1
|
Sun SY, Lee DH, Liu HC, Yang Y, Han YH, Kwon T. Identifying competing endogenous RNA regulatory networks and hub genes in alcoholic liver disease for early diagnosis and potential therapeutic target insights. Aging (Albany NY) 2024; 16:9147-9167. [PMID: 38795390 PMCID: PMC11164510 DOI: 10.18632/aging.205861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/22/2024] [Indexed: 05/27/2024]
Abstract
Alcoholic liver disease (ALD) has a complex pathogenesis. Although early-stage ALD can be reversed by ceasing alcohol consumption, early symptoms are difficult to detect, and several factors contribute to making alcohol difficult to quit. Continued alcohol abuse worsens the condition, meaning it may gradually progress into alcoholic hepatitis and cirrhosis, ultimately, resulting in irreversible consequences. Therefore, effective treatments are urgently needed for early-stage ALD. Current research mainly focuses on preventing the progression of alcoholic fatty liver to alcoholic hepatitis and cirrhosis. However, challenges remain in identifying key therapeutic targets and understanding the molecular mechanisms that underlie the treatment of alcoholic hepatitis and cirrhosis, such as the limited discovery of effective therapeutic targets and treatments. Here, we downloaded ALD microarray data from Gene Expression Omnibus and used bioinformatics to compare and identify the hub genes involved in the progression of alcoholic fatty liver to alcoholic hepatitis and cirrhosis. We also predicted target miRNAs and long non-coding RNAs (lncRNAs) to elucidate the regulatory mechanisms (the mRNA-miRNA-lncRNA axis) underlying this progression, thereby building a competitive endogenous RNA (ceRNA) mechanism for lncRNA, miRNA, and mRNA. This study provides a theoretical basis for the early treatment of alcoholic hepatitis and cirrhosis and identifies potential therapeutic targets.
Collapse
Affiliation(s)
- Shuai-Yang Sun
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Dong Hun Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hao-Cheng Liu
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yi Yang
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Ying-Hao Han
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Taeho Kwon
- Primate Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeonbuk 56216, Republic of Korea
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, Korea National University of Science and Technology, Daejeon 34113, Republic of Korea
| |
Collapse
|
2
|
Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
Collapse
Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
| |
Collapse
|
3
|
Zhang D, Jia N, Hu Z, Keqing Z, Chenxi S, Chunying S, Chen C, Chen W, Hu Y, Ruan Z. Bioinformatics identification of potential biomarkers and therapeutic targets for ischemic stroke and vascular dementia. Exp Gerontol 2024; 187:112374. [PMID: 38320734 DOI: 10.1016/j.exger.2024.112374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Ischemic stroke and vascular dementia, as common cerebrovascular diseases, with the former causing irreversible neurological damage and the latter causing cognitive and memory impairment, are closely related and have long received widespread attention. Currently, the potential causative genes of these two diseases have yet to be investigated, and effective early diagnostic tools for the diseases have not yet emerged. In this study, we screened new potential biomarkers and analyzed new therapeutic targets for both diseases from the perspective of immune infiltration. Two gene expression profiles on ischemic stroke and vascular dementia were obtained from the NCBI GEO database, and key genes were identified by LASSO regression and SVM-RFE algorithms, and key genes were analyzed by GO and KEGG enrichment. The CIBERSORT algorithm was applied to the gene expression profile species of the two diseases to quantify the 24 subpopulations of immune cells. Moreover, logistic regression modeling analysis was applied to illustrate the stability of the key genes in the diagnosis. Finally, the key genes were validated using RT-PCR assay. A total of 105 intersecting DEGs genes were obtained in the 2 sets of GEO datasets, and bioinformatics functional analysis of the intersecting DEGs genes showed that GO was mainly involved in the purine ribonucleoside triphosphate metabolic process,respiratory chain complex,DNA-binding transcription factor binding and active transmembrane transporter activity. KEGG is mainly involved in the Oxidative phosphorylation, cAMP signaling pathway. The LASSO regression algorithm and SVM-RFE algorithm finally obtained three genes, GAS2L1, ARHGEF40 and PFKFB3, and the logistic regression prediction model determined that the three genes, GAS2L1 (AUC: 0.882), ARHGEF40 (AUC: 0.867) and PFKFB3 (AUC: 0.869), had good diagnostic performance. Meanwhile, the two disease core genes and immune infiltration were closely related, GAS2L1 and PFKFB3 had the highest positive correlation with macrophage M1 (p < 0.001) and the highest negative correlation with mast cell activation (p = 0.0017); ARHGEF40 had the highest positive correlation with macrophage M1 and B cells naive (p < 0.001), the highest negative correlation with B cell memory highest correlation (p = 0.0047). RT-PCR results showed that the relative mRNA expression levels of GAS2L1, ARHGEF40, and PFKFB3 were significantly elevated in the populations of both disease groups (p < 0.05). Immune infiltration-based models can be used to predict the diagnosis of patients with ischemic stroke and vascular dementia and provide a new perspective on the early diagnosis and treatment of both diseases.
