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<p>Transcriptomics enables comprehensive, multiplexed characterization of cellular states, yet prevailing methods typically require cell fixation or lysis, precluding longitudinal analysis of RNA expression in living cells. Here, we present non-destructive transcriptomics by vesicular export (NTVE), a platform for multi-time-point monitoring of RNA expression dynamics in living cells. Stabilized RNA reporter barcodes can be selectively packaged and exported from cells <i>via</i> virus-like particles (VLPs) bearing bioorthogonal affinity handles for convenient multichannel tracking of co-cultured cells. Using an engineered poly(A)-binding protein adapter, NTVE exports endogenous transcripts from inducible human and murine cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE captures transcriptome changes in response to genetic and chemical perturbations within the same cells over time using standard sequencing workflows. NTVE can further be equipped with fusogens to deliver mRNA-encoded effectors or ribonucleoprotein gene editors from sender cells, activating gene reporters in co-cultured recipient cells. We demonstrate the utility of NTVE for monitoring hiPSC differentiation through daily non-destructive transcriptomic profiling of lineage-specific marker dynamics.</p>

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Non-destructive transcriptomics via vesicular export

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月25日

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  • Niklas Armbrust,
  • Martin Grosshauser,
  • Julian Geilenkeuser,
  • Luisa Stroppel,
  • Mattea Jozinovic,
  • Hella Levermann,
  • Tobias Panne,
  • Jannick Wißmann,
  • Lukas Goelitz,
  • Sebastian Schmidt,
  • Tanja Orschmann,
  • Ejona Rusha,
  • Emily Steinmaßl,
  • Florenc Widenmeyer,
  • Niklas Warsing,
  • Melike Sabry,
  • Asina Sultanbai,
  • Tobias Santl,
  • Arie Geerlof,
  • Oleksandr Berezin,
  • Silviu-Vasile Bodea,
  • Alessandra Moretti,
  • Steffen Schneider,
  • Fabian Theis,
  • Julien Gagneur,
  • Dong-Jiunn Jeffery Truong,
  • Gil Gregor Westmeyer

摘要

Transcriptomics enables comprehensive, multiplexed characterization of cellular states, yet prevailing methods typically require cell fixation or lysis, precluding longitudinal analysis of RNA expression in living cells. Here, we present non-destructive transcriptomics by vesicular export (NTVE), a platform for multi-time-point monitoring of RNA expression dynamics in living cells. Stabilized RNA reporter barcodes can be selectively packaged and exported from cells via virus-like particles (VLPs) bearing bioorthogonal affinity handles for convenient multichannel tracking of co-cultured cells. Using an engineered poly(A)-binding protein adapter, NTVE exports endogenous transcripts from inducible human and murine cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE captures transcriptome changes in response to genetic and chemical perturbations within the same cells over time using standard sequencing workflows. NTVE can further be equipped with fusogens to deliver mRNA-encoded effectors or ribonucleoprotein gene editors from sender cells, activating gene reporters in co-cultured recipient cells. We demonstrate the utility of NTVE for monitoring hiPSC differentiation through daily non-destructive transcriptomic profiling of lineage-specific marker dynamics.