Czechowska, K, Lannigan, J, Wang, L, Arcidiacono, J, Ashhurst, TM, Barnard, RM, Bauer, S, Bispo, C, Bonilla, DL, Brinkman, RR, Cabanski, M, Chang, H-D, Chakrabarti, L, Chojnowski, G, Cotleur, B, Degheidy, H, Dela Cruz, GV, Eck, S, Elliott, J, Errington, R, Filby, A, Gagnon, D, Gardner, R, Green, C, Gregory, M, Groves, CJ, Hall, C, Hammes, F, Hedrick, M, Hoffman, R, Icha, J, Ivaska, J, Jenner, DC, Jones, D, Kerckhof, F-M, Kukat, C, Lanham, D, Leavesley, S, Lee, M, Lin-Gibson, S, Litwin, V, Liu, Y, Molloy, J, Moore, JS, Müller, S, Nedbal, J, Niesner, R, Nitta, N, Ohlsson-Wilhelm, B, Paul, NE, Perfetto, S, Portat, Z, Props, R, Radtke, S, Rayanki, R, Rieger, A, Rogers, S, Rubbens, P, Salomon, R, Schiemann, M, Sharpe, J, Sonder, SU, Stewart, JJ, Sun, Y, Ulrich, H, Van Isterdael, G, Vitaliti, A, van Vreden, C, Weber, M, Zimmermann, J, Vacca, G, Wallace, P & Tárnok, A 2019, 'Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.', Cytometry. Part A : the journal of the International Society for Analytical Cytology, vol. 95, no. 6, pp. 598-644.View/Download from: UTS OPUS or Publisher's site
Salomon, R, Kaczorowski, D, Valdes-Mora, F, Nordon, RE, Neild, A, Farbehi, N, Bartonicek, N & Gallego-Ortega, D 2019, 'Droplet-based single cell RNAseq tools: a practical guide.', Lab on a chip, vol. 19, no. 10, pp. 1706-1727.View/Download from: UTS OPUS or Publisher's site
Droplet based scRNA-seq systems such as Drop-seq, inDrop and Chromium 10X have been the catalyst for the wide adoption of high-throughput scRNA-seq technologies in the research laboratory. In order to understand the capabilities of these systems to deeply interrogate biology; here we provide a practical guide through all the steps involved in a typical scRNA-seq experiment. Through comparing and contrasting these three main droplet based systems (and their derivatives), we provide an overview of all critical considerations in obtaining high quality and biologically relevant data. We also discuss the limitations of these systems and how they fit into the emerging field of Genomic Cytometry.
Valdes-Mora, F, Salomon, R, Gloss, B, Law, AMK, Murphy, K, Roden, D, Castillo, L, Colino-Sanguino, Y, Kikhtyak, Z, Farbehi, N, Conway, JRW, Oakes, S, Sikta, N, O’Donoghue, S, Cox, T, Timpson, P, Ormandy, C & Gallego-Ortega, D 2019, 'Single-cell RNAseq uncovers involution mimicry as an aberrant development pathway during breast cancer metastasis'.View/Download from: Publisher's site
Summary Both luminal and basal breast cancer subtypes originate in the mammary luminal progenitor cell compartment. Basal breast cancer is associated with younger age, early relapse, and high mortality rate. Here we used unbiased droplet-based single-cell RNAseq to elucidate the cellular basis of tumour progression during the specification of the basal breast cancer subtype from the luminal progenitor population. Basal–like cancer cells resembled the alveolar lineage that is specified upon pregnancy and showed molecular features indicative of an interaction with the tumour microenvironment (TME) including EMT, hypoxia, lactation and involution. Involution signatures in luminal breast cancer tumours with alveolar lineage features were associated with worse prognosis and features of basal breast cancer. Our high-resolution molecular characterisation of the tumour ecosystem also revealed a highly interactive cell-cell network reminiscent of an involution process. This involution mimicry involves malignant education of cancer-associated fibroblasts and myeloid cell recruitment to support tissue remodelling and sustained inflammation. Our study shows how luminal breast cancer acquires a post-lactation developmental program to shift molecular subtype and promote tumour progression, with potential to explain the increased risk of cancer during the post-partum period.
