Publications

For a complete list of publications see:
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Chen M, Xu R, Rai A, Suwakulsiri W, Izumikawa K, Ishikawa H, Greening DW, Takahashi N and Simpson RJ (2019) Distinct shed microvesicle and exosome microRNA signatures reveal diagnostic markers for colorectal cancerPLoS One, 14(1): e0210003.

Simpson RJ and Greening DW (2019) Special Issue on Extracellular Vesicles and Exosomes, Proteomics, 19(1-2): e1800434.

Rai A, Greening DW, Chen M, Xu R, Ji H and Simpson RJ (2019) Exosomes Derived from Human Primary and Metastatic Colorectal Cancer Cells Contribute to Functional Heterogeneity of Activated Fibroblasts by Reprogramming Their ProteomeProteomics, doi: 10.1002/pmic.201800148.

Liu SIaria J, Simpson RJ and Zhu H-J (2018) Ras enhances TGF-β signaling by decreasing cellular protein levels of its type II receptor negative regulator SPSB1, Cell Communication and Signaling, 16(1): 10.

Izumikawa K, Ishikawa H, Simpson RJ and Takahashi N (2018) Modulating the expression of Chtop, a versatile regulator of gene-specific transcription and mRNA export, RNA Biology, 15(7): 849-855.

Rooney BV, Bigley AB, LaVoy EC, Laughlin M, Pedlar C and Simpson RJ (2018) Lymphocytes and monocytes egress peripheral blood within minutes after cessation of steady state exercise: A detailed temporal analysis of leukocyte extravasation, Physiology and Behavior, 194: 260-267.

Jansson KH, Tucker JB, Stahl LE, Simmons JK, Fuller C, Beshiri ML, Agarwal S, Fang L, Hynes PG, Alilin AN, Lake R, Abbey YC, Cawley J, Tice CM, Yin J, McKnight C, Klummp-Thomas C, Zhang X, Guha R, Hoover S, Simpson RM, Nguyen HM, Corey E, Thomas CJ, Proia DA and Kelly K (2018) High-throughput screens identify HSP90 inhibitors as potent therapeutics that target inter-related growth and survival pathways in advanced prostate cancer, Scientific Reports, 8: 17239.

Kunz HE, Spielmann G, Agha NH, O'Connor DP, Bollard CM and Simpson RJ (2018) A single exercise bout augments adenovirus-specific T-cell mobilization and function, Physiology and Behavior, 194: 56-65.

Suwakulsiri W, Rai A, Xu R, Chen M, Greening DW and Simpson RJ (2018) Proteomic profiling reveals key cancer progression modulators in shed microvesicles released from isogenic human primary and metastatic colorectal cancer cell lines, Biochim Biophys Acta Proteins Proteom, pii: S1570-9639(18)30206-1.

Greening DW and Simpson RJ (2018) Understanding extracellular vesicle diversity - current statusExpert Rev Proteomics, 15(11): 887-910.

Xu R, Rai A, Chen M, Suwakulsiri W, Greening DW and Simpson RJ (2018) Extracellular vesicles in cancer — implications for future improvements in cancer care, Nature Reviews Clinical Oncology, 15: 617-638.

Ishikawa H, Nobe Y, Izumikawa K, Taoka M, Yamauchi Y, Nakayama H, Simpson RJ, Isobe T and Takahash N (2018) Truncated forms of U2 snRNA (U2-tfs) are shunted toward a novel uridylylation pathway that differs from the degradation pathway for U1-tfs, RNA Biol., 15(2): 261-268.

Greening DW, Kapp EA and Simpson RJ (2017) The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome, Enzymes, 42: 27-64.

Izumikawa K, Nobe Y, Yoshikawa H, Ishikawa H, Miura Y, Nakayama H, Nonaka T, Hasegawa M, Egawa N, Inoue H, Nishikawa K, Yamano K, Simpson RJ, Taoka M, Yamauchi Y, Isobe T and Takahashi N (2017) TDP-43 stabilises the processing intermediates of mitochondrial transcripts, Sci Rep., 7(1): 7709.

Belov L, Hallal S, Matic K, Zhou J, Wissmueller S, Ahmed N, Tanjil S, Mulligan SP, Best OG, Simpson RJ and Christopherson RI (2017) Surface Profiling of Extracellular Vesicles from Plasma or Ascites Fluid Using DotScan Antibody Microarrays, Methods Mol Biol., 1619: 263-301.

Simpson RJ (2017) Extracellular vesicles, Semin Cell Dev Biol., 67: 1-2.

Greening DW and Simpson RJ (2017) Characterization of the Low-Molecular-Weight Human Plasma Peptidome, Methods Mol Biol., 1619: 63-79.

Greening DW, Simpson RJ and Sparrow RL (2017) Preparation of Platelet Concentrates for Research and Transfusion Purposes, Methods Mol Biol., 1619: 31-42.

Sparrow RL, Simpson RJ and Greening DW (2017) A Protocol for the Preparation of Cryoprecipitate and Cryo-depleted Plasma for Proteomic Studies, Methods Mol Biol., 1619: 23-30.

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, 14(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, Nieuwland 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.