Urinary extracellular vesicles contain mature transcriptome enriched in circular and long noncoding RNAs with functional significance in prostate cancer

被引：18

作者：

Almeida, Anna ^{[1
,2
]}

Gabriel, Marc ^{[1
]}

Firlej, Virginie ^{[3
,4
]}

Martin-Jaular, Lorena ^{[5
,6
]}

Lejars, Matthieu ^{[1
]}

Cipolla, Rocco ^{[1
]}

Petit, Floriane ^{[7
]}

Vogt, Nicolas ^{[1
]}

San-Roman, Mabel ^{[8
]}

Dingli, Florent ^{[9
]}

Loew, Damarys ^{[9
]}

Destouches, Damien ^{[4
]}

Vacherot, Francis ^{[4
]}

de la Taille, Alexandre ^{[10
]}

Thery, Clotilde ^{[5
,6
]}

Morillon, Antonin ^{[1
]}

机构：

[1] Sorbonne Univ, PSL Univ, Ctr Rech, CNRS,UMR3244,Inst Curie, Paris, France

[2] PSL Univ, Ctr Rech, Inst Curie, Dept Rech Translat, Paris, France

[3] Hop H Mondor, AP HP, Plateforme Ressources Biol, Creteil, France

[4] Univ Paris Est Creteil, UR TRePCa, Creteil, France

[5] PSL Univ, Ctr Rech, Inst Curie, INSERM,U932, Paris, France

[6] Ctr Rech, Inst Curie, Curie Core Tech Extracellular Vesicles, Paris, France

[7] Sorbonne Univ, PSL Univ, Ctr Rech, INSERM,U820,Inst Curie, Paris, France

[8] Sorbonne Univ, PSL Univ, Ctr Rech, CNRS,UMR3215,Inst Curie, Paris, France

[9] PSL Res Univ, Inst Curie Ctr Rech, Lab Spectrometrie Masse Proteom, Paris, France

[10] Hop H Mondor, AP HP, Serv Urol, Inserm,CIC 1930, Creteil, France

来源：

JOURNAL OF EXTRACELLULAR VESICLES | 2022年 / 11卷 / 05期

关键词：

CircRNA; EV; lncRNA; neoantigen; TSA; EXOSOMES; BIOMARKERS; PROLIFERATION; TRANSLATION; LANDSCAPE;

D O I：

10.1002/jev2.12210

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and antitumourigenic functions by controlling the immune response. In contrast to extracellular nonvesicular RNA, few studies have addressed the full RNA content within human fluids' EVs and have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on six Formalin-Fixed-Paraffin-Embedded (FFPE) prostate cancer (PCa) tumour tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intronfree cytoplasmic transcripts and enriched lnc/circular (circ)RNAs, strikingly common to an independent 20 patients' urinary cohort. Our full cellular and EVs transcriptome comparison within three PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 28 uEV-lncRNAs belonging to the cancer-related lncRNA census (CLC2). In addition, we found 15 uEV-lncRNAs, predicted to encode 768 high-affinity neoantigens, and for which three of the encoded-ORF produced detectable unmodified peptides by mass spectrometry. Our dual analysis of EVs-lnc/circRNAs both in urines' and in vitro's EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.

引用

页数：20

共 76 条

[21] A review on the role of PCAT6 lncRNA in tumorigenesis [J].

Ghafouri-Fard, Soudeh ;

Khoshbakht, Tayyebeh ;

Taheri, Mohammad ;

Ebrahimzadeh, Kaveh .

BIOMEDICINE & PHARMACOTHERAPY, 2021, 142

[22] Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma [J].

Giraldez, Maria D. ;

Spengler, Ryan M. ;

Etheridge, Alton ;

Goicochea, Annika J. ;

Tuck, Missy ;

Choi, Sung Won ;

Galas, David J. ;

Tewari, Muneesh .

EMBO JOURNAL, 2019, 38 (11)

[23] Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity [J].

Griffin, Gabriel K. ;

Wu, Jingyi ;

Iracheta-Vellve, Arvin ;

Patti, James C. ;

Hsu, Jeffrey ;

Davis, Thomas ;

Dele-Oni, Deborah ;

Du, Peter P. ;

Halawi, Aya G. ;

Ishizuka, Jeffrey J. ;

Kim, Sarah Y. ;

Klaeger, Susan ;

Knudsen, Nelson H. ;

Miller, Brian C. ;

Nguyen, Tung H. ;

Olander, Kira E. ;

Papanastasiou, Malvina ;

Rachimi, Suzanna ;

Robitschek, Emily J. ;

Schneider, Emily M. ;

Yeary, Mitchell D. ;

Zimmer, Margaret D. ;

Jaffe, Jacob D. ;

Carr, Steven A. ;

Doench, John G. ;

Haining, W. Nicholas ;

Yates, Kathleen B. ;

Manguso, Robert T. ;

Bernstein, Bradley E. .

NATURE, 2021, 595 (7866) :309-+

[24] Natural RNA circles function as efficient microRNA sponges [J].