Collapse
Affiliation(s)
- Ding Zhang
- Guangxi university of chinese medicine Nanning, China
| | - Ni Jia
- Shaanxi University of Traditional Chinese Medicine Xianyang, China
| | - Zhihan Hu
- Shanghai University of Traditional Chinese Medicine Shanghai, China
| | - Zhou Keqing
- Guangxi university of chinese medicine Nanning, China
| | - Song Chenxi
- Guangxi university of chinese medicine Nanning, China
| | - Sun Chunying
- Guangxi university of chinese medicine Nanning, China
| | - Canrong Chen
- Guangxi university of chinese medicine Nanning, China
| | - Wei Chen
- Guangxi university of chinese medicine First Affiliated Hospital Nanning, China
| | - Yueqiang Hu
- Guangxi university of chinese medicine First Affiliated Hospital Nanning, China.
| | - Ziyun Ruan
- Guangxi university of chinese medicine Nanning, China
| |
Collapse
|
4
|
Chen X, Deng R, Su D, Ma X, Han X, Wang S, Xia Y, Yang Z, Gong N, Jia Y, Gao X, Ren X. Visual genetic typing of glioma using proximity-anchored in situ spectral coding amplification. EXPLORATION (BEIJING, CHINA) 2023; 3:20220175. [PMID: 37933281 PMCID: PMC10582607 DOI: 10.1002/exp.20220175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/21/2023] [Indexed: 11/08/2023]
Abstract
Gliomas are histologically and genetically heterogeneous tumors. However, classical histopathological typing often ignores the high heterogeneity of tumors and thus cannot meet the requirements of precise pathological diagnosis. Here, proximity-anchored in situ spectral coding amplification (ProxISCA) is proposed for multiplexed imaging of RNA mutations, enabling visual typing of brain gliomas with different pathological grades at the single-cell and tissue levels. The ligation-based padlock probe can discriminate one-nucleotide variations, and the design of proximity primers enables the anchoring of amplicons on target RNA, thus improving localization accuracy. The DNA module-based spectral coding strategy can dramatically improve the multiplexing capacity for imaging RNA mutations through one-time labelling, with low cost and simple operation. One-target-one-amplicon amplification confers ProxISCA the ability to quantify RNA mutation copy number with single-molecule resolution. Based on this approach, it is found that gliomas with higher malignant grades express more genes with high correlation at the cellular and tissue levels and show greater cellular heterogeneity. ProxISCA provides a tool for glioma research and precise diagnosis, which can reveal the relationship between cellular heterogeneity and glioma occurrence or development and assist in pathological prognosis.
