Publications

For a complete list of publications see:
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Xu R, Simpson RJ and Greening DW (2017) A protocol for isolation and proteomic characterization of distinct extracellular vesicle subtypes by sequential centrifugal ultrafiltration, Methods Mol Biol., 1545: 91-116.

Greening DW, Xu R, Gopal SK, Rai A and Simpson RJ (2017) Proteomic Insights into extracellular vesicle biology – defining exosomes and shed microvesicles, Exp Rev Proteomics, 4(1): 69-95.

Gopal SK, Greening DW, Rai A, Chen M, Xu R, Shafiq A, Mathias RA, Zhu HJ and Simpson RJ (2017) Extracellular vesicles: their role in cancer biology and epithelial-mesenchymal transition, Biochem J., 474(1): 21-45.

Ishikawa H, Yoshikawa H, Izumikawa K, Miura Y, Taoka M, Nobe Y, Yamauchi Y, Nakayama H, Simpson RJ, Isobe T and Nobuhiro T (2016) Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells, Nucleic Acids Res., 45(6): 3437-47.

Izumikawa K, Yoshikawa H, Ishikawa H, Nobe Y, Yamauchi Y, Philipsen S, Simpson RJ, Isobe T and Takahashi N (2016) Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA, Nucleic Acids Res., 44(20): 9847-59.

Khondee P, Srisomsap C, Chokchaichamnankit D, Svasti J, Simpson RJ and Kingtong S (2016) Histopathological effect and stress response of mantle proteome following TBT exposure in the Hooded oyster Saccostrea cucullata, Environ Pollut., 218: 855-62.

Chen M, Xu R, Ji H, Greening DW, Rai A, Izumikawa K, Ishikawa H, Takahashi N and Simpson RJ (2016) Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line, Sci Rep., 6: 38397.

Nguyen HPT, Simpson RJ, Salamonsen LA and Greening DW (2016) Extracellular vesicles in the intrauterine environment: challenges and potential functions, Biol Reprod., 95(5): 109.

Greening DW, Ji H, Chen M, Robinson BWS, Dick IM, Creaney J and Simpson RJ (2016) Primary human malignant mesothelioma exosome signature reflects oncogenic cargo, Sci Rep., 6: 32643.

Gopal SK, Greening DW, Zhu HJ, Simpson RJ and Mathias RA (2016) Transformed MDCK cells secrete elevated MMP1 that generates LAMA5 fragments promoting endothelial cell angiogenesis, Sci Rep., 6: 28321

Nguyen HPT, Simpson RJ, Salamonsen LA and Greening DW (2016) Extracellular vesicles in the intrauterine environment: challenges and potential functions, Biol Reprod., Sep 21. pii: biolreprod.116.143503.

Greening DW, Nguyen HP, Evans J, Simpson RJ and Salamonsen LA (2016) Modulating the endometrial epithelial proteome and secretome in preparation for pregnancy: the role of ovarian steroid and pregnancy hormones, J Proteomics, doi: 10.1016/j.jprot.2016.05.026.

Xu R, Greening DW, Takahashi N, Zhu HJ and Simpson RJ (2016) Extracellular vesicle isolation and characterization: toward clinical application, J Clin Invest., 126(4): 1152-62.

Greening DW, Nguyen H, Elgass K, Simpson RJ and Salamonsen LA (2016) Human endometrial exosomes contain hormone-specific cargo modulating trophoblast adhesive capacity: insights into endometrial-embryo interactions, Biol Repro., 94(2): 38, 1-15.

Gopal SK, Greening DW, Hanssen EG, Zhu HJ, Simpson RJ and Mathias RA (2016) Oncogenic epithelial cell-derived exosomes containing Rac1 and PAK2 induce angiogenesis in recipient endothelial cells, Oncotarget, doi: 10.18632/oncotarget.7573.

Carrasco-Ramírez P, Greening DW, Andrés G, Gopal SK, Martín-Villar E, Renart J, Simpson RJ and Quintanilla M (2016) Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation, Oncotarget, 7(13): 16070-89.

Sato S, Ishikawa H, Yoshikawa H, Izumikawa K, Simpson RJ, Takahashi N (2015) Collaborator of alternative reading frame protein (CARF) regulates early processing of pre-ribosomal RNA by retaining XRN2 (5'-3' exoribonuclease) in the nucleoplasm, Nucleic Acids Res., 43(21): 10397-410.