Hansen, Thomas B. ;

Jensen, Trine I. ;

Clausen, Bettina H. ;

Bramsen, Jesper B. ;

Finsen, Bente ;

Damgaard, Christian K. ;

Kjems, Jorgen .

NATURE, 2013, 495 (7441) :384-388

[25] Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species [J].

Hezroni, Hadas ;

Koppstein, David ;

Schwartz, Matthew G. ;

Avrutin, Alexandra ;

Bartel, David P. ;

Ulitsky, Igor .

CELL REPORTS, 2015, 11 (07) :1110-1122

[26] Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers [J].

Hoshino, Ayuko ;

Kim, Han Sang ;

Bojmar, Linda ;

Gyan, Kofi Ennu ;

Cioffi, Michele ;

Hernandez, Jonathan ;

Zambirinis, Constantinos P. ;

Rodrigues, Goncalo ;

Molina, Henrik ;

Heissel, Sren ;

Mark, Milica Tesic ;

Steiner, Loic ;

Benito-Martin, Alberto ;

Lucotti, Serena ;

Di Giannatale, Angela ;

Offer, Katharine ;

Nakajima, Miho ;

Williams, Caitlin ;

Nogues, Laura ;

Vatter, Fanny A. Pelissier ;

Hashimoto, Ayako ;

Davies, Alexander E. ;

Freitas, Daniela ;

Kenific, Candia M. ;

Ararso, Yonathan ;

Buehring, Weston ;

Lauritzen, Pernille ;

Ogitani, Yusuke ;

Sugiura, Kei ;

Takahashi, Naoko ;

Aleckovic, Masa ;

Bailey, Kayleen A. ;

Jolissant, Joshua S. ;

Wang, Huajuan ;

Harris, Ashton ;

Schaeffer, L. Miles ;

Garcia-Santos, Guillermo ;

Posner, Zoe ;

Balachandran, Vinod P. ;

Khakoo, Yasmin ;

Raju, G. Praveen ;

Scherz, Avigdor ;

Sagi, Irit ;

Scherz-Shouval, Ruth ;

Yarden, Yosef ;

Oren, Moshe ;

Malladi, Mahathi ;

Petriccione, Mary ;

De Braganca, Kevin C. ;

Donzelli, Maria .

CELL, 2020, 182 (04) :1044-+

[27] The translational landscape of mTOR signalling steers cancer initiation and metastasis [J].

Hsieh, Andrew C. ;

Liu, Yi ;

Edlind, Merritt P. ;

Ingolia, Nicholas T. ;

Janes, Matthew R. ;

Sher, Annie ;

Shi, Evan Y. ;

Stumpf, Craig R. ;

Christensen, Carly ;

Bonham, Michael J. ;

Wang, Shunyou ;

Ren, Pingda ;

Martin, Michael ;

Jessen, Katti ;

Feldman, Morris E. ;

Weissman, Jonathan S. ;

Shokat, Kevan M. ;

Rommel, Christian ;

Ruggero, Davide .

NATURE, 2012, 485 (7396) :55-U196

[28] Large non-coding RNAs: missing links in cancer? [J].

Huarte, Maite ;

Rinn, John L. .

HUMAN MOLECULAR GENETICS, 2010, 19 :R152-R161

[29] Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas [J].

Hulstaert, Eva ;

Morlion, Annelien ;

Cobos, Francisco Avila ;

Verniers, Kimberly ;

Nuytens, Justine ;

Vanden Eynde, Eveline ;

Yigit, Nurten ;

Anckaert, Jasper ;

Geerts, Anja ;

Hindryckx, Pieter ;

Jacques, Peggy ;

Brusselle, Guy ;

Bracke, Ken R. ;

Maes, Tania ;

Malfait, Thomas ;

Derveaux, Thierry ;

Ninclaus, Virginie ;

Van Cauwenbergh, Caroline ;

Roelens, Kristien ;

Roets, Ellen ;

Hemelsoet, Dimitri ;

Tilleman, Kelly ;

Brochez, Lieve ;

Kuersten, Scott ;

Simon, Lukas M. ;

Karg, Sebastian ;

Kautzky-Willers, Alexandra ;

Leutner, Michael ;

Noehammer, Christa ;

Slaby, Ondrej ;

Prins, Romeo Willinge ;

Koster, Jan ;

Lefever, Steve ;

Schroth, Gary P. ;

Vandesompele, Jo ;

Mestdagh, Pieter .

CELL REPORTS, 2020, 33 (13)

[30] The landscape of long noncoding RNAs in the human transcriptome [J].

Iyer, Matthew K. ;

Niknafs, Yashar S. ;

Malik, Rohit ;

Singhal, Udit ;

Sahu, Anirban ;

Hosono, Yasuyuki ;

Barrette, Terrence R. ;

Prensner, John R. ;

Evans, Joseph R. ;

Zhao, Shuang ;

Poliakov, Anton ;

Cao, Xuhong ;

Dhanasekaran, Saravana M. ;

Wu, Yi-Mi ;

Robinson, Dan R. ;

Beer, David G. ;

Feng, Felix Y. ;

Iyer, Hariharan K. ;

Chinnaiyan, Arul M. .

NATURE GENETICS, 2015, 47 (03) :199-+

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