Chiu, SK, Orive, SL, Moon, MJ, Saw, J, Ellis, S, Kile, BT, Huang, Y, Chacon, D, Pimanda, JE, Beck, D, Hamilton, JR, Tremblay, CS & Curtis, DJ 2019, 'Shared roles for Scl and Lyl1 in murine platelet production and function.', Blood.View/Download from: Publisher's site
The Stem Cell Leukemia (Scl or Tal1) protein forms part of a multimeric transcription factor complex required for normal megakaryopoiesis. However, unlike other members of this complex such as Gata1, Fli1 and Runx1, mutations of Scl have not been observed as a cause of inherited thrombocytopenia. We postulated that functional redundancy with its closely related family member, Lymphoblastic Leukemia 1 (Lyl1) might explain this observation. To determine if Lyl1 can substitute for Scl in megakaryopoiesis, we examined the platelet phenotype of mice lacking one or both factors in megakaryocytes. Conditional Scl knockout mice crossed with transgenic mice expressing Cre recombinase under the control of the mouse platelet factor 4 (Pf4) promoter generated megakaryocytes with markedly reduced but not absent Scl. These Pf4SclcKO mice had mild thrombocytopenia and subtle defects in platelet aggregation. However, Pf4SclcKO mice generated on a Lyl1-null background (double knockout, DKO mice) had severe macrothrombocytopenia, abnormal megakaryocyte morphology, defective pro-platelet formation and markedly impaired platelet aggregation. DKO megakaryocytes, but not single knockouts, had reduced expression of Gata1, Fli1, Nfe2 and many other genes that cause inherited thrombocytopenia. These gene expression changes were significantly associated with shared Scl and Lyl1 E-box binding sites that were also enriched for Gata1, Ets and Runx1 motifs. Thus, Scl and Lyl1 share functional roles in platelet production and function by regulating expression of partner proteins including Gata1. We propose that this functional redundancy provides one explanation for the absence of Scl and Lyl1 mutations in inherited thrombocytopenia.
Guo, D, Lui, GYL, Lai, SL, Wilmott, JS, Tikoo, S, Jackett, LA, Quek, C, Brown, DL, Sharp, DM, Kwan, RYQ, Chacon, D, Wong, JH, Beck, D, van Geldermalsen, M, Holst, J, Thompson, JF, Mann, GJ, Scolyer, RA, Stow, JL, Weninger, W, Haass, NK & Beaumont, KA 2019, 'RAB27A promotes melanoma cell invasion and metastasis via regulation of pro-invasive exosomes.', International journal of cancer.View/Download from: UTS OPUS or Publisher's site
Despite recent advances in targeted and immune-based therapies, advanced stage melanoma remains a clinical challenge with a poor prognosis. Understanding the genes and cellular processes that drive progression and metastasis is critical for identifying new therapeutic strategies. Here, we found that the GTPase RAB27A was overexpressed in a subset of melanomas, which correlated with poor patient survival. Loss of RAB27A expression in melanoma cell lines inhibited 3D spheroid invasion and cell motility in vitro, and spontaneous metastasis in vivo. The reduced invasion phenotype was rescued by RAB27A-replete exosomes, but not RAB27A-knockdown exosomes, indicating that RAB27A is responsible for the generation of pro-invasive exosomes. Furthermore, while RAB27A loss did not alter the number of exosomes secreted, it did change exosome size and altered the composition and abundance of exosomal proteins, some of which are known to regulate cancer cell movement. Our data suggest that RAB27A promotes the biogenesis of a distinct pro-invasive exosome population. These findings support RAB27A as a key cancer regulator, as well as a potential prognostic marker and therapeutic target in melanoma.