Valdes-Mora, F, Handler, K, Law, AMK, Salomon, R, Oakes, SR, Ormandy, CJ & Gallego-Ortega, D 2018, 'Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology', FRONTIERS IN IMMUNOLOGY, vol. 9.View/Download from: Publisher's site
Barsky, LW, Black, M, Cochran, M, Daniel, BJ, Davies, D, DeLay, M, Gardner, R, Gregory, M, Kunkel, D, Lannigan, J, Marvin, J, Salomon, R, Torres, C & Walker, R 2016, 'International Society for Advancement of Cytometry (ISAC) Flow Cytometry Shared Resource Laboratory (SRL) Best Practices', CYTOMETRY PART A, vol. 89A, no. 11, pp. 1017-1030.View/Download from: Publisher's site
Gallego-Ortega, D, Ledger, A, Roden, DL, Law, AMK, Magenau, A, Kikhtyak, Z, Cho, C, Allerdice, SL, Lee, HJ, Valdes-Mora, F, Herrmann, D, Salomon, R, Young, AIJ, Lee, BY, Sergio, CM, Kaplan, W, Piggin, C, Conway, JRW, Rabinovich, B, Millar, EKA, Oakes, SR, Chtanova, T, Swarbrick, A, Naylor, MJ, O'Toole, S, Green, AR, Timpson, P, Gee, JMW, Ellis, IO, Clark, SJ & Ormandy, CJ 2015, 'ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+CD11b+Myeloid-Derived Suppressor Cells', PLOS BIOLOGY, vol. 13, no. 12.View/Download from: Publisher's site
Burke, CM, Liu, MY, Britton, WJ, Triccas, JA, Thomas, T, Smith, A, Allen, S, Salomon, R & Harry, L 2013, 'Harnessing Single Cell Sorting To Identify Cell Division Genes And Regulators In Bacteria', Plos One, vol. 8, no. 4, pp. 1-13.View/Download from: UTS OPUS or Publisher's site
Cell division is an essential cellular process that requires an array of known and unknown proteins for its spatial and temporal regulation. Here we develop a novel, high-throughput screening method for the identification of bacterial cell division genes and regulators. The method combines the over-expression of a shotgun genomic expression library to perturb the cell division process with high-throughput flow cytometry sorting to screen many thousands of clones. Using this approach, we recovered clones with a filamentous morphology for the model bacterium, Escherichia coli. Genetic analysis revealed that our screen identified both known cell division genes, and genes that have not previously been identified to be involved in cell division. This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development.
Min, D, Brooks, B, Wong, J, Salomon, R, Bao, W, Harrisberg, B, Twigg, SM, Yue, DK & McLennan, SV 2012, 'Alterations in Monocyte CD16 in Association with Diabetes Complications', MEDIATORS OF INFLAMMATION.View/Download from: Publisher's site
Richards, A, McGeechan, K, Niknam, M, Salomon, R, Kurek, C, Dong, Q & Patel, MI 2009, 'Prolonging androgen sensitivity in prostate cancer - a role for COX inhibitors?', ANZ JOURNAL OF SURGERY, vol. 79, no. 9, pp. 641-647.View/Download from: Publisher's site
Gallego-Ortega, D, Ledger, A, Roden, D, Cho, C, Allerdice, SL, Lee, HJ, Valdes-Mora, F, Lee, B, Kaplan, W, Salomon, R, Piggin, C, Rabinovich, B, Millar, E, Chtanova, T, Swarbrick, A, Clark, SJ & Ormandy, CJ 2015, 'The ETS transcription factor Elf5 drives metastasis via angiogenesis and recruitment of Gr-1+CD11b+myeloid derived suppressor cells in luminal breast cancer', CLINICAL & EXPERIMENTAL METASTASIS, SPRINGER, pp. 203-203.
Ortega, DG, Ledger, A, Roden, D, Cho, C, Allerdice, S, Lee, H, Valdes-Mora, F, Salomon, R, Oakes, S & Ormandy, C 2014, 'THE ETS TRANSCRIPTION FACTOR ELF5 IS A KEY DETERMINANT OF THE LETHAL PHENOTYPE IN LUMINAL BREAST CANCER, DRIVING THE ACQUISITION OF ANTIESTROGEN RESISTANCE AND METASTATIC ACTIVITY', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 16-17.
Min, D, Brooks, B, Wong, J, Salomon, R, Bao, W, Harrisberg, B, Twigg, SM, Yue, DK & Mclennan, SV 2012, 'Alterations in Monocyte Surface Markers in Diabetes Complications', DIABETES, 72nd Scientific Sessions of the American-Diabetes-Association, AMER DIABETES ASSOC, Philadelphia, PA, pp. A120-A121.