ system involvement. We also explored on-treatment changes in TCR clonality among patients receiving combination therapy and linked our findings to the severity and timing of irAE onset. These results demonstrate circulating T cell characteristics associated with ICI-induced toxicity, with implications for improved diagnostics and clinical management.
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Affiliation(s)
- Alexander X Lozano
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Computer Science & Engineering, Washington University, St. Louis, MO, USA. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Aishwarya Nene
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Noah Earland
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Vesely
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brandon E Turner
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Chloé B Steen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Ti Badri
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Milad R Vahid
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Farnaz Khameneh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Y Chen
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Division of Dermatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kavita Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Mario Sznol
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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Imbert A, Vialaneix N, Marquis J, Vion J, Charpagne A, Metairon S, Laurens C, Moro C, Boulet N, Walter O, Lefebvre G, Hager J, Langin D, Saris WHM, Astrup A, Viguerie N, Valsesia A. Network Analyses Reveal Negative Link Between Changes in Adipose Tissue GDF15 and BMI During Dietary-induced Weight Loss. J Clin Endocrinol Metab 2022; 107:e130-e142. [PMID: 34415992 DOI: 10.1210/clinem/dgab621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Adipose tissue (AT) transcriptome studies provide holistic pictures of adaptation to weight and related bioclinical settings changes. OBJECTIVE To implement AT gene expression profiling and investigate the link between changes in bioclinical parameters and AT gene expression during 3 steps of a 2-phase dietary intervention (DI). METHODS AT transcriptome profiling was obtained from sequencing 1051 samples, corresponding to 556 distinct individuals enrolled in a weight loss intervention (8-week low-calorie diet (LCD) at 800 kcal/day) followed with a 6-month ad libitum randomized DI. Transcriptome profiles obtained with QuantSeq sequencing were benchmarked against Illumina RNAseq. Reverse transcription quantitative polymerase chain reaction was used to further confirm associations. Cell specificity was assessed using freshly isolated cells and THP-1 cell line. RESULTS During LCD, 5 modules were found, of which 3 included at least 1 bioclinical variable. Change in body mass index (BMI) connected with changes in mRNA level of genes with inflammatory response signature. In this module, change in BMI was negatively associated with changes in expression of genes encoding secreted protein (GDF15, CCL3, and SPP1). Through all phases of the DI, change in GDF15 was connected to changes in SPP1, CCL3, LIPA and CD68. Further characterization showed that these genes were specific to macrophages (with LIPA, CD68 and GDF15 expressed in anti-inflammatory macrophages) and GDF15 also expressed in preadipocytes. CONCLUSION Network analyses identified a novel AT feature with GDF15 upregulated with calorie restriction induced weight loss, concomitantly to macrophage markers. In AT, GDF15 was expressed in preadipocytes and macrophages where it was a hallmark of anti-inflammatory cells.
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Affiliation(s)
- Alyssa Imbert
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, F-31326 Castanet-Tolosan, France
| | - Nathalie Vialaneix
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, F-31326 Castanet-Tolosan, France
| | - Julien Marquis
- Université de Lausanne, Genomic Technologies Facility, 1015, Lausanne, Switzerland
| | - Julie Vion
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
| | - Aline Charpagne
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Sylviane Metairon
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Claire Laurens
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
| | - Cedric Moro
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
| | - Nathalie Boulet
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Adipose tissue, microbiota and cardiometabolic flexibility, 31400, Toulouse, France
| | - Ondine Walter
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Grégory Lefebvre
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Jörg Hager
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Dominique Langin
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
- Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France
- Toulouse University Hospitals, Laboratory of Clinical Biochemistry, 31000, Toulouse, France
| | - Wim H M Saris
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Arne Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Sciences, University of Copenhagen, Denmark
| | - Nathalie Viguerie
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
- Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France
| | - Armand Valsesia
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
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Wu H, Zeng R, Qiu X, Chen K, Zhuo Z, Guo K, Xiang Y, Yang Q, Jiang R, Leung FW, Lian Q, Sha W, Chen H. Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn's disease. Front Immunol 2022; 13:1096587. [PMID: 36685554 PMCID: PMC9849378 DOI: 10.3389/fimmu.2022.1096587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/02/2022] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Crohn's disease is characterized of dysregulated inflammatory and immune reactions. The role of the NOD-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome in Crohn's disease remains largely unknown. METHODS The microarray-based transcriptomic data and corresponding clinical information of GSE100833 and GSE16879 were obtained from the Gene Expression Omnibus (GEO) database. Identification of in the NLRP3 inflammasome-related genes and construction of LASSO regression model. Immune landscape analysis was evaluated with ssGSEA. Classification of Crohn's-disease samples based on NLRP3 inflammasome-related genes with ConsensusClusterPlus. Functional enrichment analysis, gene set variation analysis (GSVA) and drug-gene interaction network. RESULTS The expressions of NLRP3 inflammasome-related genes were increased in diseased tissues, and higher expressions of NLRP3 inflammasome-related genes were correlated with generally enhanced immune cell infiltration, immune-related pathways and human leukocyte antigen (HLA)-gene expressions. The gene-based signature showed well performance in the diagnosis of Crohn's disease. Moreover, consensus clustering identified two Crohn's disease clusters based on NLRP3 inflammasome-related genes, and cluster 2 was with higher expressions of the genes. Cluster 2 demonstrated upregulated activities of immune environment in Crohn's disease. Furthermore, four key hub genes were identified and potential drugs were explored for the treatment of Crohn's disease. CONCLUSIONS Our findings indicate that NLRP3 inflammasome and its related genes could regulate immune cells and responses, as well as involve in the pathogenesis of Crohn's disease from transcriptomic aspects. These findings provide in silico insights into the diagnosis and treatment of Crohn's disease and might assist in the clinical decision-making process.
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Affiliation(s)
- Huihuan Wu
- Department of Gastroenterology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Ruijie Zeng
- Department of Gastroenterology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, Shantou University Medical College, Shantou, China
| | - Xinqi Qiu
- Zhuguang Community Healthcare Center, Guangzhou, China
| | - Kequan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zewei Zhuo
- Department of Gastroenterology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kehang Guo
- Department of Critical Care Medicine, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yawen Xiang
- Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Qi Yang
- Department of Gastroenterology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Rui Jiang
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Felix W. Leung
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
- *Correspondence: Felix W. Leung, ; Qizhou Lian, ; Weihong Sha, ; Hao Chen,
| | - Qizhou Lian
- Department of Medicine, Queen Mary Hospital, Hong Kong, Hong Kong SAR, China
- *Correspondence: Felix W. Leung, ; Qizhou Lian, ; Weihong Sha, ; Hao Chen,
| | - Weihong Sha
- Department of Gastroenterology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Felix W. Leung, ; Qizhou Lian, ; Weihong Sha, ; Hao Chen,
| | - Hao Chen
- Department of Gastroenterology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Felix W. Leung, ; Qizhou Lian, ; Weihong Sha, ; Hao Chen,
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Dasgupta S, Maricic I, Tang J, Wandro S, Weldon K, Carpenter CS, Eckmann L, Rivera-Nieves J, Sandborn W, Knight R, Dorrestein P, Swafford AD, Kumar V. Class Ib MHC-Mediated Immune Interactions Play a Critical Role in Maintaining Mucosal Homeostasis in the Mammalian Large Intestine. Immunohorizons 2021; 5:953-971. [PMID: 34911745 PMCID: PMC10026853 DOI: 10.4049/immunohorizons.2100090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/09/2021] [Indexed: 11/19/2022] Open
Abstract
Lymphocytes within the intestinal epithelial layer (IEL) in mammals have unique composition compared with their counterparts in the lamina propria. Little is known about the role of some of the key colonic IEL subsets, such as TCRαβ+CD8+ T cells, in inflammation. We have recently described liver-enriched innate-like TCRαβ+CD8αα regulatory T cells, partly controlled by the non-classical MHC molecule, Qa-1b, that upon adoptive transfer protect from T cell-induced colitis. In this study, we found that TCRαβ+CD8αα T cells are reduced among the colonic IEL during inflammation, and that their activation with an agonistic peptide leads to significant Qa-1b-dependent protection in an acute model of colitis. Cellular expression of Qa-1b during inflammation and corresponding dependency in peptide-mediated protection suggest that Batf3-dependent CD103+CD11b- type 1 conventional dendritic cells control the protective function of TCRαβ+CD8αα T cells in the colonic epithelium. In the colitis model, expression of the potential barrier-protective gene, Muc2, is enhanced upon administration of a Qa-1b agonistic peptide. Notably, in steady state, the mucin metabolizing Akkermansia muciniphila was found in significantly lower abundance amid a dramatic change in overall microbiome and metabolome, increased IL-6 in explant culture, and enhanced sensitivity to dextran sulfate sodium in Qa-1b deficiency. Finally, in patients with inflammatory bowel disease, we found upregulation of HLA-E, a Qa-1b analog with inflammation and biologic non-response, in silico, suggesting the importance of this regulatory mechanism across species.
