Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms

  • Nat Commun. 2026 May 29. doi: 10.1038/s41467-026-73661-5.
Alejandra Bodelón  1 ,  Maurice J H van Haaren  1  2 ,  Paula Sobrevals Alcaraz  3 ,  Lyanne J P M Sijbers  1 ,  Rianne C Scholman  1 ,  Lucas W Picavet  1  2 ,  Aafke de Ligt  1 ,  Daphne van Ginneken  1 ,  Remco G A Erkens  1  2 ,  Harmjan R Vos  3 ,  Jorg J A Calis  1 ,  Sebastiaan J Vastert  1  2 ,  Jorg van Loosdregt  4  5
Affiliations
  • 1. Center for Translational Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.
  • 2. Division of Pediatric Rheumatology and Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.
  • 3. Center for Molecular Medicine, University Medical Center Utrecht, Oncode Institute, Utrecht, the Netherlands.
  • 4. Center for Translational Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands. [email protected].
  • 5. Division of Pediatric Rheumatology and Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands. [email protected].
PMID: 42215459 DOI: 10.1038/s41467-026-73661-5
Abstract

Alternative splicing is a key mechanism for expanding transcriptomic and proteomic complexity, yet its role in innate immune activation remains incompletely understood. Here, we applied Oxford Nanopore native RNA-sequencing to generate an isoform-level transcriptome of primary human monocytes before and after activation with lipopolysaccharide. We identify over 24,000 expressed isoforms, including thousands of previously unannotated variants. Activation induced widespread isoform-specific expression changes, leading to extensive isoform switching events, which were validated using matched short-read RNA-Seq. These activation-induced shifts enhanced transcript immune-regulatory functions: activated monocytes preferentially express longer, coding-competent isoforms with complete open reading frames, fewer retained introns, and increased domain complexity. By integrating matched Ribo-seq and proteomic data, we demonstrate that these isoform modulations are associated with enhanced translation of immune effector proteins. Together, our findings position alternative splicing as a dynamic and functional regulator of monocyte activation, emphasizing the need for isoform-level resolution to fully understand immune cell function.

Products