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De La Torre-Tarazona E, Ayala-Suárez R, Díez-Fuertes F, Alcamí J. Omic Technologies in HIV: Searching Transcriptional Signatures Involved in Long-Term Non-Progressor and HIV Controller Phenotypes. Front Immunol 2022; 13:926499. [PMID: 35844607 PMCID: PMC9284212 DOI: 10.3389/fimmu.2022.926499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
This article reviews the main discoveries achieved by transcriptomic approaches on HIV controller (HIC) and long-term non-progressor (LTNP) individuals, who are able to suppress HIV replication and maintain high CD4+ T cell levels, respectively, in the absence of antiretroviral therapy. Different studies using high throughput techniques have elucidated multifactorial causes implied in natural control of HIV infection. Genes related to IFN response, calcium metabolism, ribosome biogenesis, among others, are commonly differentially expressed in LTNP/HIC individuals. Additionally, pathways related with activation, survival, proliferation, apoptosis and inflammation, can be deregulated in these individuals. Likewise, recent transcriptomic studies include high-throughput sequencing in specific immune cell subpopulations, finding additional gene expression patterns associated to viral control and/or non-progression in immune cell subsets. Herein, we provide an overview of the main differentially expressed genes and biological routes commonly observed on immune cells involved in HIV infection from HIC and LTNP individuals, analyzing also different technical aspects that could affect the data analysis and the future perspectives and gaps to be addressed in this field.
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Affiliation(s)
- Erick De La Torre-Tarazona
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rubén Ayala-Suárez
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Francisco Díez-Fuertes
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Francisco Díez-Fuertes,
| | - José Alcamí
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Human Immunodeficiency Virus (HIV) Unit, Hospital Clínic de Barcelona, Barcelona, Spain
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Ma L, Zhang H, Zhang Y, Li H, An M, Zhao B, Ding H, Xu J, Shang H, Han X. Integrated analysis of lncRNA, miRNA and mRNA profiles reveals potential lncRNA functions during early HIV infection. J Transl Med 2021; 19:135. [PMID: 33794921 PMCID: PMC8015739 DOI: 10.1186/s12967-021-02802-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) can regulate gene expression in a cis-regulatory fashion or as “microRNA sponges”. However, the expression and functions of lncRNAs during early human immunodeficiency virus (HIV) infection (EHI) remain unclear. Methods 3 HAART-naive EHI patients and 3 healthy controls (HCs) were recruited in this study to perform RNA sequencing and microRNA (miRNA) sequencing. The expression profiles of lncRNAs, mRNAs and miRNAs were obtained, and the potential roles of lncRNAs were analysed based on discovering lncRNA cis-regulatory target mRNAs and constructing lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) networks. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on 175 lncRNA-associated differentially expressed (DE) mRNAs to investigate the potential functions of DE lncRNAs in ceRNA networks. Results A total of 242 lncRNAs, 1240 mRNAs and 21 mature known miRNAs were determined as differentially expressed genes in HAART-naive EHI patients compared to HCs. Among DE lncRNAs, 44 lncRNAs were predicted to overlap with 41 target mRNAs, and 107 lncRNAs might regulate their nearby DE mRNAs. Two DE lncRNAs might regulate their cis-regulatory target mRNAs BTLA and ZAP70, respectively, which were associated with immune activation. In addition, the ceRNA networks comprised 160 DE lncRNAs, 21 DE miRNAs and 175 DE mRNAs. Seventeen DE lncRNAs were predicted to regulate HIF1A and TCF7L2, which are involved in the process of HIV-1 replication. Twenty DE lncRNAs might share miRNA response elements (MREs) with FOS, FOSB and JUN, which are associated with both immune activation and HIV-1 replication. Conclusions This study revealed that lncRNAs might play a critical role in HIV-1 replication and immune activation during EHI. These novel findings are helpful for understanding of the pathogenesis of HIV infection and provide new insights into antiviral therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02802-9.
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Affiliation(s)
- Lianwei Ma
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Hui Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Yue Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Hailong Li
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Junjie Xu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China. .,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China. .,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China. .,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China. .,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
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