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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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Meshref M, Ghaith HS, Hammad MA, Shalaby MMM, Ayasra F, Monib FA, Attia MS, Ebada MA, Elsayed H, Shalash A, Bahbah EI. The Role of RIN3 Gene in Alzheimer's Disease Pathogenesis: a Comprehensive Review. Mol Neurobiol 2024; 61:3528-3544. [PMID: 37995081 PMCID: PMC11087354 DOI: 10.1007/s12035-023-03802-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
Alzheimer's disease (AD) is a globally prevalent form of dementia that impacts diverse populations and is characterized by progressive neurodegeneration and impairments in executive memory. Although the exact mechanisms underlying AD pathogenesis remain unclear, it is commonly accepted that the aggregation of misfolded proteins, such as amyloid plaques and neurofibrillary tau tangles, plays a critical role. Additionally, AD is a multifactorial condition influenced by various genetic factors and can manifest as either early-onset AD (EOAD) or late-onset AD (LOAD), each associated with specific gene variants. One gene of particular interest in both EOAD and LOAD is RIN3, a guanine nucleotide exchange factor. This gene plays a multifaceted role in AD pathogenesis. Firstly, upregulation of RIN3 can result in endosomal enlargement and dysfunction, thereby facilitating the accumulation of beta-amyloid (Aβ) peptides in the brain. Secondly, RIN3 has been shown to impact the PICLAM pathway, affecting transcytosis across the blood-brain barrier. Lastly, RIN3 has implications for immune-mediated responses, notably through its influence on the PTK2B gene. This review aims to provide a concise overview of AD and delve into the role of the RIN3 gene in its pathogenesis.
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Affiliation(s)
- Mostafa Meshref
- Department of Neurology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | | | | | | | - Faris Ayasra
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | | | - Mohamed S Attia
- Department of Pharmaceutics, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | | | - Hanaa Elsayed
- Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ali Shalash
- Department of Neurology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Eshak I Bahbah
- Faculty of Medicine, Al-Azhar University, Damietta, Egypt.
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He D, Yu Q, Zeng X, Feng J, Yang R, Wan H, Zhong Y, Yang Y, Zhao R, Lu J, Zhang J. Single-Cell RNA Sequencing and Transcriptome Analysis Revealed the Immune Microenvironment and Gene Markers of Acute Respiratory Distress Syndrome. J Inflamm Res 2023; 16:3205-3217. [PMID: 37547124 PMCID: PMC10404049 DOI: 10.2147/jir.s419576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023] Open
Abstract
Background Acute respiratory distress syndrome (ARDS) is caused by severe pulmonary inflammation and the leading cause of death in the intensive care unit. Methods We used single-cell RNA sequencing to compare peripheral blood mononuclear cells from sepsis-induced ARDS (SEP-ARDS) and pneumonic ARDS (PNE-ARDS) patient. Then, we used the GSE152978 and GSE152979 datasets to identify molecular dysregulation mechanisms at the transcriptional level in ARDS. Results Markedly increased CD14 cells were the predominant immune cell type observed in SEP-ARDS and PNE-ARDS patients. Cytotoxic cells and natural killer (NK) T cells were exclusively identified in patients with PNE-ARDS. An enrichment analysis of differentially expressed genes (DEGs) suggested that Th1 cell differentiation and Th2 cell differentiation were enriched in cytotoxic cells, and that the IL-17 signaling pathway, NOD receptor signaling pathway, and complement and coagulation cascades were enriched in CD14 cells. Furthermore, according to GSE152978 and GSE152979, 1939 DEGs were identified in patients with ARDS and controls; they were mainly enriched in the Kyoto Encyclopedia of Genes and Genomes pathways. RBP7 had the highest area under the curve values among the 12 hub genes and was mainly expressed in CD14 cells. Additionally, hub genes were negatively correlated with NK cells and positively correlated with neutrophils, cytotoxic cells, B cells, and macrophages. Conclusion A severe imbalance in the proportion of immune cells and immune dysfunction were observed in SEP-ARDS and PNE-ARDS patients. RBP7 may be immunologically associated with CD14 cells and serve as a potential marker of ARDS.