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Affiliation(s)
- Suryasarathi Dasgupta
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Igor Maricic
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Jay Tang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Kelly Weldon
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Carolina S Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Lars Eckmann
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Jesus Rivera-Nieves
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - William Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA; and
- Department of Bioengineering, University of California San Diego, La Jolla, CA
| | - Peter Dorrestein
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Vipin Kumar
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA;
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
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75
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Etwebi Z, Goldsmith JR, Bou-Dargham M, Tian Y, Hood R, Spitofsky N, Li M, Sun H, Lou Y, Liu S, Lengner C, Chen YH. TIPE2 Promotes Tumor Initiation But Inhibits Tumor Progression in Murine Colitis-Associated Colon Cancer. Inflamm Bowel Dis 2021; 28:764-774. [PMID: 34894222 PMCID: PMC9074867 DOI: 10.1093/ibd/izab306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third leading cause of cancer in the United States, and inflammatory bowel disease patients have an increased risk of developing CRC due to chronic intestinal inflammation with it being the cause of death in 10% to 15% of inflammatory bowel disease patients. TIPE2 (TNF-alpha-induced protein 8-like 2) is a phospholipid transporter that is highly expressed in immune cells and is an important regulator of immune cell function. METHODS The azoxymethane/dextran sulfate sodium murine model of colitis-associated colon cancer (CAC) was employed in Tipe2 -/- and wild-type mice, along with colonoid studies, to determine the role of TIPE2 in CAC. RESULTS Early on, loss of TIPE2 led to significantly less numbers of visible tumors, which was in line with its previously described role in myeloid-derived suppressor cells. However, as time went on, loss of TIPE2 promoted tumor progression, with larger tumors appearing in Tipe2 -/- mice. This was associated with increased interleukin-22/STAT3 phosphorylation signaling. Similar effects were also observed in primary colonoid cultures, together demonstrating that TIPE2 also directly regulated colonocytes in addition to immune cells. CONCLUSIONS This work demonstrates that TIPE2 has dual effects in CAC. In the colonocytes, it works as a tumor suppressor. However, in the immune system, TIPE2 may promote tumorigenesis through suppressor cells or inhibit it through IL-22 secretion. Going forward, this work suggests that targeting TIPE2 for CRC therapy requires cell- and pathway-specific approaches and serves as a cautionary tale for immunotherapy approaches in general in terms of colon cancer, as intestinal inflammation can both promote and inhibit cancer.
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Affiliation(s)
- Zienab Etwebi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason R Goldsmith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Address correspondence to: Jason Rosenbaum Goldsmith, MD, PhD, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA ()
| | - Mayassa Bou-Dargham
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhua Tian
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Ryan Hood
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nina Spitofsky
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Honghong Sun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yunwei Lou
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
| | - Suxia Liu
- Institute of Immunology, Shandong University School of Medicine, Jinan, China
| | - Christopher Lengner
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Youhai H Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Faculty of Pharmaceutical Sciences, CAS Shenzhen Institute of Advanced Technology, Shenzhen, China
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76
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Argmann C, Tokuyama M, Ungaro RC, Huang R, Hou R, Gurunathan S, Kosoy R, Di’Narzo A, Wang W, Losic B, Irizar H, Peters L, Stojmirovic A, Wei G, Comella PH, Curran M, Brodmerkel C, Friedman JR, Hao K, Schadt EE, Zhu J, Cho J, Harpaz N, Dubinsky MC, Sands BE, Kasarskis A, Mehandru S, Colombel JF, Suárez-Fariñas M. Molecular Characterization of Limited Ulcerative Colitis Reveals Novel Biology and Predictors of Disease Extension. Gastroenterology 2021; 161:1953-1968.e15. [PMID: 34480882 PMCID: PMC8640960 DOI: 10.1053/j.gastro.2021.08.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Disease extent varies in ulcerative colitis (UC) from proctitis to left-sided colitis to pancolitis and is a major prognostic factor. When the extent of UC is limited there is often a sharp demarcation between macroscopically involved and uninvolved areas and what defines this or subsequent extension is unknown. We characterized the demarcation site molecularly and determined genes associated with subsequent disease extension. METHODS We performed RNA sequence analysis of biopsy specimens from UC patients with endoscopically and histologically confirmed limited disease, of which a subset later extended. Biopsy specimens were obtained from the endoscopically inflamed upper (proximal) limit of disease, immediately adjacent to the uninvolved colon, as well as at more proximal, endoscopically uninflamed colonic segments. RESULTS Differentially expressed genes were identified in the endoscopically inflamed biopsy specimens taken at each patient's most proximal diseased site relative to healthy controls. Expression of these genes in the more proximal biopsy specimens transitioned back to control levels abruptly or gradually, the latter pattern supporting the concept that disease exists beyond the endoscopic disease demarcation site. The gradually transitioning genes were associated with inflammation, angiogenesis, glucuronidation, and homeodomain pathways. A subset of these genes in inflamed biopsy specimens was found to predict disease extension better than clinical features and were responsive to biologic therapies. Network analysis revealed critical roles for interferon signaling in UC inflammation and poly(ADP-ribose) polymerase 14 (PARP14) was a predicted key driver gene of extension. Higher PARP14 protein levels were found in inflamed biopsy specimens of patients with limited UC that subsequently extended. CONCLUSION Molecular predictors of disease extension reveal novel strategies for disease prognostication and potential therapeutic targeting.
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Affiliation(s)
- Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, New York, New York.
| | - Minami Tokuyama
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C. Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruiqi Huang
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruixue Hou
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sakteesh Gurunathan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York
| | - Antonio Di’Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York,Sema4, Stamford, Connecticut
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York
| | | | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York
| | - Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York
| | | | | | | | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York,Sema4, Stamford, Connecticut
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York,Sema4, Stamford, Connecticut
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York,Sema4, Stamford, Connecticut
| | - Judy Cho
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marla C. Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce E. Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York, New York,Sema4, Stamford, Connecticut,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Saurabh Mehandru
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York.
