Identification of Potential Diagnostic Genes of HIV-Infected Immunological Non-Responders on Bioinformatics Analysis

References

• Takuva S, Maskew M, Brennan AT, Long L, Sanne I, Fox MP. Poor CD4 recovery and risk of subsequent progression to AIDS or death despite viral suppression in a South African cohort. J Int AIDS Soc. 2014;17(1):18651. doi:10.7448/IAS.17.1.18651
   PubMedGoogle Scholar
• Saag MS, Gandhi RT, Hoy JF, et al. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2020 Recommendations of the International Antiviral Society-USA Panel. JAMA. 2020;324(16):1651–1669.
   PubMed Web of Science ®Google Scholar
• Yang X, Su B, Zhang X, Liu Y, Wu H, Zhang T. Incomplete immune reconstitution in HIV/AIDS patients on antiretroviral therapy: challenges of immunological non-responders. J Leukoc Biol. 2020;107(4):597–612.
   PubMed Web of Science ®Google Scholar
• Prabhu S, Harwell JI, Kumarasamy N. Advanced HIV: diagnosis, treatment, and prevention. Lancet HIV. 2019;6(8):e540–e51.
   PubMedGoogle Scholar
• Corbeau P, Reynes J. Immune reconstitution under antiretroviral therapy: the new challenge in HIV-1 infection. Blood. 2011;117(21):5582–5590.
   PubMed Web of Science ®Google Scholar
• Baker JV, Peng G, Rapkin J, et al. CD4+ count and risk of non-AIDS diseases following initial treatment for HIV infection. Aids. 2008;22(7):841–848.
   PubMed Web of Science ®Google Scholar
• Lapadula G, Cozzi-Lepri A, Marchetti G, et al. Risk of clinical progression among patients with immunological nonresponse despite virological suppression after combination antiretroviral treatment. Aids. 2013;27(5):769–779.
   PubMedGoogle Scholar
• Pacheco YM, Jarrin I, Rosado I, et al. Increased risk of non-AIDS-related events in HIV subjects with persistent low CD4 counts despite cART in the CoRIS cohort. Antiviral Res. 2015;117:69–74.
   PubMed Web of Science ®Google Scholar
• Engsig FN, Zangerle R, Katsarou O, et al. Long-term mortality in HIV-positive individuals virally suppressed for >3 years with incomplete CD4 recovery. Clin Infect Dis. 2014;58(9):1312–1321.
   PubMed Web of Science ®Google Scholar
• Yong YK, Shankar EM, Solomon A, et al. Polymorphisms in the CD14 and TLR4 genes independently predict CD4+ T-cell recovery in HIV-infected individuals on antiretroviral therapy. Aids. 2016;30(14):2159–2168.
   PubMedGoogle Scholar
• Qian S, Chen X, Wu T, et al. The accumulation of plasma acylcarnitines are associated with poor immune recovery in HIV-infected individuals. BMC Infect Dis. 2021;21(1):808.
   PubMed Web of Science ®Google Scholar
• Utay NS, Hunt PW. Role of immune activation in progression to AIDS. Curr Opin HIV AIDS. 2016;11(2):131–137.
   PubMedGoogle Scholar
• Massanella M, Negredo E, Clotet B, Blanco J. Immunodiscordant responses to HAART--mechanisms and consequences. Expert Rev Clin Immunol. 2013;9(11):1135–1149.
   PubMed Web of Science ®Google Scholar
• Wang Z, Monteiro CD, Jagodnik KM, et al. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat Commun. 2016;7:12846.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. j Integrative Biol. 2012;16(5):284–287.
   Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559.
   PubMed Web of Science ®Google Scholar
• Huang L, Ye T, Wang J, et al. Identification of Survival-Associated Hub Genes in Pancreatic Adenocarcinoma Based on WGCNA. Front Genet. 2021;12:814798.