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Affiliation(s)
- Dan He
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Qiao Yu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Xiaona Zeng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Ruiqi Yang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Huan Wan
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Ying Zhong
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Yanli Yang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Ruzhi Zhao
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
| | - Junyu Lu
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
- Guangxi Health Commission Key Laboratory of Emergency and Critical Medicine, Nanning, 530007, People’s Republic of China
| | - Jianfeng Zhang
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People’s Republic of China
- Guangxi Health Commission Key Laboratory of Emergency and Critical Medicine, Nanning, 530007, People’s Republic of China
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Suarez-Pajes E, Tosco-Herrera E, Ramirez-Falcon M, Gonzalez-Barbuzano S, Hernandez-Beeftink T, Guillen-Guio B, Villar J, Flores C. Genetic Determinants of the Acute Respiratory Distress Syndrome. J Clin Med 2023; 12:3713. [PMID: 37297908 PMCID: PMC10253474 DOI: 10.3390/jcm12113713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung condition that arises from multiple causes, including sepsis, pneumonia, trauma, and severe coronavirus disease 2019 (COVID-19). Given the heterogeneity of causes and the lack of specific therapeutic options, it is crucial to understand the genetic and molecular mechanisms that underlie this condition. The identification of genetic risks and pharmacogenetic loci, which are involved in determining drug responses, could help enhance early patient diagnosis, assist in risk stratification of patients, and reveal novel targets for pharmacological interventions, including possibilities for drug repositioning. Here, we highlight the basis and importance of the most common genetic approaches to understanding the pathogenesis of ARDS and its critical triggers. We summarize the findings of screening common genetic variation via genome-wide association studies and analyses based on other approaches, such as polygenic risk scores, multi-trait analyses, or Mendelian randomization studies. We also provide an overview of results from rare genetic variation studies using Next-Generation Sequencing techniques and their links with inborn errors of immunity. Lastly, we discuss the genetic overlap between severe COVID-19 and ARDS by other causes.
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Eva Tosco-Herrera
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Melody Ramirez-Falcon
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Silvia Gonzalez-Barbuzano
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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Mo J, Yang Y, Feng J, Lei Y, Huang S, Cen W, Wei S, Huang H, Lu J, Zhang J. Single-cell analysis reveals dysregulated inflammatory response in peripheral blood immunity in patients with acute respiratory distress syndrome. Front Cell Dev Biol 2023; 11:1199122. [PMID: 37283946 PMCID: PMC10239863 DOI: 10.3389/fcell.2023.1199122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction: Acute respiratory distress syndrome (ARDS) remains a major clinical challenge for patients in intensive care units. Determining the differential mechanisms underlying ARDS with different etiologies is a key goal to improve the effectiveness of ARDS therapy. Despite growing evidence that different immune cell types are involved in ARDS, the role of altered immune cell subpopulations in disease progression is unelucidated. Methods: In this study, we combined scRNA-seq and bulk-level sequencing to analyze the transcriptomes of peripheral blood mononuclear cells from healthy volunteers and patients with septic ARDS (sep-ARDS) and pneumonic ARDS (PNE-ARDS). Results: Our data revealed differential alterations at the cellular and molecular levels and within biological signaling pathways in ARDS with different etiologies. The dynamics of neutrophils, macrophages (Macs), classical dendritic cells (cDCs), myeloid-derived suppressive cells (MDSCs), and CD8+ T cells varied significantly among groups of different samples, with neutrophils and cDCs at higher, and Macs at significantly lower, amounts in the patients with sep-ARDS. Furthermore, MDSCs were highly enriched only in the sep-ARDS patients, whereas a higher abundance of CD8+ T cells was observed in patients with PNE-ARDS. In addition, these cell subpopulations were found to be significantly involved in apoptosis, inflammatory, and immune-related pathways. In particular, a significant enhancement of the oxidative stress response was observed in the neutrophil subpopulation. Conclusion: Our study shows that the composition of cells involved in the main peripheral circulation differs in patients with ARDS with different etiologies. Studying the role and mechanism of action of these cells during ARDS will provide new opportunities for the treatment of this condition.
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Affiliation(s)
- Jingjia Mo
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yanli Yang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yanhua Lei
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Suhong Huang
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weiluan Cen
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shanshan Wei
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hao Huang
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Junyu Lu
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jianfeng Zhang
- Department of General Practice, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
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Ramji HF, Hafiz M, Altaq HH, Hussain ST, Chaudry F. Acute Respiratory Distress Syndrome; A Review of Recent Updates and a Glance into the Future. Diagnostics (Basel) 2023; 13:diagnostics13091528. [PMID: 37174920 PMCID: PMC10177247 DOI: 10.3390/diagnostics13091528] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/15/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a rapidly progressive form of respiratory failure that accounts for 10% of admissions to the ICU and is associated with approximately 40% mortality in severe cases. Despite significant mortality and healthcare burden, the mainstay of management remains supportive care. The recent pandemic of SARS-CoV-2 has re-ignited a worldwide interest in exploring the pathophysiology of ARDS, looking for innovative ideas to treat this disease. Recently, many trials have been published utilizing different pharmacotherapy targets; however, the long-term benefits of these agents remain unknown. Metabolomics profiling and stem cell transplantation offer strong enthusiasm and may completely change the outlook of ARDS management in the near future.
