{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T15:32:38Z","timestamp":1785857558377,"version":"3.56.0"},"reference-count":83,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T00:00:00Z","timestamp":1762041600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Program for Basic Research in the Russian Federation","award":["124050800018-9"],"award-info":[{"award-number":["124050800018-9"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Human immunodeficiency virus (HIV) remains a global public health challenge. Antiretroviral therapy (ART) improves outcomes by suppressing viral replication and enabling immune recovery, yet the early molecular mechanisms of immune-related transcriptional change after ART remain insufficiently characterized. We enrolled eight ART-na\u00efve male patients with HIV aged 18\u201335. Peripheral blood mononuclear cells (PBMCs) were collected before and after 24 weeks of combination ART (TDF, 3TC, DTG) and underwent bulk RNA-seq (Illumina HiSeq 1500, Illumina, Inc., San Diego, CA, USA). Differential expression was assessed with DESeq2 (paired design); gene set enrichment analysis (GSEA), principal component analysis (PCA), hierarchical clustering, and protein\u2013protein interaction (PPI) networks (STRING\/NetworkX) explored functional patterns and transcriptomic shifts. We identified 87 differentially expressed genes, including 67 downregulated interferon-stimulated genes (e.g., IFI44L, ISG15, STAT1) and 20 upregulated transcripts, mostly pseudogenes related to ribosomal proteins. Functional enrichment revealed suppression of type I interferon and other antiviral signaling pathways. PCA and hierarchical clustering indicated a post-ART transcriptional shift. These findings suggest that early immune recovery following ART involves downregulation of chronic interferon-driven activation. This observation may correspond to partial restoration of T-cell functional capacity, reduced immune exhaustion, and a rebalanced antiviral immune environment.<\/jats:p>","DOI":"10.3390\/ijms262110678","type":"journal-article","created":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T13:15:14Z","timestamp":1762175714000},"page":"10678","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Early Transcriptomic Signatures of Immune Response Modulation Following Antiretroviral Therapy in HIV-Infected Patients"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-0569-4967","authenticated-orcid":false,"given":"Ekaterina A.","family":"Stolbova","sequence":"first","affiliation":[{"name":"Laboratory of Big Data Analysis for Digital Pharmacology, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Street 10-8, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia V.","family":"Pokrovskaya","sequence":"additional","affiliation":[{"name":"Federal Budget Institution of Science \u201cCentral Research Institute for Epidemiology\u201d of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Novogireevskaya Street, 3A, 111123 Moscow, Russia"},{"name":"Department of Infectious Diseases with Courses of Epidemiology and Physiology, Medical Institute, Peoples\u2019 Friendship University of Russia, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1637-4229","authenticated-orcid":false,"given":"Andrey B.","family":"Shemshura","sequence":"additional","affiliation":[{"name":"Federal Budget Public Health Institution \u201cClinical Center of HIV\/AIDS Treatment and Prevention\u201d of the Ministry of Health of Krasnodar Region, 204\/2, Mitrofana Sedina Street, 350000 Krasnodar, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7896-2379","authenticated-orcid":false,"given":"Dmitry E.","family":"Kireev","sequence":"additional","affiliation":[{"name":"Federal Budget Institution of Science \u201cCentral Research Institute for Epidemiology\u201d of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Novogireevskaya Street, 3A, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1757-8004","authenticated-orcid":false,"given":"Alexey A.","family":"Lagunin","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117513 Moscow, Russia"},{"name":"Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya St. 10-8, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7843-5272","authenticated-orcid":false,"given":"Boris N.","family":"Sobolev","sequence":"additional","affiliation":[{"name":"Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya St. 10-8, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3177-6237","authenticated-orcid":false,"given":"Sergey M.","family":"Ivanov","sequence":"additional","affiliation":[{"name":"Laboratory of Big Data Analysis for Digital Pharmacology, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Street 10-8, 119121 Moscow, Russia"},{"name":"Department of Bioinformatics, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117513 Moscow, Russia"},{"name":"Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya St. 10-8, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga A.","family":"Tarasova","sequence":"additional","affiliation":[{"name":"Laboratory of Big Data Analysis for Digital Pharmacology, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Street 10-8, 119121 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,2]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2025, September 19). 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