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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022; 5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored. OBJECTIVE To assess the association between loss-of-function (LOF) variants and pediatric critical illness. DESIGN, SETTING, AND PARTICIPANTS This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022. EXPOSURE Critical illness. MAIN OUTCOMES AND MEASURES Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment. RESULTS This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05). CONCLUSIONS AND RELEVANCE In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.
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Affiliation(s)
- Joshua E. Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Natalie C. Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Evin Feldman
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Matthew Nelligan
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
| | | | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Steven G. Kernie
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
- NewYork-Presbyterian Hospital, New York, New York
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Huang S, Wang J, Zhang L, Tian S, Wang Y, Shao X, Zhou S, Yu P. Ras guanine nucleotide-releasing protein-4 promotes renal inflammatory injury in type 2 diabetes mellitus. Metabolism 2022; 131:155177. [PMID: 35218794 DOI: 10.1016/j.metabol.2022.155177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/31/2022] [Accepted: 02/18/2022] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Ras guanine nucleotide-releasing protein-4 (RasGRP4) is an activator of Ras protein, which plays significant roles in both the inflammatory response and immune activation. This study determined the role of RasGRP4 in diabetic kidney disease (DKD) progression. METHODS CRISPR/Cas9 technology was used to establish RasGRP4 knockout (KO) mice. Diabetes was induced by a high-fat diet combined with five consecutive daily intraperitoneal injections of streptozotocin (60 mg/kg) in C57BL/6J wild-type (WT) mice and RasGRP4 KO mice. Hematoxylin and eosin, periodic acid-Schiff, and Masson's trichrome staining were used to observe the histology of pathological injury. Immunohistochemical staining was used to analyze inflammatory cell infiltration. Quantitative PCR and Western blotting were used to detect the expression of inflammatory mediators and the activation of signaling pathways in renal tissues. In vitro cell co-culture experiments were performed to explore the interactions between peripheral blood mononuclear cells (PBMCs) and glomerular endothelial cells (GEnCs). RESULTS RasGRP4 KO mice developed less severe diabetic kidney injury compared to WT mice, exhibiting lower proteinuria, reduced CD3+ T lymphocyte and F4/80+ macrophage infiltration, less inflammatory mediator expression including interleukin 6, tumor necrosis alpha, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1, and lower expression levels of critical signal transduction molecules in the NLR family pyrin domain-containing 3 inflammasome and mitogen-activated protein kinase (MAPK)/nuclear factor kappa B (NF-κB) signaling pathways in the diabetic kidney. In vitro experiments showed that the adhesion function of PBMCs of RasGRP4 KO mice was reduced compared to that of WT mice. Moreover, the expression of adhesion molecules and critical signal transduction molecules in the NLRP3 inflammasome and MAPK/NF-κB signaling pathways in GEnCs was stimulated by the supernatant of PBMCs, which were derived from RasGRP4 KO mice treated with high glucose and were also significantly reduced compared to those derived from WT mice. CONCLUSION RasGRP4 promotes the inflammatory injury mediated by PBMCs in diabetes, probably by regulating the interaction between PBMCs and GEnCs and further activating the NLRP3 inflammasome and MAPK/NF-κB signaling pathways.
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Affiliation(s)
- Shuai Huang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Junmei Wang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Li Zhang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Shasha Tian
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Yao Wang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Xian Shao
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Saijun Zhou
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Pei Yu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China.
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Benoit A, Bou-Petit E, Chou H, Lu M, Guilbert C, Luo VM, Assouline S, Morin RD, Dmitrienko S, Estrada-Tejedor R, Johnson NA, Mann KK. Mutated RAS-associating proteins and ERK activation in relapse/refractory diffuse large B cell lymphoma. Sci Rep 2022; 12:779. [PMID: 35039569 PMCID: PMC8764096 DOI: 10.1038/s41598-021-04736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is successfully treated with combination immuno-chemotherapy, but relapse with resistant disease occurs in ~ 40% of patients. However, little is known regarding relapsed/refractory DLBCL (rrDLBCL) genetics and alternative therapies. Based on findings from other tumors, we hypothesized that RAS-MEK-ERK signaling would be upregulated in resistant tumors, potentially correlating with mutations in RAS, RAF, or associated proteins. We analyzed mutations and phospho-ERK levels in tumor samples from rrDLBCL patients. Unlike other tumor types, rrDLBCL is not mutated in any Ras or Raf family members, despite having increased expression of p-ERK. In paired biopsies comparing diagnostic and relapsed specimens, 33% of tumors gained p-ERK expression, suggesting a role in promoting survival. We did find mutations in several Ras-associating proteins, including GEFs, GAPs, and downstream effectors that could account for increased ERK activation. We further investigated mutations in one such protein, RASGRP4. In silico modeling indicated an increased interaction between H-Ras and mutant RASGRP4. In cell lines, mutant RASGRP4 increased basal p-ERK expression and lead to a growth advantage in colony forming assays when challenged with doxorubicin. Relapsed/refractory DLBCL is often associated with increased survival signals downstream of ERK, potentially corresponding with mutations in protein controlling RAS/MEK/ERK signaling.
