Extracellular vesicles carry distinct proteo-transcriptomic signatures that are different from their cancer cell of origin

Tzu-Yi Chen; Edgar Gonzalez-Kozlova; Taliah Soleymani; Sabrina La Salvia; Natasha Kyprianou; Susmita Sahoo; Ashutosh K Tewari; Carlos Cordon-Cardo; Gustavo Stolovitzky; Navneet Dogra

doi:10.1016/j.isci.2022.104414

Extracellular vesicles carry distinct proteo-transcriptomic signatures that are different from their cancer cell of origin

iScience. 2022 May 18;25(6):104414. doi: 10.1016/j.isci.2022.104414. eCollection 2022 Jun 17.

Authors

Tzu-Yi Chen^{1

2}, Edgar Gonzalez-Kozlova^{2

3}, Taliah Soleymani^{1

2}, Sabrina La Salvia⁴, Natasha Kyprianou^{3

5}, Susmita Sahoo⁴, Ashutosh K Tewari^{3

5}, Carlos Cordon-Cardo^{1

2

3}, Gustavo Stolovitzky^{2

6

7}, Navneet Dogra^{1

2

6}

Affiliations

¹ Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
² Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
³ Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁴ Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
⁵ Department of Urology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
⁶ IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
⁷ Sema4, Stamford, CT 06902, USA.

Abstract

Circulating extracellular vesicles (EVs) contain molecular footprints-lipids, proteins, RNA, and DNA-from their cell of origin. Consequently, EV-associated RNA and proteins have gained widespread interest as liquid-biopsy biomarkers. Yet, an integrative proteo-transcriptomic landscape of EVs and comparison with their cell of origin remains obscure. Here, we report that EVs enrich distinct proteo-transcriptome that does not linearly correlate with their cell of origin. We show that EVs enrich endosomal and extracellular proteins, small RNA (∼13-200 nucleotides) associated with cell differentiation, development, and Wnt signaling. EVs cargo specific RNAs (RNY3, vtRNA, and MIRLET-7) and their complementary proteins (YBX1, IGF2BP2, and SRSF1/2). To ensure an unbiased and independent analyses, we studied 12 cancer cell lines, matching EVs (inhouse and exRNA database), and serum EVs of patients with prostate cancer. Together, we show that EV-RNA-protein complexes may constitute a functional interaction network to protect and regulate molecular access until a function is achieved.

Keywords: Cancer systems biology; Microenvironment; Transcriptomics.

Abstract

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