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77
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He M, Li C, Tang W, Kang Y, Zuo Y, Wang Y. Machine learning gene expression predicting model for ustekinumab response in patients with Crohn's disease. Immun Inflamm Dis 2021; 9:1529-1540. [PMID: 34469062 PMCID: PMC8589399 DOI: 10.1002/iid3.506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background Recent studies reported the responses of ustekinumab (UST) for the treatment of Crohn's disease (CD) differ among patients, while the cause was unrevealed. The study aimed to develop a prediction model based on the gene transcription profiling of patients with CD in response to UST. Methods The GSE112366 dataset, which contains 86 CD and 26 normal samples, was downloaded for analysis. Differentially expressed genes (DEGs) were identified first. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were administered. Least absolute shrinkage and selection operator regression analysis was performed to build a model for UST response prediction. Results A total of 122 DEGs were identified. GO and KEGG analyses revealed that immune response pathways are significantly enriched in patients with CD. A multivariate logistic regression equation that comprises four genes (HSD3B1, MUC4, CF1, and CCL11) for UST response prediction was built. The area under the receiver operator characteristic curve for patients in training set and testing set were 0.746 and 0.734, respectively. Conclusions This study is the first to build a gene expression prediction model for UST response in patients with CD and provides valuable data sources for further studies.
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Affiliation(s)
- Manrong He
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wanxin Tang
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yingxi Kang
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongdi Zuo
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yufang Wang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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78
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Manthey CF, Reher D, Huber S. [What is confirmed in the treatment of chronic inflammatory bowel diseases]. Internist (Berl) 2021; 62:1269-1279. [PMID: 34727190 PMCID: PMC8561375 DOI: 10.1007/s00108-021-01207-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/07/2022]
Abstract
The prevalence of the chronic inflammatory bowel diseases (CIBD) Crohn's disease (CD) and ulcerative colitis (UC) is on the rise worldwide. In Germany CIBDs are also a significant healthcare problem. The pathogenesis is complex and involves genetic factors, environmental aspects and changes in the immunological constitution. Furthermore, the gut microbiota plays a role in the maintenance of intestinal inflammation. Fortunately, several new drugs, in particular biologicals, have been approved for the treatment of CIBDs. The treatment of UC is mainly based on 5‑aminosalicylic acid formulations, preferably as a topical form for distal colitis and proctitis as well as local budesonide formulations. In the case of extensive spread, high disease activity and refractory disease antibodies (biologicals) are successfully used, similar to CD. In addition to anti-tumor necrosis factor antibodies (infliximab, adalimumab, golimumab), vedolizumab, an anti-integrin antibody and the interleukin 12/23 antibody ustekinumab can be successfully used. The intravenous and also subcutaneous administration of antibodies are increasing in importance and are now available for all forms. Furthermore, the Janus kinase inhibitor tofacitinib is an orally administered option for UC. Clinical scores, endoscopy, ultrasound, laboratory parameters and calprotectin determination in stool are employed to evaluate treatment response (treat to target approach). Ultimately, the long-term goal is mucosal healing. Despite advances in the pharmaceutical treatment, a significant number of patients with CIBD still suffer from treatment refractory courses and need surgery at some time during the disease.
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Affiliation(s)
- Carolin F Manthey
- I. Medizinische Klinik und Poliklinik, Universitätsklinikum Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Deutschland.
| | - Dominik Reher
- I. Medizinische Klinik und Poliklinik, Universitätsklinikum Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Deutschland
| | - Samuel Huber
- I. Medizinische Klinik und Poliklinik, Universitätsklinikum Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Deutschland.
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79
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Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers SJ, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Thomas T, Ravindran R, Tandon R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Attar M, McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom SN, Easton A, Raychaudhuri S, Travis SP, Powrie FM. IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nat Med 2021; 27:1970-1981. [PMID: 34675383 PMCID: PMC8604730 DOI: 10.1038/s41591-021-01520-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
Current inflammatory bowel disease (IBD) therapies are ineffective in a high proportion of patients. Combining bulk and single-cell transcriptomics, quantitative histopathology and in situ localization across three cohorts of patients with IBD (total n = 376), we identify coexpressed gene modules within the heterogeneous tissular inflammatory response in IBD that map to distinct histopathological and cellular features (pathotypes). One of these pathotypes is defined by high neutrophil infiltration, activation of fibroblasts and vascular remodeling at sites of deep ulceration. Activated fibroblasts in the ulcer bed display neutrophil-chemoattractant properties that are IL-1R, but not TNF, dependent. Pathotype-associated neutrophil and fibroblast signatures are increased in nonresponders to several therapies across four independent cohorts (total n = 343). The identification of distinct, localized, tissular pathotypes will aid precision targeting of current therapeutics and provides a biological rationale for IL-1 signaling blockade in ulcerating disease.
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Affiliation(s)
- Matthias Friedrich
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathilde Pohin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Matthew A Jackson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ilya Korsunsky
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel J Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Kevin Rue-Albrecht
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Zoe Christoforidou
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Dharshan Sathananthan
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Tom Thomas
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Rahul Ravindran
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Ruchi Tandon
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Raphael Sanches Peres
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Hannah Sharpe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Wei
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth H Mann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Moustafa Attar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah McCuaig
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lloyd Thomas
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Elena Collantes
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Department of Paediatrics, John Radcliffe Hospital, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alistair Easton
- Old Road Campus Research Building, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Simon P Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Fiona M Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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80
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Thomas JP, Modos D, Korcsmaros T, Brooks-Warburton J. Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. Front Genet 2021; 12:760501. [PMID: 34745229 PMCID: PMC8566351 DOI: 10.3389/fgene.2021.760501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/08/2021] [Indexed: 12/22/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated condition arising due to complex interactions between multiple genetic and environmental factors. Despite recent advances, the pathogenesis of the condition is not fully understood and patients still experience suboptimal clinical outcomes. Over the past few years, investigators are increasingly capturing multi-omics data from patient cohorts to better characterise the disease. However, reaching clinically translatable endpoints from these complex multi-omics datasets is an arduous task. Network biology, a branch of systems biology that utilises mathematical graph theory to represent, integrate and analyse biological data through networks, will be key to addressing this challenge. In this narrative review, we provide an overview of various types of network biology approaches that have been utilised in IBD including protein-protein interaction networks, metabolic networks, gene regulatory networks and gene co-expression networks. We also include examples of multi-layered networks that have combined various network types to gain deeper insights into IBD pathogenesis. Finally, we discuss the need to incorporate other data sources including metabolomic, histopathological, and high-quality clinical meta-data. Together with more robust network data integration and analysis frameworks, such efforts have the potential to realise the key goal of precision medicine in IBD.
