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Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral

Oleg D Fateev1, Vasily E Akimov1, Olga V Glushkova1

  • 1Federal State Budgetary Institution "Center for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical-Biological Agency (FSBI "CSP" of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia.

International Journal of Molecular Sciences
|February 13, 2026
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) regulate immunity. This study found unique non-LTR TE expression patterns in viral infections like HIV and SARS-CoV-2, aiding disease assessment and identifying potential biomarkers.

Keywords:
COVID-19HIVinfluenza AscRNA-seqtransposable elementsviral infection

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Area of Science:

  • Immunology
  • Genomics
  • Virology

Background:

  • Transposable elements (TEs) are crucial for immune regulation, with increased activity during viral infections.
  • Non-LTR TEs (LINE, SINE, SVA) show altered expression correlating with antiviral responses.

Purpose of the Study:

  • Investigate non-LTR TE transcriptomic signatures in human PBMCs during influenza A, HIV, and SARS-CoV-2 infections.
  • Identify cell-specific TE patterns for disease severity assessment, progression prediction, and therapy evaluation.
  • Analyze TE co-expression networks in cytotoxic T cells to find diagnostic and therapeutic targets.

Main Methods:

  • Single-cell RNA sequencing (scRNA-seq) on 98 patient samples.
  • Bioinformatic analysis of transcriptomic data.
  • Co-expression network analysis of TEs and transcription factors.

Main Results:

  • Unique cell-specific non-LTR TE expression patterns identified in HIV and SARS-CoV-2 cohorts.
  • TE expression linked to disease severity, progression, and treatment efficacy.
  • Precursor cytotoxic T cells showed the most variable TE expression, dependent on virus and disease severity.
  • Key regulatory players in TE networks identified as potential biomarkers.

Conclusions:

  • Non-LTR TEs are involved in mediating antiviral responses.
  • Cell-specific TE signatures can differentiate disease severity and predict progression.
  • Identified TE-associated networks and transcription factors offer potential diagnostic biomarkers and therapeutic targets for viral infections.