   PubMedGoogle Scholar
• Zeng H, Luo M, Chen L, Ma X, Ma X. Machine learning analysis of DNA methylation in a hypoxia-immune model of oral squamous cell carcinoma. Int Immunopharmacol. 2020;89(Pt B):107098.
   PubMedGoogle Scholar
• Wang ZL, Zhou ZG, Chen Y, Li XT, Sun YS. Support Vector Machines Model of Computed Tomography for Assessing Lymph Node Metastasis in Esophageal Cancer with Neoadjuvant Chemotherapy. J Comput Assist Tomogr. 2017;41(3):455–460.
   PubMedGoogle Scholar
• Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12:77.
   PubMed Web of Science ®Google Scholar
• Liu X, Lin L, Lu L, et al. Comparative Transcriptional Analysis Identified Characteristic Genes and Patterns in HIV-Infected Immunological Non-Responders. Front Immunol. 2022;13:807890.
   PubMedGoogle Scholar
• Zhang Y, Jiang T, Li A, et al. Adjunct Therapy for CD4(+) T-Cell Recovery, Inflammation and Immune Activation in People Living With HIV: a Systematic Review and Meta-Analysis. Front Immunol. 2021;12:632119.
   PubMedGoogle Scholar
• Young J, Psichogiou M, Meyer L, et al.; Opportunistic Infections Project Team of the Collaboration of Observational HIVERiEiE. CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE. PLoS Med. 2012;9(3):e1001194.
   PubMed Web of Science ®Google Scholar
• Baker JV, Peng G, Rapkin J, et al. Poor initial CD4+ recovery with antiretroviral therapy prolongs immune depletion and increases risk for AIDS and non-AIDS diseases. J Acquir Immune Defic Syndr. 2008;48(5):541–546.
   PubMed Web of Science ®Google Scholar
• van der Windt GJ, Everts B, Chang CH, et al. Mitochondrial respiratory capacity is a critical regulator of CD8+ T cell memory development. Immunity. 2012;36(1):68–78.
   PubMed Web of Science ®Google Scholar
• Buck MD, O’Sullivan D, Klein Geltink RI, et al. Mitochondrial Dynamics Controls T Cell Fate through Metabolic Programming. Cell. 2016;166(1):63–76.
   PubMed Web of Science ®Google Scholar
• Ron-Harel N, Sharpe AH, Haigis MC. Mitochondrial metabolism in T cell activation and senescence: a mini-review. Gerontology. 2015;61(2):131–138.
   PubMedGoogle Scholar
• Zhao J, Schank M, Wang L, et al. Mitochondrial Functions Are Compromised in CD4 T Cells From ART-Controlled PLHIV. Front Immunol. 2021;12:658420.
   PubMedGoogle Scholar
• Vlasova VV, Saidakova EV, Korolevskaya LB, Shmagel NG, Chereshnev VA, Shmagel KV. Metabolic Features of Activated Memory CD4(+) T-Cells Derived from HIV-Infected Immunological Non-responders to Highly Active Antiretroviral Therapy. Doklady biol sci. 2021;501(1):206–209.
   PubMedGoogle Scholar
• Younes SA, Talla A, Pereira Ribeiro S, et al. Cycling CD4+ T cells in HIV-infected immune nonresponders have mitochondrial dysfunction. J Clin Invest. 2018;128(11):5083–5094.
   PubMedGoogle Scholar
• O’Neill LA, Kishton RJ, Rathmell J. A guide to immunometabolism for immunologists. Nat Rev Immunol. 2016;16(9):553–565.
   PubMed Web of Science ®Google Scholar
• Ferrari B, Da Silva AC, Liu KH, et al. Gut-derived bacterial toxins impair memory CD4+ T cell mitochondrial function in HIV-1 infection. J Clin Invest. 2022;132(9):543.
   Google Scholar
• Huang H, Lv J, Huang Y, et al. IFI27 is a potential therapeutic target for HIV infection. Ann Med. 2022;54(1):314–325.