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Affiliation(s)
- John P Thomas
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
- Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Dezso Modos
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Johanne Brooks-Warburton
- Department of Gastroenterology, Lister Hospital, Stevenage, United Kingdom
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
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81
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Tian L, Zhao JL, Kang JQ, Guo SB, Zhang N, Shang L, Zhang YL, Zhang J, Jiang X, Lin Y. Astragaloside IV Alleviates the Experimental DSS-Induced Colitis by Remodeling Macrophage Polarization Through STAT Signaling. Front Immunol 2021; 12:740565. [PMID: 34589089 PMCID: PMC8473681 DOI: 10.3389/fimmu.2021.740565] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/26/2021] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic and relapsing intestinal inflammation, which currently lacks safe and effective medicine. Some previous studies indicated that Astragaloside IV (AS-IV), a natural saponin extracted from the traditional Chinese medicine herb Ligusticum chuanxiong, alleviates the experimental colitis symptoms in vitro and in vivo. However, the mechanism of AS-IV on IBD remains unclear. Accumulating evidence suggests that M2-polarized intestinal macrophages play a pivotal role in IBD progression. Here, we found that AS-IV attenuated clinical activity of DSS-induced colitis that mimics human IBD and resulted in the phenotypic transition of macrophages from immature pro-inflammatory macrophages to mature pro-resolving macrophages. In vitro, the phenotype changes of macrophages were observed by qRT-PCR after bone marrow-derived macrophages (BMDMs) were induced to M1/M2 and incubated with AS-IV, respectively. In addition, AS-IV was effective in inhibiting pro-inflammatory macrophages and promoting the pro-resolving macrophages to ameliorate experimental colitis via the regulation of the STAT signaling pathway. Hence, we propose that AS-IV can ameliorate experimental colitis partially by modulating macrophage phenotype by remodeling the STAT signaling, which seems to have an essential function in the ability of AS-IV to alleviate the pathological progress of IBD.
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Affiliation(s)
- Lianlian Tian
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jun-Long Zhao
- State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Air Force Medical University, Xi'an, China
| | - Jian-Qin Kang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Shi-Bo Guo
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Nini Zhang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Lei Shang
- Department of Health Statistics and Ministry of Education, Key Laboratory of Hazard Assessment and Control in Special Operational Environment, Air Force Medical University, Xi'an, China
| | - Ya-Long Zhang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jian Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China
| | - Xun Jiang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yan Lin
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi'an, China
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82
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Fiocchi C, Dragoni G, Iliopoulos D, Katsanos K, Ramirez VH, Suzuki K, Torres J, Scharl M. Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-What, Why, and How. J Crohns Colitis 2021; 15:1410-1430. [PMID: 33733656 DOI: 10.1093/ecco-jcc/jjab051] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many diseases that affect modern humans fall in the category of complex diseases, thus called because they result from a combination of multiple aetiological and pathogenic factors. Regardless of the organ or system affected, complex diseases present major challenges in diagnosis, classification, and management. Current forms of therapy are usually applied in an indiscriminate fashion based on clinical information, but even the most advanced drugs only benefit a limited number of patients and to a variable and unpredictable degree. This 'one measure does not fit all' situation has spurred the notion that therapy for complex disease should be tailored to individual patients or groups of patients, giving rise to the notion of 'precision medicine' [PM]. Inflammatory bowel disease [IBD] is a prototypical complex disease where the need for PM has become increasingly clear. This prompted the European Crohn's and Colitis Organisation to focus the Seventh Scientific Workshop on this emerging theme. The articles in this special issue of the Journal address the various complementary aspects of PM in IBD, including what PM is; why it is needed and how it can be used; how PM can contribute to prediction and prevention of IBD; how IBD PM can aid in prognosis and improve response to therapy; and the challenges and future directions of PM in IBD. This first article of this series is structured on three simple concepts [what, why, and how] and addresses the definition of PM, discusses the rationale for the need of PM in IBD, and outlines the methodology required to implement PM in IBD in a correct and clinically meaningful way.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, and Department of Gastroenterology, Hepatology & Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gabriele Dragoni
- Gastroenterology Research Unit, Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Florence, Florence,Italy.,IBD Referral Center, Gastroenterology Department, Careggi University Hospital, Florence,Italy
| | | | - Konstantinos Katsanos
- Division of Gastroenterology, Department of Internal Medicine, University of Ioannina School of Health Sciences, Ioannina,Greece
| | - Vicent Hernandez Ramirez
- Department of Gastroenterology, Xerencia Xestión Integrada de Vigo, and Research Group in Digestive Diseases, Galicia Sur Health Research Institute [IIS Galicia Sur], SERGAS-UVIGO, Vigo, Spain
| | - Kohei Suzuki
- Division of Digestive and Liver Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX,USA
| | | | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
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83
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Skok DJ, Hauptman N, Jerala M, Zidar N. Expression of Cytokine-Coding Genes BMP8B, LEFTY1 and INSL5 Could Distinguish between Ulcerative Colitis and Crohn's Disease. Genes (Basel) 2021; 12:genes12101477. [PMID: 34680872 PMCID: PMC8535226 DOI: 10.3390/genes12101477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
Ulcerative colitis (UC) and Crohn’s disease (CD) are characterized by an imbalance between pro-inflammatory and anti-inflammatory cytokines, interfering with the resolution of inflammation. Due to the crucial role of cytokines, new insights into their profiles in UC and CD would help to improve our understanding of pathogenesis and enable the development of new treatment modalities. We provide an expression profile of cytokines in UC and CD, using bioinformatics approach, and experimental validation of expression of the selected genes. We retrieved data and analyzed the cytokine gene expression profiles of UC and CD. From ten genes with inverse expression, common to CD and UC, BMP8B, LEFTY1 and INSL5 were selected for gene expression experimental validation. Experimentally, BMP8B and INSL5 were down-regulated in both CD and UC but followed the bioinformatics trend. The expression of genes LEFTY1 and BMP8B was statistically significant when comparing UC and CD in colon and the expression of gene LEFTY1 showed statistical significance when CD in ileum and colon were compared. Using the bioinformatics approach and experimental validation, we found differences in expression profiles between UC and CD for INSL5, LEFTY1 and BMP8B. These three promising candidate genes need to be further explored at different levels, such as DNA methylation and protein expression, to provide more evidence on their potential diagnostic role in CD and UC.
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Affiliation(s)
- Daša Jevšinek Skok
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia; (D.J.S.); (N.H.); (M.J.)
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, SI-1000 Ljubljana, Slovenia
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia; (D.J.S.); (N.H.); (M.J.)
| | - Miha Jerala
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia; (D.J.S.); (N.H.); (M.J.)
| | - Nina Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia; (D.J.S.); (N.H.); (M.J.)
- Correspondence: ; Tel.: +386-1-543-7149
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84
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Majidova K, Handfield J, Kafi K, Martin RD, Kubinski R. Role of Digital Health and Artificial Intelligence in Inflammatory Bowel Disease: A Scoping Review. Genes (Basel) 2021; 12:1465. [PMID: 34680860 PMCID: PMC8535572 DOI: 10.3390/genes12101465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD), subdivided into Crohn's disease (CD) and ulcerative colitis (UC), are chronic diseases that are characterized by relapsing and remitting periods of inflammation in the gastrointestinal tract. In recent years, the amount of research surrounding digital health (DH) and artificial intelligence (AI) has increased. The purpose of this scoping review is to explore this growing field of research to summarize the role of DH and AI in the diagnosis, treatment, monitoring and prognosis of IBD. A review of 21 articles revealed the impact of both AI algorithms and DH technologies; AI algorithms can improve diagnostic accuracy, assess disease activity, and predict treatment response based on data modalities such as endoscopic imaging and genetic data. In terms of DH, patients utilizing DH platforms experienced improvements in quality of life, disease literacy, treatment adherence, and medication management. In addition, DH methods can reduce the need for in-person appointments, decreasing the use of healthcare resources without compromising the standard of care. These articles demonstrate preliminary evidence of the potential of DH and AI for improving the management of IBD. However, the majority of these studies were performed in a regulated clinical environment. Therefore, further validation of these results in a real-world environment is required to assess the efficacy of these methods in the general IBD population.