Greening DW, Lee ST, Ji H, Simpson RJ, Rigopoulos A, Murone C, Fang C, Gong S, O'Keefe G and Scott A (2015) Molecular profiling of cetuximab and bevacizumab treatment of colorectal tumours reveals perturbations in metabolic and hypoxic response pathways, Oncotarget, 6(35): 38166-80.

Kim DK, Lee J, Simpson RJ, Lötvall J and Gho YS (2015) EVpedia: A community web resource for prokaryotic and eukaryotic extracellular vesicles research, Semin Cell Dev Biol., 40: 4-7.

Luwor RB, Hakmana D, Iaria J, Nheu TV, Simpson RJ and Zhu HJ (2015) Single live cell TGF-β signalling imaging: breast cancer cell motility and migration is driven by sub-populations of cells with dynamic TGF-β-Smad3 activity, Mol Cancer, 14:50, doi: 10.1186/s12943-015-0309-1.

Greening DW, Gopal SK, Mathias RA, Liu L, Sheng J, Zhu HJ and Simpson RJ (2015) Emerging roles of exosomes during epithelial-mesenchymal transition and cancer progression, Sem Cell Dev Biol., 40:  60-71.

Greening DW, Gopal SK, Xu R, Simpson RJ and Chen W (2015) Exosomes and their roles in immune regulation and cancer, Sem Cell Dev Biol., 40: 72-81.

Greening DW, Xu R, Ji H, Tauro BJ and Simpson RJ (2015) A protocol for exosome isolation and characterisation: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods, Methods Mol Biol., 1295: 179-209.

Gopal SK, Greening DW, Mathias RA, Ji H, Rai A, Chen M, Zhu HJ and Simpson RJ (2015) YBX1/YB-1 induces partial EMT and tumourigenicity through secretion of angiogenic factors into the extracellular microenvironment, Oncotarget., 6(15): 13718-30.

Xu R, Greening DW, Rai A, Ji H and Simpson RJ (2015) Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct, Methods, pii: dS1046-2023(15)00154-1.

Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill A, Stroud DA, Ryan MT, Agbinya JI, Mariadasson JM, Burgess AW and Mathivanan S (2015) FunRich: an open access standalone functional enrichment and interaction network analysis tool Proteomics, 15(15): 2597-601.

Simpson RJ (2015) Editorial, Sem Cell Dev Biol., 40: 1-3.

Yoshikawa H, Ishikawa H, Izumikawa K, Miura Y, Hayano T, Isobe T, Simpson RJ and Takahashi N (2015) Human nucleolar protein Nop52 (RRP1/NNP-1) is involved in site 2 cleavage in internal transcribed spacer 1 of pre-rRNAs at early stages of ribosome biogenesis, Nucleic Acids Res., doi: 10.1093/nar/gkv470.

Feng J, He W, Song Y, Wang Y, Simpson RJ, Zhang X, Luo G, Wu J and Huang C (2014) Platelet-derived growth factor receptor beta: a novel urinary biomarker for recurrence of non-muscle-invasive bladder cancer, PLoS One, 9: e96671.

He W, Kuang Y, Xing X, Simpson RJ, Huang H, Yang T, Chen J, Yang L, Liu E, He W and Gu J (2014) Proteomic comparison of 3D and 2D glioma models reveals increased HLA-E expression in 3D models is associated with resistance to NK cell-mediated cytotoxicity, J Proteome Res., 13(5): 2272-81.

Ji H, Chen M, Greening DW, He W, Rai A, Zhang W and Simpson RJ (2014) Deep sequencing of RNA from three different extracellular vesicle (EV) subtypes released from the human LIM1863 colon cancer cell line uncovers distinct miRNA-enrichment signatures, PLoS One, 9: e110314.

