Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture

Sandipan Dasgupta; Daniella Y. Dayagi; Gal Haimovich; Emanuel Wyler; Tsviya Olender; Robert H. Singer; Markus Landthaler; Jeffrey E. Gerst

doi:10.7554/eLife.83584

Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture

Sandipan Dasgupta, Daniella Y. Dayagi, Gal Haimovich^*, Emanuel Wyler, Tsviya Olender, Robert H. Singer, Markus Landthaler, Jeffrey E. Gerst^*

^*Corresponding author for this work

Department of Molecular Genetics

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically,<1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.

Original language	English
Article number	e83584
Number of pages	32
Journal	eLife
Volume	12
DOIs	https://doi.org/10.7554/eLife.83584
Publication status	Published - 30 May 2023

Bibliographical note

Funding Information:
We thank Ester Feldmesser and Igor Ulitsky (Weizmann Institute of Science, Israel) for assistance with the bioinformatics analysis; Michael Wigler and Siran Li (Cold Spring Harbor Laboratories, NY, USA) for generously performing scBAG-seq experiments to detect mRNA transfer; and Shalev Itzkovitz (Weizmann Institute of Science, Israel) for the gift of reagents. This work was funded by grants to JEG from the Joel and Mady Dukler Fund for Cancer Research, the Jean-Jacques Brunschwig Fund for the Molecular Genetics of Cancer, a Proof-of-Principle Grant from the Moross Integrated Cancer Center, the Kekst Family Institute for Medical Genetics (Weizmann Institute of Science), the German-Israel Foundation (GIF; I-1461–412.13/2018) (JEG and ML), and the US-Israel Binational Science Foundation-National Science Foundation (#2015846) (JEG and RHS).

Publisher Copyright:
© 2023, eLife Sciences Publications Ltd. All rights reserved.

All Science Journal Classification (ASJC) codes

General Neuroscience
General Biochemistry,Genetics and Molecular Biology
General Immunology and Microbiology

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10.7554/eLife.83584

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@article{2bddb814295a465dbc51595ec9ddb573,

title = "Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture",

abstract = "Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically,<1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.",

author = "Sandipan Dasgupta and Dayagi, {Daniella Y.} and Gal Haimovich and Emanuel Wyler and Tsviya Olender and Singer, {Robert H.} and Markus Landthaler and Gerst, {Jeffrey E.}",

note = "Funding Information: We thank Ester Feldmesser and Igor Ulitsky (Weizmann Institute of Science, Israel) for assistance with the bioinformatics analysis; Michael Wigler and Siran Li (Cold Spring Harbor Laboratories, NY, USA) for generously performing scBAG-seq experiments to detect mRNA transfer; and Shalev Itzkovitz (Weizmann Institute of Science, Israel) for the gift of reagents. This work was funded by grants to JEG from the Joel and Mady Dukler Fund for Cancer Research, the Jean-Jacques Brunschwig Fund for the Molecular Genetics of Cancer, a Proof-of-Principle Grant from the Moross Integrated Cancer Center, the Kekst Family Institute for Medical Genetics (Weizmann Institute of Science), the German-Israel Foundation (GIF; I-1461–412.13/2018) (JEG and ML), and the US-Israel Binational Science Foundation-National Science Foundation (#2015846) (JEG and RHS). Publisher Copyright: {\textcopyright} 2023, eLife Sciences Publications Ltd. All rights reserved.",

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AU - Dasgupta, Sandipan

AU - Dayagi, Daniella Y.

AU - Haimovich, Gal

AU - Wyler, Emanuel

AU - Olender, Tsviya

AU - Singer, Robert H.

AU - Landthaler, Markus

AU - Gerst, Jeffrey E.

N1 - Funding Information: We thank Ester Feldmesser and Igor Ulitsky (Weizmann Institute of Science, Israel) for assistance with the bioinformatics analysis; Michael Wigler and Siran Li (Cold Spring Harbor Laboratories, NY, USA) for generously performing scBAG-seq experiments to detect mRNA transfer; and Shalev Itzkovitz (Weizmann Institute of Science, Israel) for the gift of reagents. This work was funded by grants to JEG from the Joel and Mady Dukler Fund for Cancer Research, the Jean-Jacques Brunschwig Fund for the Molecular Genetics of Cancer, a Proof-of-Principle Grant from the Moross Integrated Cancer Center, the Kekst Family Institute for Medical Genetics (Weizmann Institute of Science), the German-Israel Foundation (GIF; I-1461–412.13/2018) (JEG and ML), and the US-Israel Binational Science Foundation-National Science Foundation (#2015846) (JEG and RHS). Publisher Copyright: © 2023, eLife Sciences Publications Ltd. All rights reserved.

PY - 2023/5/30

Y1 - 2023/5/30

N2 - Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically,<1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.

AB - Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically,<1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.

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Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture

Abstract

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