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Affiliation(s)
| | | | | | | | - Ryszard Kubinski
- Phyla Technologies Inc., Montréal, QC H3C 4J9, Canada; (K.M.); (J.H.); (K.K.); (R.D.M.)
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85
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Mo A, Nagpal S, Gettler K, Haritunians T, Giri M, Haberman Y, Karns R, Prince J, Arafat D, Hsu NY, Chuang LS, Argmann C, Kasarskis A, Suarez-Farinas M, Gotman N, Mengesha E, Venkateswaran S, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, LeLeiko NS, Heyman MB, Griffiths AM, Patel AS, Noe JD, Davis Thomas S, Aronow BJ, Walters TD, McGovern DPB, Hyams JS, Kugathasan S, Cho JH, Denson LA, Gibson G. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. Am J Hum Genet 2021; 108:1765-1779. [PMID: 34450030 DOI: 10.1016/j.ajhg.2021.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of individuals with ulcerative colitis (UC) require colectomy within 5 years of diagnosis, but polygenic risk scores (PRSs) utilizing findings from genome-wide association studies (GWASs) are unable to provide meaningful prediction of this adverse status. By contrast, in Crohn disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a transcriptional risk score (TRS). Here, we demonstrate that a measured TRS based on bulk rectal gene expression in the PROTECT inception cohort study has a positive predictive value approaching 50% for colectomy. Single-cell profiling demonstrates that the genes are active in multiple diverse cell types from both the epithelial and immune compartments. Expression quantitative trait locus (QTL) analysis identifies genes with differential effects at baseline and week 52 follow-up, but for the most part, differential expression associated with colectomy risk is independent of local genetic regulation. Nevertheless, a predicted polygenic transcriptional risk score (PPTRS) derived by summation of transcriptome-wide association study (TWAS) effects identifies UC-affected individuals at 5-fold elevated risk of colectomy with data from the UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with TWASs for stratification of risk of disease complications.
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Affiliation(s)
- Angela Mo
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sini Nagpal
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kyle Gettler
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Giri
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yael Haberman
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Sheba Medical Center, Tel Hashomer, Tel Aviv University, Tel Aviv 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dalia Arafat
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nai-Yun Hsu
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Nathan Gotman
- University of North Carolina, Chapel Hill, NC 27516, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Paul A Rufo
- Harvard University-Children's Hospital Boston, Boston, MA 02115, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo, Buffalo, NY 14222, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, New Hyde Park, NY 11040, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, NJ 07960, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, ON K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Neal S LeLeiko
- Department of Pediatrics, Columbia University, New York City, NY 10032, USA
| | - Melvin B Heyman
- University of California at San Francisco, San Francisco, CA 94143, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, CT 06106, USA
| | | | - Judy H Cho
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Greg Gibson
- Georgia Institute of Technology, Atlanta, GA 30332, USA.
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86
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Jung SM, Park KS, Kim KJ. Deep phenotyping of synovial molecular signatures by integrative systems analysis in rheumatoid arthritis. Rheumatology (Oxford) 2021; 60:3420-3431. [PMID: 33230538 DOI: 10.1093/rheumatology/keaa751] [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: 05/19/2020] [Revised: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE RA encompasses a complex, heterogeneous and dynamic group of diseases arising from molecular and cellular perturbations of synovial tissues. The aim of this study was to decipher this complexity using an integrative systems approach and provide novel insights for designing stratified treatments. METHODS An RNA sequencing dataset of synovial tissues from 152 RA patients and 28 normal controls was imported and subjected to filtration of differentially expressed genes, functional enrichment and network analysis, non-negative matrix factorization, and key driver analysis. A naïve Bayes classifier was applied to the independent datasets to investigate the factors associated with treatment outcome. RESULTS A matrix of 1241 upregulated differentially expressed genes from RA samples was classified into three subtypes (C1-C3) with distinct molecular and cellular signatures. C3 with prominent immune cells and proinflammatory signatures had a stronger association with the presence of ACPA and showed a better therapeutic response than C1 and C2, which were enriched with neutrophil and fibroblast signatures, respectively. C2 was more occupied by synovial fibroblasts of destructive phenotype and carried highly expressed key effector molecules of invasion and osteoclastogenesis. CXCR2, JAK3, FYN and LYN were identified as key driver genes in C1 and C3. HDAC, JUN, NFKB1, TNF and TP53 were key regulators modulating fibroblast aggressiveness in C2. CONCLUSIONS Deep phenotyping of synovial heterogeneity captured comprehensive and discrete pathophysiological attributes of RA regarding clinical features and treatment response. This result could serve as a template for future studies to design stratified approaches for RA patients.
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Affiliation(s)
- Seung Min Jung
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea
| | - Kyung-Su Park
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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87
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Jung SM, Park KS, Kim KJ. Integrative analysis of lung molecular signatures reveals key drivers of systemic sclerosis-associated interstitial lung disease. Ann Rheum Dis 2021; 81:108-116. [PMID: 34380701 DOI: 10.1136/annrheumdis-2021-220493] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/25/2021] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Interstitial lung disease is a significant comorbidity and the leading cause of mortality in patients with systemic sclerosis. Transcriptomic data of systemic sclerosis-associated interstitial lung disease (SSc-ILD) were analysed to evaluate the salient molecular and cellular signatures in comparison with those in related pulmonary diseases and to identify the key driver genes and target molecules in the disease module. METHODS A transcriptomic dataset of lung tissues from patients with SSc-ILD (n=52), idiopathic pulmonary fibrosis (IPF) (n=549), non-specific interstitial pneumonia (n=49) and pulmonary arterial hypertension (n=81) and from normal healthy controls (n=331) was subjected to filtration of differentially expressed genes, functional enrichment analysis, network-based key driver analysis and kernel-based diffusion scoring. The association of enriched pathways with clinical parameters was evaluated in patients with SSc-ILD. RESULTS SSc-ILD shared key pathogenic pathways with other fibrosing pulmonary diseases but was distinguishable in some pathological processes. SSc-ILD showed general similarity with IPF in molecular and cellular signatures but stronger signals for myofibroblasts, which in SSc-ILD were in a senescent and apoptosis-resistant state. The p53 signalling pathway was the most enriched signature in lung tissues and lung fibroblasts of SSc-ILD, and was significantly correlated with carbon monoxide diffusing capacity of lung, cellular senescence and apoptosis. EEF2, EFF2K, PHKG2, VCAM1, PRKACB, ITGA4, CDK1, CDK2, FN1 and HDAC1 were key regulators with high diffusion scores in the disease module. CONCLUSIONS Integrative transcriptomic analysis of lung tissues revealed key signatures of fibrosis in SSc-ILD. A network-based Bayesian approach provides deep insights into key regulatory genes and molecular targets applicable to treating SSc-ILD.
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Affiliation(s)
- Seung Min Jung
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung-Su Park
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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88
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Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA. A proteogenomic portrait of lung squamous cell carcinoma. Cell 2021; 184:4348-4371.e40. [PMID: 34358469 PMCID: PMC8475722 DOI: 10.1016/j.cell.2021.07.016] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.