Kim DK, Lee J, Kim SR, Choi DS, Yoon YJ, Kim JH, Go G, Nhung D, Hong K, Jang SC, Kim SH, Park KS, Kim OY, Park HT, Seo JH, Aikawa E, Baj-Krzyworzeka M, Van Balkom BW, Belting M, Blanc L, Bond V, Bongiovanni A, Borràs FE, Buée L, Buzás EI, Cheng L, Clayton A, Cocucci E, Dela Cruz CS, Desiderio DM, Di Vizio D, Ekström K, Falcon-Perez JM, Gardiner C, Giebel B, Greening DW, Gross JC, Gupta D, Hendrix A, Hill AF, Hill MM, Hoen EN, Hwang DW, Inal J, Jagannadham MV, Jayachandran M, Jee YK, Jørgensen M, Kim KP, Kim YK, Kislinger T, Lässer C, Lee DS, Lee H, Van Leeuwen J, Lener T, Liu ML, Lötvall J, Marcilla A, Mathivanan S, Möller A, Morhayim J, Mullier F, Nazarenko I, N ieuwland R, Nunes DN, Pang K, Park J, Patel T, Pocsfalvi G, Del Portillo H, Putz U, Ramirez MI, Rodrigues ML, Roh TY, Royo F, Sahoo S, Schiffelers R, Sharma S, Siljander P, Simpson RJ, Soekmadji C, Stahl P, Stensballe A, Stępień E, Tahara H, Trummer A, Valadi H, Vella LJ, Wai SN, Witwer K, Yáñez-Mó M, Youn H, Zeidler R and Gho YS (2015) EVpedia as a resource for extracellular vesicles biology, Bioinformatics, 31(6): 933-39.

Nanjappa V, Thomas JK, Marimuthu A, Muthusamy B, Radhakrishnan A, Sharma R, Khan AA, Balakrishnan L, Sahasrabuddhe N, Kumar S, Jhaveri BN, Sheth KV, Khatana RK, Shaw PG, Srikanth SM, Mathur PP, Shankar S, Nagaraja D, Christopher R, Mathivanan S, Raju R, Sirdeshmukh R, Chatterjee A, Simpson RJ, Harsha HC, Pandey A and Prasad TSK (2014) Plasma Proteome Database as a resource for proteomics research: 2014 update, Nucleic Acids Res., doi: 10.1093/nar/gkt1251.

Bernhard OK, Greening DW, Barnes TW, Ji H and Simpson RJ (2013) Detection of cadherin-17 in human colon cancer LIM1215 cell secretome and tumour xenograft-derived interstitial fluid and plasma, Biochim Biophys Acta, 1834(11): 2372-79.

Fanayan S, Smith JT, Sethi MK, Cantor D, Goode R, Simpson RJ, Baker MS, Hancock WS and Nice E (2013) Chromosome 7-centric analysis of proteomics data from a panel of human colon carcinoma cell lines, J Proteome Res., 12(1): 89-96.

Greening DW, Ji H, Kapp EA and Simpson RJ (2013) Sulindac modulates secreted protein expression from LIM1215 colon carcinoma cells prior to apoptosis, Biochim Biophys Acta, 1834(11): 2293-307.

Greening DW, Kapp EA, Ji H, Speed TP and Simpson RJ (2013) Colon tumour secretopeptidome: insights into endogenous proteolytic cleavage events in the colon tumour microenvironment, Biochim Biophys Acta, 1834(11): 2396-407.

Greening DW and Simpson RJ (2013) An updated secretome, Biochim Biophys Acta, 1834(11): 2225.

Ji H, Greening DW, Barnes TW, Lim JW, Tauro BJ, Rai A, Xu R, Adda C, Mathivanan S, Zhao W, Xue Y, Xu T, Zhu HJ and Simpson RJ (2013) Proteome profiling of exosomes derived from human primary and metastatic colorectal cells reveal differential expression of key metastatic factors and signal transduction components, Proteomics, 13(10-11): 1672-86.

Kalra H, Adda CG, Liem M, Ang CS, Mechler A, Simpson RJ, Hulett MD and Mathivanan S (2013) Comparative proteomics evaluation of plasma exosome isolation techniques and assessment of the stability of exosomes in normal human blood plasma, Proteomics, 13(22): 3354-64.

Lee ST, Ji H, Greening DW, Speirs RW, Rigopoulos A, Pillay V, Murone C, Vitali A, Stuhler K, Johns TG, Corner GA, Mariadason JM, Simpson RJ and Scott AM (2013) Global protein profiling reveals anti-EGFR monoclonal antibody 806-modulated proteins in A431 tumor xenografts, Growth Factors, 31(5): 154-64.