   PubMed Web of Science ®Google Scholar
• Gonzalez-Amaro R, Cortes JR, Sanchez-Madrid F, Martin P. Is CD69 an effective brake to control inflammatory diseases? Trends Mol Med. 2013;19(10):625–632.
   PubMedGoogle Scholar
• Okhrimenko A, Grun JR, Westendorf K, et al. Human memory T cells from the bone marrow are resting and maintain long-lasting systemic memory. Proc Natl Acad Sci U S A. 2014;111(25):9229–9234.
   PubMedGoogle Scholar
• Martin P, Gomez M, Lamana A, et al. CD69 association with Jak3/Stat5 proteins regulates Th17 cell differentiation. Mol Cell Biol. 2010;30(20):4877–4889.
   PubMed Web of Science ®Google Scholar
• Conde M, Montano R, Moreno-Aurioles VR, et al. Anti-CD69 antibodies enhance phorbol-dependent glucose metabolism and Ca2+ levels in human thymocytes. J Leukocyte Biol. 1996;60(2):278–284.
   PubMedGoogle Scholar
• Labiano S, Meléndez-Rodríguez F, Palazón A, et al. CD69 is a direct HIF-1α target gene in hypoxia as a mechanism enhancing expression on tumor-infiltrating T lymphocytes. Oncoimmunology. 2017;6(4):e1283468.
   PubMedGoogle Scholar
• Jiang H, He X, Wang S, et al. A microtubule-associated zinc finger protein, BuGZ, regulates mitotic chromosome alignment by ensuring Bub3 stability and kinetochore targeting. Dev Cell. 2014;28(3):268–281.
   PubMedGoogle Scholar
• Fang F, Xia N, Angulo B, et al. A distinct isoform of ZNF207 controls self-renewal and pluripotency of human embryonic stem cells. Nat Commun. 2018;9(1):4384.
   PubMedGoogle Scholar
• Pahl PM, Hodges YK, Meltesen L, Perryman MB, Horwitz KB, Horwitz LD. ZNF207, a ubiquitously expressed zinc finger gene on chromosome 6p21.3. Genomics. 1998;53(3):410–412.
   PubMedGoogle Scholar
• Wan Y, Zheng X, Chen H, et al. Splicing function of mitotic regulators links R-loop-mediated DNA damage to tumor cell killing. J Cell Biol. 2015;209(2):235–246.
   PubMedGoogle Scholar
• Wang X, Zhou T, Chen X, et al. System analysis based on the cancer-immunity cycle identifies ZNF207 as a novel immunotherapy target for hepatocellular carcinoma. J Immunother Cancer. 2022;10(3):85.
   Google Scholar
• Chen J, Xun J, Yang J, et al. Plasma Indoleamine 2,3-Dioxygenase Activity Is Associated With the Size of the Human Immunodeficiency Virus Reservoir in Patients Receiving Antiretroviral Therapy. Clin Infect Dis. 2019;68(8):1274–1281.
   PubMedGoogle Scholar
• Yamamoto H, Williams EG, Mouchiroud L, et al. NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell. 2011;147(4):827–839.
   PubMedGoogle Scholar
• Lederman MM, Calabrese L, Funderburg NT, et al. Immunologic failure despite suppressive antiretroviral therapy is related to activation and turnover of memory CD4 cells. J Infect Dis. 2011;204(8):1217–1226.
   PubMedGoogle Scholar
• Piconi S, Trabattoni D, Gori A, et al. Immune activation, apoptosis, and Treg activity are associated with persistently reduced CD4+ T-cell counts during antiretroviral therapy. Aids. 2010;24(13):1991–2000.
   PubMed Web of Science ®Google Scholar
• Bai R, Li Z, Hou Y, et al. Identification of Diagnostic Markers Correlated With HIV(+) Immune Non-response Based on Bioinformatics Analysis. Front Mol Biosci. 2021;8:809085.
   PubMedGoogle Scholar