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Affiliation(s)
- Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pierre M Jean Beltran
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yongchao Dou
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shayan C Avanessian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Suhas V Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Song Cao
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yize Li
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tanvi H Visal
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria G Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tobias Schraink
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Houxiang Zhu
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Chia-Kuei Mo
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chen Huang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Stephan Schurer
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - James Suh
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Qing Kay Li
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Ramaswamy Govindan
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Li Ding
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02115, USA.
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89
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease. Nat Commun 2021; 12:4246. [PMID: 34253728 PMCID: PMC8275683 DOI: 10.1038/s41467-021-24470-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here we outline an unbiased AI-assisted approach for target identification and validation. A network was built in which clusters of genes are connected by directed edges that highlight asymmetric Boolean relationships. Using machine-learning, a path of continuum states was pinpointed, which most effectively predicted disease outcome. This path was enriched in gene-clusters that maintain the integrity of the gut epithelial barrier. We exploit this insight to prioritize one target, choose appropriate pre-clinical murine models for target validation and design patient-derived organoid models. Potential for treatment efficacy is confirmed in patient-derived organoids using multivariate analyses. This AI-assisted approach identifies a first-in-class gut barrier-protective agent in IBD and predicted Phase-III success of candidate agents. Traditional drug discovery process use differential, Bayesian and other network based approaches. We developed a Boolean approach for building disease maps and prioritizing pre-clinical models to discover a first-in-class therapy to restore and protect the leaky gut barrier in inflammatory bowel disease.
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90
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Koppens MAJ, Davis H, Valbuena GN, Mulholland EJ, Nasreddin N, Colombe M, Antanaviciute A, Biswas S, Friedrich M, Lee L, Wang LM, Koelzer VH, East JE, Simmons A, Winton DJ, Leedham SJ. Bone Morphogenetic Protein Pathway Antagonism by Grem1 Regulates Epithelial Cell Fate in Intestinal Regeneration. Gastroenterology 2021; 161:239-254.e9. [PMID: 33819486 PMCID: PMC7613733 DOI: 10.1053/j.gastro.2021.03.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS In homeostasis, intestinal cell fate is controlled by balanced gradients of morphogen signaling. The bone morphogenetic protein (BMP) pathway has a physiological, prodifferentiation role, predominantly inferred through previous experimental pathway inactivation. Intestinal regeneration is underpinned by dedifferentiation and cell plasticity, but the signaling pathways that regulate this adaptive reprogramming are not well understood. We assessed the BMP signaling landscape and investigated the impact and therapeutic potential of pathway manipulation in homeostasis and regeneration. METHODS A novel mouse model was generated to assess the effect of the autocrine Bmp4 ligand on individual secretory cell fate. We spatiotemporally mapped BMP signaling in mouse and human regenerating intestine. Transgenic models were used to explore the functional impact of pathway manipulation on stem cell fate and intestinal regeneration. RESULTS In homeostasis, ligand exposure reduced proliferation, expedited terminal differentiation, abrogated secretory cell survival, and prevented dedifferentiation. After ulceration, physiological attenuation of BMP signaling arose through upregulation of the secreted antagonist Grem1 from topographically distinct populations of fibroblasts. Concomitant expression supported functional compensation after Grem1 deletion from tissue-resident cells. BMP pathway manipulation showed that antagonist-mediated BMP attenuation was obligatory but functionally submaximal, because regeneration was impaired or enhanced by epithelial overexpression of Bmp4 or Grem1, respectively. Mechanistically, Bmp4 abrogated regenerative stem cell reprogramming despite a convergent impact of YAP/TAZ on cell fate in remodeled wounds. CONCLUSIONS BMP signaling prevents epithelial dedifferentiation, and pathway attenuation through stromal Grem1 upregulation was required for adaptive reprogramming in intestinal regeneration. This intercompartmental antagonism was functionally submaximal, raising the possibility of therapeutic pathway manipulation in inflammatory bowel disease.
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Affiliation(s)
- Martijn A J Koppens
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Hayley Davis
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gabriel N Valbuena
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eoghan J Mulholland
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nadia Nasreddin
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mathilde Colombe
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Agne Antanaviciute
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom; Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Sujata Biswas
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthias Friedrich
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, United Kingdom
| | - Lennard Lee
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Lai Mun Wang
- Department of Laboratory Medicine, Changi General Hospital, SingHealth, Singapore, Singapore
| | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland; Department of Oncology and Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - James E East
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, and Oxford National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Alison Simmons
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom; Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, and Oxford National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Douglas J Winton
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Simon J Leedham
- Intestinal Stem Cell Biology Lab, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom; Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, and Oxford National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom.
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91
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Nowak JK, Kalla R, Satsangi J. Reply. Gastroenterology 2021; 160:2622-2623. [PMID: 33549534 PMCID: PMC7859710 DOI: 10.1053/j.gastro.2021.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/14/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022]
Affiliation(s)
| | - Rahul Kalla
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK and, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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92
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Abstract
BACKGROUND Systems biology is a rapidly advancing field of science that allows us to look into disease mechanisms, patient diagnosis and stratification, and drug development in a completely new light. It is based on the utilization of unbiased computational systems free of the traditional experimental approaches based on personal choices of what is important and what select experiments should be performed to obtain the expected results. METHODS Systems biology can be applied to inflammatory bowel disease (IBD) by learning basic concepts of omes and omics and how omics-derived "big data" can be integrated to discover the biological networks underlying highly complex diseases like IBD. Once these biological networks (interactomes) are identified, then the molecules controlling the disease network can be singled out and specific blockers developed. RESULTS The field of systems biology in IBD is just emerging, and there is still limited information on how to best utilize its power to advance our understanding of Crohn disease and ulcerative colitis to develop novel therapeutic strategies. Few centers have embraced systems biology in IBD, but the creation of international consortia and large biobanks will make biosamples available to basic and clinical IBD investigators for further research studies. CONCLUSIONS The implementation of systems biology is indispensable and unavoidable, and the patient and medical communities will both benefit immensely from what it will offer in the near future.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
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93
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Scarallo L, Lionetti P. Dietary Management in Pediatric Patients with Crohn's Disease. Nutrients 2021; 13:1611. [PMID: 34064976 PMCID: PMC8150738 DOI: 10.3390/nu13051611] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
It has been widely endorsed that a multifactorial etiology, including interaction between genetic and environmental factors, can contribute to Crohn's Disease (CD) pathogenesis. More specifically, diet has proven to be able to shape gut microbiota composition and thus is suspected to play a significant role in inflammatory bowel disease (IBD) pathogenesis. Moreover, poor nutritional status and growth retardation, arising from several factors such as reduced dietary intake or nutrient leakage from the gastrointestinal tract, represent the hallmarks of pediatric CD. For these reasons, multiple research lines have recently focused on the utilization of dietary therapies for the management of CD, aiming to target concurrently mucosal inflammation, intestinal dysbiosis and optimization of nutritional status. The forerunner of such interventions is represented by exclusive enteral nutrition (EEN), a robustly supported nutritional therapy; however, it is burdened by monotony and low tolerance in the long term. Novel dietary interventions, such as Crohn's Disease Exclusion Diet or Crohn's Disease treatment with eating, have shown their efficacy in the induction of remission in pediatric patients with CD. The aim of the present narrative review is to provide a synopsis of the available nutritional strategies in the management of pediatric CD and to discuss their application in the dietary management of these patients.