Mathias RA, Gopal SK and Simpson RJ (2013) Contribution of cells undergoing epithelial-mesenchymal transition to the tumour microenvironment, J Proteomics, 78: 545-57.

Mercier SK, Donaghy H, Botting RA, Turville SG, Harman AN, Nasr N, Ji H, Kusebauch U, Mendoza L, Shteynberg D, Sandgren K, Simpson RJ, Moritz RL and Cunningham AL (2013) The microvesicle component of HIV-1 inocula modulates dendritic cell infection and maturation and enhances adhesion to and activation of T lymphocytes, PLoS Pathog., 9: e1003700.

Tauro BJ, Greening DW, Mathias RA, Mathivanan S, Ji H and Simpson RJ (2013) Two distinct populations of exosomes are released from LIM1863 colon carcinoma cell-derived organoids, Mol Cell Proteomics, 12(3): 587-98.

Tauro BJ, Mathias RA, Greening DW, Gopal SK, Ji H, Kapp EA, Coleman BM, Hill AF, Kusebauch U, Hallows JL, Shteynberg D, Moritz RL, Zhu HJ and Simpson RJ (2013) Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition, Mol Cell Proteomics, 12(8): 2148-59.

Fhaner CJ, Liu S, Ji H, Simpson RJ and Reid GE (2012) Comprehensive lipidome profiling of isogenic primary and metastatic colon adenocarcinoma cell lines, Anal Chem., 84(21): 8917-26.

Kalra H, Simpson RJ, Ji H, Aikawa E, Altevogt P, Askenase P, Bond VC, Borras FE, Breakefield X, Budnik V, Buzas E, Camussi G, Clayton A, Cocucci E, Falcon-Perez JM, Gabrielsson S, Gho YS, Gupta D, Harsha HC, Hendrix A, Hill AF, Inal JM, Jenster G, Kramer-Albers EM, Lim SK, Llorente A, Lotvall J, Marcilla A, Mincheva-Nilsson L, Nazarenko I, Nieuwland R, Nolte-'t Hoen EN, Pandey A, Patel T, Piper MG, Pluchino S, Prasad TS, Rajendran L, Raposo G, Record M, Reid GE, Sanchez-Madrid F, Schiffelers RM, Siljander P, Stensballe A, Stoorvogel W, Taylor D, Thery C, Valadi H, van Balkom BW, Vazquez J, Vidal M, Wauben MH, Yanez-Mo M, Zoeller M and Mathivanan S (2012) Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation, PLoS Biol., 10: e1001450.

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR and Rodriguez H (2012) Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles), J Proteome Res., 11(2): 1412-19.

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR and Rodriguez H (2012) Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles), Proteomics, 12(1): 11-20.

Layton MJ, Church NL, Faux MC, Ji H, Goode RJ, Kapp EA, Burgess AW and Simpson RJ (2012) Solubilisation of the armadillo-repeat protein beta-catenin using a zwitterionic detergent allows resolution of phosphorylated forms by 2DE, Electrophoresis, 33(12): 1804-13.

Layton MJ, Faux MC, Church NL, Catimel B, Kershaw NJ, Kapp EA, Nowell C, Coates JL, Burgess AW and Simpson RJ (2012) Identification of a Wnt-induced protein complex by affinity proteomics using an antibody that recognizes a sub-population of beta-catenin, Biochim Biophys Acta, 1824(7): 925-37.

Lim JW, Mathias RA, Kapp EA, Layton MJ, Faux MC, Burgess AW, Ji H and Simpson RJ (2012) Restoration of full-length APC protein in SW480 colon cancer cells induces exosome-mediated secretion of DKK-4, Electrophoresis, 33(12): 1873-80.

Mathivanan S, Fahner CJ, Reid GE and Simpson RJ (2012) ExoCarta 2012: database of exosomal proteins, RNA and lipids, Nucleic Acids Res., 40: D1241-44.

Mathias RA, Ji H and Simpson RJ (2012) Proteomic profiling of the epithelial-mesenchymal transition using 2D DIGE, Methods Mol Biol., 854: 269-86.

