VAP-A and Its Binding Partner CERT Drive Biogenesis of RNA-containing Extracellular Vesicles at ER Membrane Contact Sites

Overview

Journal Dev Cell

Publisher Cell Press

Specialties Cell Biology
Reproductive Medicine

Date 2022 Apr 14

PMID 35421371

Authors

Bahnisikha Barman

Bong Hwan Sung

Evan Krystofiak

Jie Ping

Marisol Ramirez

Bryan Millis

Ryan Allen

Nripesh Prasad

Sergei Chetyrkin

M Wade Calcutt

Kasey Vickers

James G Patton

Qi Liu

Alissa M Weaver

Affiliations

Soon will be listed here.

Abstract

RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCSs) as platforms for the generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes luminal filling of multivesicular bodies (MVBs), CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives the biogenesis of a select RNA-containing EV population.

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References

Lucero R, Zappulli V, Sammarco A, Murillo O, Cheah P, Srinivasan S . Glioma-Derived miRNA-Containing Extracellular Vesicles Induce Angiogenesis by Reprogramming Brain Endothelial Cells. Cell Rep. 2020; 30(7):2065-2074.e4. PMC: 7148092. DOI: 10.1016/j.celrep.2020.01.073. View

Quaresma A, Bressan G, Gava L, Lanza D, Ramos C, Kobarg J . Human hnRNP Q re-localizes to cytoplasmic granules upon PMA, thapsigargin, arsenite and heat-shock treatments. Exp Cell Res. 2009; 315(6):968-80. DOI: 10.1016/j.yexcr.2009.01.012. View

Mantel P, Hjelmqvist D, Walch M, Kharoubi-Hess S, Nilsson S, Ravel D . Infected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria. Nat Commun. 2016; 7:12727. PMC: 5062468. DOI: 10.1038/ncomms12727. View

Maas S, Breakefield X, Weaver A . Extracellular Vesicles: Unique Intercellular Delivery Vehicles. Trends Cell Biol. 2016; 27(3):172-188. PMC: 5318253. DOI: 10.1016/j.tcb.2016.11.003. View

Friedman J, Dibenedetto J, West M, Rowland A, Voeltz G . Endoplasmic reticulum-endosome contact increases as endosomes traffic and mature. Mol Biol Cell. 2013; 24(7):1030-40. PMC: 3608491. DOI: 10.1091/mbc.E12-10-0733. View

Skog J, Wurdinger T, van Rijn S, Meijer D, Gainche L, Sena-Esteves M . Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat Cell Biol. 2008; 10(12):1470-6. PMC: 3423894. DOI: 10.1038/ncb1800. View

Holland W, Summers S . Sphingolipids, insulin resistance, and metabolic disease: new insights from in vivo manipulation of sphingolipid metabolism. Endocr Rev. 2008; 29(4):381-402. PMC: 2528849. DOI: 10.1210/er.2007-0025. View

Ghosh S, Dellibovi-Ragheb T, Kerviel A, Pak E, Qiu Q, Fisher M . β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway. Cell. 2020; 183(6):1520-1535.e14. PMC: 7590812. DOI: 10.1016/j.cell.2020.10.039. View

Stalder L, Heusermann W, Sokol L, Trojer D, Wirz J, Hean J . The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing. EMBO J. 2013; 32(8):1115-27. PMC: 3630355. DOI: 10.1038/emboj.2013.52. View

10.

Santangelo L, Giurato G, Cicchini C, Montaldo C, Mancone C, Tarallo R . The RNA-Binding Protein SYNCRIP Is a Component of the Hepatocyte Exosomal Machinery Controlling MicroRNA Sorting. Cell Rep. 2016; 17(3):799-808. DOI: 10.1016/j.celrep.2016.09.031. View

11.

Fukushima M, Dasgupta D, Mauer A, Kakazu E, Nakao K, Malhi H . StAR-related lipid transfer domain 11 (STARD11)-mediated ceramide transport mediates extracellular vesicle biogenesis. J Biol Chem. 2018; 293(39):15277-15289. PMC: 6166717. DOI: 10.1074/jbc.RA118.002587. View

12.

Pathan M, Fonseka P, Chitti S, Kang T, Sanwlani R, Van Deun J . Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles. Nucleic Acids Res. 2018; 47(D1):D516-D519. PMC: 6323905. DOI: 10.1093/nar/gky1029. View

13.

Hinger S, Cha D, Franklin J, Higginbotham J, Dou Y, Ping J . Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells. Cell Rep. 2018; 25(3):715-725.e4. PMC: 6248336. DOI: 10.1016/j.celrep.2018.09.054. View

14.

Ghamloush F, Ghayad S, Rammal G, Fahs A, Ayoub A, Merabi Z . The PAX3-FOXO1 oncogene alters exosome miRNA content and leads to paracrine effects mediated by exosomal miR-486. Sci Rep. 2019; 9(1):14242. PMC: 6775163. DOI: 10.1038/s41598-019-50592-4. View

15.

Barman B, Bhattacharyya S . mRNA Targeting to Endoplasmic Reticulum Precedes Ago Protein Interaction and MicroRNA (miRNA)-mediated Translation Repression in Mammalian Cells. J Biol Chem. 2015; 290(41):24650-6. PMC: 4598978. DOI: 10.1074/jbc.C115.661868. View

16.

Alpy F, Rousseau A, Schwab Y, Legueux F, Stoll I, Wendling C . STARD3 or STARD3NL and VAP form a novel molecular tether between late endosomes and the ER. J Cell Sci. 2013; 126(Pt 23):5500-12. DOI: 10.1242/jcs.139295. View

17.

Nishimura A, Mitne-Neto M, Silva H, Richieri-Costa A, Middleton S, Cascio D . A mutation in the vesicle-trafficking protein VAPB causes late-onset spinal muscular atrophy and amyotrophic lateral sclerosis. Am J Hum Genet. 2004; 75(5):822-31. PMC: 1182111. DOI: 10.1086/425287. View

18.

Gibbings D, Ciaudo C, Erhardt M, Voinnet O . Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat Cell Biol. 2009; 11(9):1143-9. DOI: 10.1038/ncb1929. View

19.

Lasser C, Shelke G, Yeri A, Kim D, Crescitelli R, Raimondo S . Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing. RNA Biol. 2016; 14(1):58-72. PMC: 5270547. DOI: 10.1080/15476286.2016.1249092. View

20.

Mukherjee K, Ghoshal B, Ghosh S, Chakrabarty Y, Shwetha S, Das S . Reversible HuR-microRNA binding controls extracellular export of miR-122 and augments stress response. EMBO Rep. 2016; 17(8):1184-203. PMC: 4967961. DOI: 10.15252/embr.201541930. View