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Affiliation(s)
- Husayn F Ramji
- University of Oklahoma College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Maida Hafiz
- Department of Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Hiba Hammad Altaq
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Syed Talal Hussain
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Fawad Chaudry
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Vanhorebeek I, Van den Berghe G. The epigenetic legacy of ICU feeding and its consequences. Curr Opin Crit Care 2023; 29:114-122. [PMID: 36794929 PMCID: PMC9994844 DOI: 10.1097/mcc.0000000000001021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
PURPOSE OF REVIEW Many critically ill patients face physical, mental or neurocognitive impairments up to years later, the etiology remaining largely unexplained. Aberrant epigenetic changes have been linked to abnormal development and diseases resulting from adverse environmental exposures like major stress or inadequate nutrition. Theoretically, severe stress and artificial nutritional management of critical illness thus could induce epigenetic changes explaining long-term problems. We review supporting evidence. RECENT FINDINGS Epigenetic abnormalities are found in various critical illness types, affecting DNA-methylation, histone-modification and noncoding RNAs. They at least partly arise de novo after ICU-admission. Many affect genes with functions relevant for and several associate with long-term impairments. As such, de novo DNA-methylation changes in critically ill children statistically explained part of their disturbed long-term physical/neurocognitive development. These methylation changes were in part evoked by early-parenteral-nutrition (early-PN) and statistically explained harm by early-PN on long-term neurocognitive development. Finally, long-term epigenetic abnormalities beyond hospital-discharge have been identified, affecting pathways highly relevant for long-term outcomes. SUMMARY Epigenetic abnormalities induced by critical illness or its nutritional management provide a plausible molecular basis for their adverse effects on long-term outcomes. Identifying treatments to further attenuate these abnormalities opens perspectives to reduce the debilitating legacy of critical illness.
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Affiliation(s)
- Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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Li C, Wang W, Xie SS, Ma WX, Fan QW, Chen Y, He Y, Wang JN, Yang Q, Li HD, Jin J, Liu MM, Meng XM, Wen JG. The Programmed Cell Death of Macrophages, Endothelial Cells, and Tubular Epithelial Cells in Sepsis-AKI. Front Med (Lausanne) 2021; 8:796724. [PMID: 34926535 PMCID: PMC8674574 DOI: 10.3389/fmed.2021.796724] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
Sepsis is a systemic inflammatory response syndrome caused by infection, following with acute injury to multiple organs. Sepsis-induced acute kidney injury (AKI) is currently recognized as one of the most severe complications related to sepsis. The pathophysiology of sepsis-AKI involves multiple cell types, including macrophages, vascular endothelial cells (ECs) and renal tubular epithelial cells (TECs), etc. More significantly, programmed cell death including apoptosis, necroptosis and pyroptosis could be triggered by sepsis in these types of cells, which enhances AKI progress. Moreover, the cross-talk and connections between these cells and cell death are critical for better understanding the pathophysiological basis of sepsis-AKI. Mitochondria dysfunction and oxidative stress are traditionally considered as the leading triggers of programmed cell death. Recent findings also highlight that autophagy, mitochondria quality control and epigenetic modification, which interact with programmed cell death, participate in the damage process in sepsis-AKI. The insightful understanding of the programmed cell death in sepsis-AKI could facilitate the development of effective treatment, as well as preventive methods.
