Evidence map›Paper›PMID 41226717›Full record

ArticleInternational journal of molecular sciences2025

Early Transcriptomic Signatures of Immune Response Modulation Following Antiretroviral Therapy in HIV-Infected Patients.

Ekaterina A Stolbova, Anastasia V Pokrovskaya, Andrey B Shemshura, Dmitry E Kireev, Alexey A Lagunin, Boris N Sobolev, Sergey M Ivanov, Olga A Tarasova

Abstract read
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In one paragraph

Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Ekaterina A StolbovaLaboratory of Big Data Analysis for Digital Pharmacology, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Street 10-8, 119121 Moscow, Russia.ORCID 0009-0001-0569-4967
Anastasia V PokrovskayaFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Novogireevskaya Street, 3A, 111123 Moscow, Russia.
Andrey B ShemshuraFederal Budget Public Health Institution "Clinical Center of HIV/AIDS Treatment and Prevention" of the Ministry of Health of Krasnodar Region, 204/2, Mitrofana Sedina Street, 350000 Krasnodar, Russia.ORCID 0000-0003-1637-4229
Dmitry E KireevFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Novogireevskaya Street, 3A, 111123 Moscow, Russia.ORCID 0000-0002-7896-2379
Alexey A LaguninDepartment of Bioinformatics, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117513 Moscow, Russia.ORCID 0000-0003-1757-8004
Boris N SobolevLaboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya St. 10-8, 119121 Moscow, Russia.ORCID 0000-0001-7843-5272
Sergey M IvanovLaboratory of Big Data Analysis for Digital Pharmacology, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Street 10-8, 119121 Moscow, Russia.ORCID 0000-0002-3177-6237
Olga A TarasovaLaboratory of Big Data Analysis for Digital Pharmacology, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Street 10-8, 119121 Moscow, Russia.

Funding

Program for Basic Research in the Russian Federation for a long-term period (2021-2030) No. 124050800018-9
6 · The paper itself

Abstract

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-naïve male patients with HIV aged 18-35. 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-protein 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.

Indexed as

Anti-Retroviral AgentsHIV InfectionsTranscriptomeAdolescentAdultGene Expression ProfilingHIV-1HumansImmunityLeukocytes, MononuclearMaleProtein Interaction MapsYoung AdultAnti-Retroviral Agentsantiretroviral therapygene expressionHIVpaired analysisRNA seq

Identifiers

PMID41226717
PMCPMC12608518

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.