Mathivanan S, Ji H, Tauro BJ, Chen YS and Simpson RJ (2012) Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry, J Proteomics, 76: 141-49.

Nicholls C, Pinto AR, Li H, Li L, Wang L, Simpson RJ and Liu JP (2012) Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) induces cancer cell senescence by interacting with telomerase RNA component, Proc Natl Acad Sci USA, 109(33): 13308-13.

Simpson RJ, Kalra H and Mathivanan S (2012) ExoCarta as a resource for exosomal research, J Extracell Vesicles, 1: 10.3402/jev.v1i0.18374.

Tauro BJ, Greening DW, Mathias RA, Ji H, Mathivavan S, Scott AM and Simpson RJ (2012) Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes, Methods, 56(2): 293-304.

Xu Z, He Y, Ju J, Rank G, Cerruti L, Ma C, Simpson RJ, Moritz RL, Jane SM and Zhao Q (2012) The role of WDR5 in silencing human fetal globin gene expression, Haematologica, 97(11): 1632-40.

Bernhard OK, Mathias RA, Barnes TW and Simpson RJ (2011) A fluorescent microsphere-based method for assay of multiple analytes in plasma, Methods Mol Biol., 728: 195-206.

Breakefield XO, Frederickson RM and Simpson RJ (2011) Gesicles: Microvesicle "cookies" for transient information transfer between cells, Mol Ther., 19(9): 1574-76.

Chen Y, Mathias RA, Mathivanan S, Kapp EA, Moritz RL, Zhu H and Simpson RJ (2011) Proteomic profiling of MDCK plasma membranes reveals Wnt-5a involvement during oncogenic H-Ras/TGF-β-mediated epithelial-mesenchymal transition, Mol Cell Proteomics, 10(2): M110.001131.

Gorman MA, Uboldi AD, Walsh PJ, Tan KS, Hansen G, Huyton T, Ji H, Curtis J, Kedzierski L, Papenfuss AT, Dogovski C, Perugini MA, Simpson RJ, Handman E and Parker MW (2011) Crystal structure of the Leishmania major MIX protein: a scaffold protein that mediates protein-protein interactions, Protein Sci., 20(6): 1060-68.

Greening DW and Simpson RJ (2011) Low-molecular weight plasma proteome analysis using centrifugal ultrafiltration, Methods Mol Biol., 728: 109-24.

Greening DW, Sparrow RL and Simpson RJ (2011) Preparation of platelet concentrates, Methods Mol Biol., 728, 267-278.

Ji H, Goode RJ, Vaillant F, Mathivanan S, Kapp EA, Mathias RA, Lindeman GJ, Visvader JE and Simpson RJ (2011) Proteomic profiling of secretome and adherent plasma membranes from distinct mammary epithelial cell subpopulations, Proteomics, 11(20): 4029-39.

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR and Rodriguez H (2011) Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles), Proteomics Clin Appl., 5(11-12): 580-89.

Mathias RA, Chen YS, Goode RJ, Kapp EA, Mathivanan S, Moritz RL, Zhu HJ and Simpson RJ (2011) Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: towards developing an MDCK protein database, Proteomics, 11(7): 1238-53.

Mathias RA, Chen Y, Kapp EA, Greening DW, Mathivanan S and Simpson RJ (2011) Triton X-114 phase separation in the isolation and purification of mouse liver microsomal membrane proteins, Methods, 54(4): 396-406.

Sakthianandeswaren A, Christie M, D'Andreti C, Tsui C, Jorissen RN, Li S, Fleming NI, Gibbs P, Lipton L, Malaterre J, Ramsay RG, Phesse TJ, Ernst M, Jeffery RE, Poulsom R, Leedham SJ, Segditsas S, Tomlinson IP, Bernhard OK, Simpson RJ, Walker F, Faux MC, Church N, Catimel B, Flanagan DJ, Vincan E and  Sieber OM (2011) PHLDA1 expression marks the putative epithelial stem cells and contributes to intestinal tumorigenesis, Cancer Res., 71(10): 3709-19.

Sparrow RL, Greening DW and Simpson RJ (2011) A protocol for the preparation of cryoprecipitate and cryodepleted plasma, Methods Mol Biol., 728: 259-65.