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Affiliation(s)
- Luca Scarallo
- Gastroenterology and Nutrition Unit, Meyer Children’s Hospital, 50139 Florence, Italy;
| | - Paolo Lionetti
- Gastroenterology and Nutrition Unit, Meyer Children’s Hospital, 50139 Florence, Italy;
- Department NEUROFARBA, University of Florence, 50139 Florence, Italy
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94
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Kosinsky RL, Saul D, Ammer-Herrmenau C, Faubion WA, Neesse A, Johnsen SA. USP22 Suppresses SPARC Expression in Acute Colitis and Inflammation-Associated Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13081817. [PMID: 33920268 PMCID: PMC8070211 DOI: 10.3390/cancers13081817] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Intestinal inflammation leads to an increased risk of developing colorectal cancer (CRC) and incidences are expected to rise. Therefore, it is crucial to identify molecular factors contributing to these medical conditions. In an earlier study, we identified USP22 as a tumor suppressor in CRC since the loss of Usp22 resulted in severe tumor burden in mice. Moreover, Usp22-deficient mice displayed inflammation-associated symptoms. Therefore, we aimed to elucidate the function of USP22 in intestinal inflammation and inflammation-associated CRC. Indeed, mice with an intestine-specific loss of Usp22 displayed more severe colitis compared to wild type controls. In addition, the loss of Usp22 in a mouse model for CRC resulted in increased numbers of inflammation-associated tumors. Finally, we observed that the loss of USP22 induces the expression of Sparc, a factor previously linked to inflammation. Together, our results suggest that USP22 suppresses Sparc expression in acute colitis and inflammation-associated CRC. Abstract As a member of the 11-gene “death-from-cancer” gene expression signature, ubiquitin-specific protease 22 (USP22) has been considered an oncogene in various human malignancies, including colorectal cancer (CRC). We recently identified an unexpected tumor-suppressive function of USP22 in CRC and detected intestinal inflammation after Usp22 deletion in mice. We aimed to investigate the function of USP22 in intestinal inflammation as well as inflammation-associated CRC. We evaluated the effects of a conditional, intestine-specific knockout of Usp22 during dextran sodium sulfate (DSS)-induced colitis and in a model for inflammation-associated CRC. Mice were analyzed phenotypically and histologically. Differentially regulated genes were identified in USP22-deficient human CRC cells and the occupancy of active histone markers was determined using chromatin immunoprecipitation. The knockout of Usp22 increased inflammation-associated symptoms after DSS treatment locally and systemically. In addition, Usp22 deletion resulted in increased inflammation-associated colorectal tumor growth. Mechanistically, USP22 depletion in human CRC cells induced a profound upregulation of secreted protein acidic and rich in cysteine (SPARC) by affecting H3K27ac and H2Bub1 occupancy on the SPARC gene. The induction of SPARC was confirmed in vivo in our intestinal Usp22-deficient mice. Together, our findings uncover that USP22 controls SPARC expression and inflammation intensity in colitis and CRC.
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Affiliation(s)
- Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075 Goettingen, Germany
- Correspondence: ; Tel.: +1-507-293-2386
| | - Dominik Saul
- Kogod Center on Aging and Division of Endocrinology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of Trauma, Orthopedics and Reconstructive Surgery, Georg-August-University Goettingen, 37075 Goettingen, Germany
| | - Christoph Ammer-Herrmenau
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075 Goettingen, Germany; (C.A.-H.); (A.N.)
| | - William A. Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
| | - Albrecht Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075 Goettingen, Germany; (C.A.-H.); (A.N.)
| | - Steven A. Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA;
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Liu M, Zhang J, Pinder BD, Liu Q, Wang D, Yao H, Gao Y, Toker A, Gao J, Peterson A, Qu J, Siminovitch KA. WAVE2 suppresses mTOR activation to maintain T cell homeostasis and prevent autoimmunity. Science 2021; 371:371/6536/eaaz4544. [PMID: 33766857 DOI: 10.1126/science.aaz4544] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/25/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
Cytoskeletal regulatory protein dysfunction has been etiologically linked to inherited diseases associated with immunodeficiency and autoimmunity, but the mechanisms involved are incompletely understood. Here, we show that conditional Wave2 ablation in T cells causes severe autoimmunity associated with increased mammalian target of rapamycin (mTOR) activation and metabolic reprogramming that engender spontaneous activation and accelerated differentiation of peripheral T cells. These mice also manifest diminished antigen-specific T cell responses associated with increased inhibitory receptor expression, dysregulated mitochondrial function, and reduced cell survival upon activation. Mechanistically, WAVE2 directly bound mTOR and inhibited its activation by impeding mTOR interactions with RAPTOR (regulatory-associated protein of mTOR) and RICTOR (rapamycin-insensitive companion of mTOR). Both the T cell defects and immunodysregulatory disease were ameliorated by pharmacological mTOR inhibitors. Thus, WAVE2 restraint of mTOR activation is an absolute requirement for maintaining the T cell homeostasis supporting adaptive immune responses and preventing autoimmunity.
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Affiliation(s)
- Ming Liu
- Mount Sinai Hospital, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinyi Zhang
- Mount Sinai Hospital, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Benjamin D Pinder
- Mount Sinai Hospital, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Qingquan Liu
- Mount Sinai Hospital, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Dingyan Wang
- Mount Sinai Hospital, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hao Yao
- Mount Sinai Hospital, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yubo Gao
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Aras Toker
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,The Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre University Health Network, Toronto, Ontario, Canada
| | - Jimin Gao
- Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Alan Peterson
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Jia Qu
- Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Katherine A Siminovitch
- Mount Sinai Hospital, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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96
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Bayesian Model Infers Drug Repurposing Candidates for Treatment of COVID-19. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of COVID-19 progressed into a global pandemic that has functionally put the world at a standstill and catapulted major healthcare systems into an overburdened state. The dire need for therapeutic strategies to mitigate and successfully treat COVID-19 is now a public health crisis with national security implications for many countries. The current study employed Bayesian networks to a longitudinal proteomic dataset generated from Caco-2 cells transfected with SARS-CoV-2 (isolated from patients returning from Wuhan to Frankfurt). Two different approaches were employed to assess the Bayesian models, a titer-center topology analysis and a drug signature enrichment analysis. Topology analysis identified a set of proteins directly linked to the SAR-CoV2 titer, including ACE2, a SARS-CoV-2 binding receptor, MAOB and CHECK1. Aligning with the topology analysis, MAOB and CHECK1 were also identified within the enriched drug-signatures. Taken together, the data output from this network has identified nodal host proteins that may be connected to 18 chemical compounds, some already marketed, which provides an immediate opportunity to rapidly triage these assets for safety and efficacy against COVID-19.