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Affiliation(s)
- Chao Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Wei Wang
- Anhui Province Key Laboratory of Genitourinary Diseases, Department of Urology and Institute of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Shuai-Shuai Xie
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Wen-Xian Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Qian-Wen Fan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Ying Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Yuan He
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jia-Nan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Qin Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Hai-di Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Juan Jin
- Key Laboratory of Anti-inflammatory and Immunopharmacology (Ministry of Education), Department of Pharmacology, Anhui Medical University, Hefei, China
| | - Ming-Ming Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-Inflammatory of Immune Medicines (Ministry of Education), Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
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Zhao C, Mo J, Zheng X, Wu Z, Li Q, Feng J, Luo J, Lu J, Zhang J. Identification of an Alveolar Macrophage-Related Core Gene Set in Acute Respiratory Distress Syndrome. J Inflamm Res 2021; 14:2353-2361. [PMID: 34103966 PMCID: PMC8179830 DOI: 10.2147/jir.s306136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose Acute respiratory distress syndrome (ARDS) is a rapidly progressive diffuse lung injury that is characterized by high mortality and acute onset. The pathological mechanisms of ARDS are still unclear. But alveolar macrophages have been shown to play an important role in inflammatory responses during ARDS. We aimed to find the biomarkers for ARDS for early diagnosis, to give ARDS patients timely treatment. Methods Gene expression profiles were downloaded from Gene Expression Omnibus (GEO) and screened for differentially expressed genes (DEGs). The common upregulated genes in all the datasets were defined as circulating ARDS alveolar macrophage-related genes (cARDSAMGs). We performed a functional enrichment analysis to explore potential biological functions of cARDSAMGs, and we built protein–protein interaction networks. Gene set variation analysis (GSVA) was used to calculate the core gene set variation analysis (CGSVA) score for individual samples. Receiver operating characteristic (ROC) curve analysis was applied on the CGSVA score to evaluate its ability for diagnosis of ARDS. Results A total of 60 genes were upregulated in all ARDS datasets and were therefore denominated as cARDSAMGs. The cARDSAMGs were significantly involved in multiple inflammation-, immunity- and phagocytosis-related biological processes and pathways. In the protein–protein interaction network associated with host responses to ADRS, eight genes were identified as a core gene set: PTCRA, JAG1, C1QB, ADAM17, C1QA, MMP9, VSIG4 and TNFAIP3. ROC curve analysis showed that the CGSVA score may be considered as a biomarker for ARDS: it was significantly higher in patients with ARDS than those in healthy in both alveolar lavage fluid and whole blood. Conclusion The ARDS alveolar macrophage-related CGSVA score may be useful as a biomarker for ARDS.
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Affiliation(s)
- Chunling Zhao
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jingjia Mo
- Department of General Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Xiaowen Zheng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Zimeng Wu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Qian Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jiefeng Luo
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Junyu Lu
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jianfeng Zhang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
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10
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Zeng X, Feng J, Yang Y, Zhao R, Yu Q, Qin H, Wei L, Ji P, Li H, Wu Z, Zhang J. Screening of Key Genes of Sepsis and Septic Shock Using Bioinformatics Analysis. J Inflamm Res 2021; 14:829-841. [PMID: 33737824 PMCID: PMC7962593 DOI: 10.2147/jir.s301663] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
Objective Sepsis is a disease associated with high mortality. We performed bioinformatic analysis to identify key biomarkers associated with sepsis and septic shock. Methods The top 20% of genes showing the greatest variance between sepsis and controls in the GSE13904 dataset (children) were screened by co-expression network analysis. The differentially expressed genes (DEGs) were identified through analyzing differential gene expression between sepsis patients and control in the GSE13904 (children) and GSE154918 (adult) data sets. Intersection analysis of module genes and DEGs was performed to identify common DEGs for enrichment analysis, protein-protein interaction network (PPI network) analysis, and Short Time-series Expression Miner (STEM) analysis. The PPI network genes were ranked by degree of connectivity, and the top 100 sepsis-associated genes were identified based on the area under the receiver operating characteristic curve (AUC). In addition, we evaluated differences in immune cell infiltration between sepsis patients and controls in children (GSE13904, GSE25504) and adults (GSE9960, GSE154918). Finally, we analyzed differences in DNA methylation levels between sepsis patients and controls in GSE138074 (adults). Results The common genes were associated mainly with up-regulated inflammatory and metabolic responses, as well as down-regulated immune responses. Sepsis patients showed lower infiltration by most types of immune cells. Genes in the PPI network with AUC values greater than 0.9 in both GSE13904 (children) and GSE154918 (adults) were screened as key genes for diagnosis. These key genes (MAPK14, FGR, RHOG, LAT, PRKACB, UBE2Q2, ITK, IL2RB, and CD247) were also identified in STEM analysis to be progressively dysregulated across controls, sepsis patients and patients with septic shock. In addition, the expression of MAPK14, FGR, and CD247 was modified by methylation. Conclusion This study identified several potential diagnostic genes and inflammatory and metabolic responses mechanisms associated with the development of sepsis.
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Affiliation(s)
- Xiaoliang Zeng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Yanli Yang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Ruzhi Zhao
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Qiao Yu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Han Qin
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Lile Wei
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Pan Ji
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Hongyuan Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Zimeng Wu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jianfeng Zhang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
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