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<p>Phenotyping cells at transcriptomic and proteomic levels is an essential step to understanding cellular contributions to development, aging, injury, and disease. Since proteome and transcriptome level abundances modestly correlate, complementary profiling of both is needed. We report a method called simultaneous protein and RNA -omics (SPARO) to capture the cell type-specific transcriptome and proteome simultaneously in vitro using BV2 microglial and HEK293 cell lines and in vivo using astrocytic and neuronal Cre driver mice crossed with Rosa26-TurboID knock-in mice. SPARO leverages TurboID to biotinylate RNA-interacting cytosolic proteins, enabling enrichment of proteins for proteomics and protein-associated RNA for transcriptomics. We validate SPARO first using well-controlled in vitro systems to verify that the proteomes and transcriptomes obtained reflect the global proteomes and transcriptomes. The effect of neuroinflammatory activation by lipopolysaccharide is also faithfully captured. We apply SPARO to obtain native-state proteomes and transcriptomes from astrocytes and neurons, thereby validating the approach in vivo. We interrogate mRNA-protein concordance and discordance, providing insights into molecular processes that exhibit uniform or cell type-specific patterns.</p>

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Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月31日

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  • Christina C. Ramelow,
  • Eric B. Dammer,
  • Hailian Xiao,
  • Lihong Cheng,
  • Prateek Kumar,
  • Claudia Espinosa-Garcia,
  • Maureen M. Sampson,
  • Dilpreet Kour,
  • Ruth S. Nelson,
  • Sneha Malepati,
  • Rashmi Kumari,
  • Wooyoung Eric Jang,
  • Qi Guo,
  • Pritha Bagchi,
  • Duc M. Duong,
  • Nicholas T. Seyfried,
  • Steven A. Sloan,
  • Srikant Rangaraju

摘要

Phenotyping cells at transcriptomic and proteomic levels is an essential step to understanding cellular contributions to development, aging, injury, and disease. Since proteome and transcriptome level abundances modestly correlate, complementary profiling of both is needed. We report a method called simultaneous protein and RNA -omics (SPARO) to capture the cell type-specific transcriptome and proteome simultaneously in vitro using BV2 microglial and HEK293 cell lines and in vivo using astrocytic and neuronal Cre driver mice crossed with Rosa26-TurboID knock-in mice. SPARO leverages TurboID to biotinylate RNA-interacting cytosolic proteins, enabling enrichment of proteins for proteomics and protein-associated RNA for transcriptomics. We validate SPARO first using well-controlled in vitro systems to verify that the proteomes and transcriptomes obtained reflect the global proteomes and transcriptomes. The effect of neuroinflammatory activation by lipopolysaccharide is also faithfully captured. We apply SPARO to obtain native-state proteomes and transcriptomes from astrocytes and neurons, thereby validating the approach in vivo. We interrogate mRNA-protein concordance and discordance, providing insights into molecular processes that exhibit uniform or cell type-specific patterns.