TRACE-seq: A transgenic system for unbiased and non-invasive transcriptome profiling of living cells

François Cherbonneau; Guoping Li; Priyanka Gokulnath; Parul Sahu; Aurore Prunevieille; Robert Kitchen; Gilles Benichou; Jérôme Larghero; Ibrahim Domian; Saumya Das

iScience (Feb 2022)

TRACE-seq: A transgenic system for unbiased and non-invasive transcriptome profiling of living cells

François Cherbonneau,
Guoping Li,
Priyanka Gokulnath,
Parul Sahu,
Aurore Prunevieille,
Robert Kitchen,
Gilles Benichou,
Jérôme Larghero,
Ibrahim Domian,
Saumya Das

Affiliations

François Cherbonneau: Université de Paris, AP-HP, Hôpital Saint-Louis, Unité de Thérapie Cellulaire, U976, CICBT CBT501, INSERM, Paris, France; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
Guoping Li: Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
Priyanka Gokulnath: Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
Parul Sahu: Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
Aurore Prunevieille: Université de Paris, AP-HP, Hôpital Saint-Louis, Human Immunology and Immunopathology, UMR976, INSERM, Paris, France; Transplant Research Center, Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
Robert Kitchen: Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
Gilles Benichou: Transplant Research Center, Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
Jérôme Larghero: Université de Paris, AP-HP, Hôpital Saint-Louis, Unité de Thérapie Cellulaire, U976, CICBT CBT501, INSERM, Paris, France
Ibrahim Domian: Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
Saumya Das: Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA; Corresponding author

Journal volume & issue: Vol. 25, no. 2
p. 103806

Abstract

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Summary: Dynamic profiling of changes in gene expression in response to stressors in specific microenvironments without requiring cellular destruction remains challenging. Current methodologies that seek to interrogate gene expression at a molecular level require sampling of cellular transcriptome and therefore lysis of the cell, preventing serial analysis of cellular transcriptome. To address this area of unmet need, we have recently developed a technology allowing transcriptomic analysis over time without cellular destruction. Our method, TRACE-seq (TRanscriptomic Analysis Captured in Extracellular vesicles using sequencing), is characterized by a cell-type specific transgene expression. It provides data on the transcriptome inside extracellular vesicles that provides an accurate representation of stress-responsive cellular transcriptomic changes. Thus, the transcriptome of cells expressing TRACE can be followed over time without destroying the source cell, which is a powerful tool for many fields of fundamental and translational biology research.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

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