Collapse
Affiliation(s)
- Xiaolei Chen
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Ruijie Deng
- College of Biomass Science and EngineeringHealthy Food Evaluation Research CenterSichuan UniversityChengduChina
| | - Dongdong Su
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Xiaochen Ma
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Xu Han
- Institute of High Energy PhysicsChinese Academy of SciencesBeijingChina
| | - Shizheng Wang
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Yuqing Xia
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Zifu Yang
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Ningqiang Gong
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaUSA
| | - Yanwei Jia
- State‐Key Laboratory of Analog and Mixed‐Signal VLSIInstitute of MicroelectronicsUniversity of MacauMacauChina
| | - Xueyun Gao
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Xiaojun Ren
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| |
Collapse
|
5
|
Zhang C, Chen Z, Zhang M, Jia S. KEGG_Extractor: An Effective Extraction Tool for KEGG Orthologs. Genes (Basel) 2023; 14:genes14020386. [PMID: 36833314 PMCID: PMC9956942 DOI: 10.3390/genes14020386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
The KEGG Orthology (KO) database is a widely used molecular function reference database which can be used to conduct functional annotation of most microorganisms. At present, there are many KEGG tools based on the KO entries for annotating functional orthologs. However, determining how to efficiently extract and sort the annotation results of KEGG still hinders the subsequent genome analysis. There is a lack of effective measures used to quickly extract and classify the gene sequences and species information of the KEGG annotations. Here, we present a supporting tool: KEGG_Extractor for species-specific genes extraction and classification, which can output the results through an iterative keyword matching algorithm. It can not only extract and classify the amino acid sequences, but also the nucleotide sequences, and it has proved to be fast and efficient for microbial analysis. Analysis of the ancient Wood Ljungdahl (WL) pathway through the KEGG_Extractor reveals that ~226 archaeal strains contained the WL pathway-related genes. Most of them were Methanococcus maripaludis, Methanosarcina mazei and members of the Methanobacterium, Thermococcus and Methanosarcina genus. Using the KEGG_Extractor, the ARWL database was constructed, which had a high accuracy and complement. This tool helps to link genes with the KEGG pathway and promote the reconstruction of molecular networks. Availability and implementation: KEGG_Extractor is freely available from the GitHub.
Collapse
Affiliation(s)
- Chao Zhang
- Marine Sustainable Development Research Center, Third Institute of Oceanography, Xiamen 361102, China
| | - Zhongwei Chen
- Nantong Marine Environmental Monitoring Center, Ministry of Natural Resources, Nantong 226002, China
| | - Miming Zhang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shulei Jia
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence:
| |
Collapse
|
6
|
Huang R, Tang J, Wang S, Liu Y, Zhang M, Jin M, Qin H, Qian W, Lu Y, Yang Y, Lu B, Yao Y, Yan P, Huang J, Zhang W, Lu J, Gu M, Zhu Y, Guo X, Xian S, Liu X, Huang Z. Sequencing technology as a major impetus in the advancement of studies into rheumatism: A bibliometric study. Front Immunol 2023; 14:1067830. [PMID: 36875117 PMCID: PMC9982012 DOI: 10.3389/fimmu.2023.1067830] [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: 10/12/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023] Open
Abstract
Background Rheumatism covers a wide range of diseases with complex clinical manifestations and places a tremendous burden on humans. For many years, our understanding of rheumatism was seriously hindered by technology constraints. However, the increasing application and rapid advancement of sequencing technology in the past decades have enabled us to study rheumatism with greater accuracy and in more depth. Sequencing technology has made huge contributions to the field and is now an indispensable component and powerful tool in the study of rheumatism. Methods Articles on sequencing and rheumatism, published from 1 January 2000 to 25 April 2022, were retrieved from the Web of Science™ (Clarivate™, Philadelphia, PA, USA) database. Bibliometrix, the open-source tool, was used for the analysis of publication years, countries, authors, sources, citations, keywords, and co-words. Results The 1,374 articles retrieved came from 62 countries and 350 institutions, with a general increase in article numbers during the last 22 years. The leading countries in terms of publication numbers and active cooperation with other countries were the USA and China. The most prolific authors and most popular documents were identified to establish the historiography of the field. Popular and emerging research topics were assessed by keywords and co-occurrence analysis. Immunological and pathological process in rheumatism, classification, risks and susceptibility, and biomarkers for diagnosis were among the hottest themes for research. Conclusions Sequencing technology has been widely applied in the study of rheumatism and propells research in the area of discovering novel biomarkers, related gene patterns and physiopathology. We suggest that further efforts be made to advance the study of genetic patterns related to rheumatic susceptibility, pathogenesis, classification and disease activity, and novel biomarkers.
Collapse
Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jieling Tang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Yifan Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengyi Zhang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minghao Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hengwei Qin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weijin Qian
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuwei Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiting Yang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingnan Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuntao Yao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Huang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Wei Zhang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jianyu Lu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Minyi Gu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yushu Zhu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xinya Guo
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Shuyuan Xian
- Department of Orthopedics, Shibei Hospital, Shanghai, China
| | - Xin Liu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
7
|
Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
Collapse
Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
| |
Collapse
|