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97
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Fecal g. Streptococcus and g. Eubacterium_coprostanoligenes_group combined with sphingosine to modulate the serum dyslipidemia in high-fat diet mice. Clin Nutr 2021; 40:4234-4245. [PMID: 33608131 DOI: 10.1016/j.clnu.2021.01.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/04/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Although high-fat diet (HFD) could impact the composition of fecal microbiome and their metabolites, it is still largely unknown which fecal bacteria and metabolites are relatively important in responding to the HFD. This study aimed to identify the crucial fecal bacteria and metabolites in the HFD mice using a microbial-metabolite network, and to investigate the synergistic mediation effect of the crucial fecal bacteria and metabolites on serum dyslipidemia induced by the HFD. METHODS The 16srDNA sequencing and the ultra-performance liquid chromatography (UPLC/TOF MSMS) platform were performed to characterize the composition and function of fecal microbiome, and metabolites in the HFD. The microbial-metabolite network, correlation and mediation analyses were performed to examine the relationships among fecal microbiome, metabolites, and serum dyslipidemia indicators. Mice models were conducted to evaluate the effect of fecal metabolite on dyslipidemia. RESULTS Compared to the control, 32 genera were altered in the HFD, including 26 up-regulated and 6 down-regulated. A total of 42 altered pathways were observed between the control and HFD, and the "Glycosphingolipid biosynthesis" was identified as the most significant pathway (fold change = 0.64; p < 0.001). Meanwhile, 49 fecal metabolites were altered in the HFD, and the fecal microbiome was associated with the fecal metabolism (M2 = 0.776, p = 0.008). Based on the microbial-metabolite network, two major hub genera were screened (HUB1: g. Streptococcus, HUB2: g. Eubacterium_coprostanoligenes_group), and one bacterial metabolite, sphingosine, was found in this study. Further, the HUB2 was positively associated with fecal sphingosine (r = 0.646, p = 0.001), and its downstream metabolic pathway, "Glycosphingolipid biosynthesis" pathway (r = 0.544, p = 0.009). The regulatory relationship between the HUB2 and sphingosine synergistically mediated the effect of HFD on TCHO (33.7%), HDL-C (37.3%), and bodyweight (36.7%). Besides, compared to the HFD, the HFD with sphingosine supplementation had lower bodyweight (35.12 ± 1.23 vs. 39.42 ± 1.25, p < 0.001), TG (0.44 ± 0.08 vs. 0.52 ± 0.05, p = 0.002), TCHO (3.81 ± 0.34 vs. 4.51 ± 0.38, p = 0.002), and LDL-c (0.82 ± 0.09 vs. 0.97 ± 0.15, p = 0.016). CONCLUSIONS The g. Streptococcus and g. Eubacterium_coprostanoligenes are two hub genera in the fecal micro-ecosystem of the HFD, and the g. Eubacterium_coprostanoligenes mediates the effect of HFD on dyslipidemia through sphingosine. Sphingosine supplementation can improve dyslipidemia induced by HFD.
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98
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Yang Y, Zhang C, Jing D, He H, Li X, Wang Y, Qin Y, Xiao X, Xiong H, Zhou G. IRF5 Acts as a Potential Therapeutic Marker in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2021; 27:407-417. [PMID: 32737976 DOI: 10.1093/ibd/izaa200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are chronic inflammatory disorders. As is well known, interferon regulatory factor (IRF) 5 is closely associated with the pathogenesis of various inflammatory diseases. But the exact role of IRF5 in IBD remains unclear. METHODS In this study, we detected IRF5 expression in peripheral blood mononuclear cells (PBMCs) and inflamed mucosa from IBD patients by immunohistochemistry, western blot, and quantitative real-time polymerase chain reaction. Peripheral blood CD4+ T cells were stimulated with inflammatory cytokines and transfected by lentivirus. RESULTS In active IBD patients, the expression of IRF5 in PBMCs and inflamed colonic tissues was obviously increased and significantly associated with disease activity. Ectopic overexpression of IRF5 could promote the differentiation of IBD CD4+ T cells into Th1 and Th17 cells by regulating T-bet and RAR related orphan receptor C, whereas knockdown of IRF5 had the opposite effects. Tumor necrosis factor (TNF)-α upregulated expression of IRF5 in CD4+ T cells, but anti-TNF treatment with infliximab could markedly reduce IRF5 expression in CD4+ T cells and intestinal mucosa of CD patients. CONCLUSION Our study reveals a novel mechanism that IRF5 levels are correlated with disease activity in IBD and might function as a possible marker for the management of IBD via regulating Th1 and Th17 immune responses and cytokine production.
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Affiliation(s)
- Yonghong Yang
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China.,Department of Central Laboratory, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Cui Zhang
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University, Shanghai, P.R. China
| | - Dehuai Jing
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Heng He
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Xiaoyu Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P.R. China
| | - Yibo Wang
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Yufen Qin
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Xiao Xiao
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Huabao Xiong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong, P.R. China
| | - Guangxi Zhou
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China.,Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong, P.R. China
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99
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Comella PH, Gonzalez-Kozlova E, Kosoy R, Charney AW, Peradejordi IF, Chandrasekar S, Tyler SR, Wang W, Losic B, Zhu J, Hoffman GE, Kim-Schulze S, Qi J, Patel M, Kasarskis A, Suarez-Farinas M, Gümüş ZH, Argmann C, Merad M, Becker C, Beckmann ND, Schadt EE. A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.29.21250755. [PMID: 33564792 PMCID: PMC7872387 DOI: 10.1101/2021.01.29.21250755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
IntroThe molecular mechanisms of chronic fatigue syndrome (CFS, or Myalgic encephalomyelitis), a disease defined by extreme, long-term fatigue, remain largely uncharacterized, and presently no molecular diagnostic test and no specific treatments exist to diagnose and treat CFS patients. While CFS has historically had an estimated prevalence of 0.1-0.5% [1], concerns of a “long hauler” version of Coronavirus disease 2019 (COVID-19) that symptomatically overlaps CFS to a significant degree(Supplemental Table-1)and appears to occur in 10% of COVID-19 patients[2], has raised concerns of a larger spike in CFS [3]. Here, we established molecular signatures of CFS and a corresponding network-based disease context from RNA-sequencing data generated on whole blood and FACs sorted specific peripheral blood mononuclear cells (PBMCs) isolated from CFS cases and non-CFS controls. The immune cell type specific molecular signatures of CFS we identified, overlapped molecular signatures from other fatiguing illnesses, demonstrating a common molecular etiology. Further, after constructing a probabilistic causal model of the CFS gene expression data, we identified master regulator genes modulating network states associated with CFS, suggesting potential therapeutic targets for CFS.
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Affiliation(s)
- Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Irene Font Peradejordi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Shreya Chandrasekar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Scott R. Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jingjing Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Population Health Science and Policy at the Icahn School of Medicine at Mount Sinai
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
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100
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Wahane S, Zhou X, Zhou X, Guo L, Friedl MS, Kluge M, Ramakrishnan A, Shen L, Friedel CC, Zhang B, Friedel RH, Zou H. Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity. SCIENCE ADVANCES 2021; 7:eabd8811. [PMID: 33637528 PMCID: PMC7909890 DOI: 10.1126/sciadv.abd8811] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
The innate immune response influences neural repair after spinal cord injury (SCI). Here, we combined myeloid-specific transcriptomics and single-cell RNA sequencing to uncover not only a common core but also temporally distinct gene programs in injury-activated microglia and macrophages (IAM). Intriguingly, we detected a wide range of microglial cell states even in healthy spinal cord. Upon injury, IAM progressively acquired overall reparative, yet diversified transcriptional profiles, each comprising four transcriptional subtypes with specialized tasks. Notably, IAM have both distinct and common gene signatures as compared to neurodegeneration-associated microglia, both engaging phagocytosis, autophagy, and TyroBP pathways. We also identified an immediate response microglia subtype serving as a source population for microglial transformation and a proliferative subtype controlled by the epigenetic regulator histone deacetylase 3 (HDAC3). Together, our data unveil diversification of myeloid and glial subtypes in SCI and an extensive influence of HDAC3, which may be exploited to enhance functional recovery.
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Affiliation(s)
- Shalaka Wahane
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiang Zhou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lei Guo
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marie-Sophie Friedl
- Institut für Informatik, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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