2. Academic Validation
  3. Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms

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

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.

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