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Affiliation(s)
- Alexandre Benoit
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Elisabeth Bou-Petit
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Barcelona, Spain
| | - Hsiang Chou
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Melissa Lu
- Université de Montréal-Faculté de Médecine, Montreal, Canada
| | - Cynthia Guilbert
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Vincent Mingyi Luo
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Sarit Assouline
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Svetlana Dmitrienko
- Division of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Roger Estrada-Tejedor
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Barcelona, Spain
| | - Nathalie A Johnson
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Koren K Mann
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada. .,Division of Experimental Medicine, McGill University, Montreal, QC, Canada. .,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
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Immunomodulation by epigenome alterations in Mycobacterium tuberculosis infection. Tuberculosis (Edinb) 2021; 128:102077. [PMID: 33812175 DOI: 10.1016/j.tube.2021.102077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/07/2021] [Indexed: 12/14/2022]
Abstract
Mycobacterium tuberculosis (MTB) has co-evolved with humans for decades and developed several mechanisms to evade host immunity. It can efficiently alter the host epigenome, thus playing a major role in immunomodulation by either activating or suppressing genes responsible for mounting an immune response against the pathogen. Epigenetic modifications such as DNA methylation and chromatin remodelling regulate gene expression and influence several cellular processes. The involvement of epigenetic factors in disease onset and development had been overlooked upon in comparison to genetic mutations. It is now believed that assessment of epigenetic changes hold great potential in diagnosis, prevention and treatment strategies for a wide range of diseases. In this review, we unravel the principles of epigenetics and the numerous ways by which MTB re-shapes the host epigenetic landscape as a strategy to overpower the host immune system for its survival and persistence.
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Chen YC, Hsiao CC, Chen TW, Wu CC, Chao TY, Leung SY, Eng HL, Lee CP, Wang TY, Lin MC. Whole Genome DNA Methylation Analysis of Active Pulmonary Tuberculosis Disease Identifies Novel Epigenotypes: PARP9/ miR-505/ RASGRP4/ GNG12 Gene Methylation and Clinical Phenotypes. Int J Mol Sci 2020; 21:ijms21093180. [PMID: 32365959 PMCID: PMC7246806 DOI: 10.3390/ijms21093180] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
We hypothesized that DNA methylation patterns may contribute to the development of active pulmonary tuberculosis (TB). Illumina’s DNA methylation 450 K assay was used to identify differentially methylated loci (DML) in a discovery cohort of 12 active pulmonary TB patients and 6 healthy subjects (HS). DNA methylation levels were validated in an independent cohort of 64 TB patients and 24 HS. Microarray analysis identified 1028 DMLs in TB patients versus HS, and 3747 DMLs in TB patients after versus before anti-TB treatment, while autophagy was the most enriched signaling pathway. In the validation cohort, PARP9 and miR505 genes were hypomethylated in the TB patients versus HS, while RASGRP4 and GNG12 genes were hypermethylated, with the former two further hypomethylated in those with delayed sputum conversion, systemic symptoms, or far advanced lesions. MRPS18B and RPTOR genes were hypomethylated in TB patients with pleural involvement. RASGRP4 gene hypermethylation and RPTOR gene down-regulation were associated with high mycobacterial burden. TB patients with WIPI2/GNG12 hypermethylation or MRPS18B/FOXO3 hypomethylation had lower one-year survival. In vitro ESAT6 and CFP10 stimuli of THP-1 cells resulted in DNA de-methylation changes of the PARP9, RASGRP4, WIPI2, and FOXO3 genes. In conclusions, aberrant DNA methylation over the PARP9/miR505/RASGRP4/GNG12 genes may contribute to the development of active pulmonary TB disease and its clinical phenotypes, while aberrant DNA methylation over the WIPI2/GNG12/MARPS18B/FOXO3 genes may constitute a determinant of long-term outcomes.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
- Graduate Institute of Clinical Medical Sciences and Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Correspondence: (Y.-C.C.); (M.-C.L.); Tel.: +886-975056041 (Y.-C.C.); +886-7-731-7123 (ext 8199) (M.-C.L.)
| | - Chang-Chun Hsiao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
- Graduate Institute of Clinical Medical Sciences and Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, and Bioinformatics Center, Chang Gung University, Taoyuan 33302, Taiwan;
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chao-Chien Wu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Tung-Ying Chao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Sum-Yee Leung
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Hock-Liew Eng
- Division of Clinical Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan;
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Ting-Ya Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
- Correspondence: (Y.-C.C.); (M.-C.L.); Tel.: +886-975056041 (Y.-C.C.); +886-7-731-7123 (ext 8199) (M.-C.L.)
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