Beck, D, Thoms, JAI, Palu, C, Herold, T, Shah, A, Olivier, J, Boelen, L, Huang, Y, Chacon, D, Brown, A, Babic, M, Hahn, C, Perugini, M, Zhou, X, Huntly, BJ, Schwarzer, A, Klusmann, J-H, Berdel, WE, Wörmann, B, Büchner, T, Hiddemann, W, Bohlander, SK, To, LB, Scott, HS, Lewis, ID, D'Andrea, RJ, Wong, JWH & Pimanda, JE 2018, 'A four-gene LincRNA expression signature predicts risk in multiple cohorts of acute myeloid leukemia patients.', Leukemia, vol. 32, no. 2, pp. 263-272.View/Download from: UTS OPUS or Publisher's site
Prognostic gene expression signatures have been proposed as clinical tools to clarify therapeutic options in acute myeloid leukemia (AML). However, these signatures rely on measuring large numbers of genes and often perform poorly when applied to independent cohorts or those with older patients. Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of cell identity and oncogenesis, but knowledge of their utility as prognostic markers in AML is limited. Here we analyze transcriptomic data from multiple cohorts of clinically annotated AML patients and report that (i) microarrays designed for coding gene expression can be repurposed to yield robust lincRNA expression data, (ii) some lincRNA genes are located in close proximity to hematopoietic coding genes and show strong expression correlations in AML, (iii) lincRNA gene expression patterns distinguish cytogenetic and molecular subtypes of AML, (iv) lincRNA signatures composed of three or four genes are independent predictors of clinical outcome and further dichotomize survival in European Leukemia Net (ELN) risk groups and (v) an analytical tool based on logistic regression analysis of quantitative PCR measurement of four lincRNA genes (LINC4) can be used to determine risk in AML.
Chacon, D, Beck, D, Perera, D, Wong, JW & Pimanda, JE 2014, 'BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells.', Nucleic Acids Research, vol. 42, no. D1, pp. D172-D177.View/Download from: UTS OPUS or Publisher's site
The BloodChIP database (http://www.med.unsw.edu.au/CRCWeb.nsf/page/BloodChIP) supports exploration and visualization of combinatorial transcription factor (TF) binding at a particular locus in human CD34-positive and other normal and leukaemic cells or retrieval of target gene sets for user-defined combinations of TFs across one or more cell types. Increasing numbers of genome-wide TF binding profiles are being added to public repositories, and this trend is likely to continue. For the power of these data sets to be fully harnessed by experimental scientists, there is a need for these data to be placed in context and easily accessible for downstream applications. To this end, we have built a user-friendly database that has at its core the genome-wide binding profiles of seven key haematopoietic TFs in human stem/progenitor cells. These binding profiles are compared with binding profiles in normal differentiated and leukaemic cells. We have integrated these TF binding profiles with chromatin marks and expression data in normal and leukaemic cell fractions. All queries can be exported into external sites to construct TF-gene and protein-protein networks and to evaluate the association of genes with cellular processes and tissue expression.
Perera, D, Chacon, D, Thoms, JAI, Poulos, RC, Shlien, A, Beck, D, Campbell, PJ, Pimanda, JE & Wong, JWH 2014, 'OncoCis: annotation of cis-regulatory mutations in cancer.', Genome Biology, vol. 15, no. 10, pp. 1-14.View/Download from: UTS OPUS or Publisher's site
Whole genome sequencing has enabled the identification of thousands of somatic mutations within non-coding genomic regions of individual cancer samples. However, identification of mutations that potentially alter gene regulation remains a major challenge. Here we present OncoCis, a new method that enables identification of potential cis-regulatory mutations using cell type-specific genome and epigenome-wide datasets along with matching gene expression data. We demonstrate that the use of cell type-specific information and gene expression can significantly reduce the number of candidate cis-regulatory mutations compared with existing tools designed for the annotation of cis-regulatory SNPs. The OncoCis webserver is freely accessible at https://powcs.med.unsw.edu.au/OncoCis/.
Beck, D, Thoms, J, Palu, C, Herold, T, Shah, A, Olivier, J, Boelen, L, Huang, Y, Chacon, D, Brown, A, Babic, M, Hahn, C, Perugini, M, Zhou, X, Huntly, B, Berdel, W, Woermann, B, Buechner, T, Hiddemann, W, Bohlander, S, Scott, H, Lewis, I, D'Andrea, R, Wong, J & Pimanda, J 2016, 'Integrative analysis of lincrna expression in 922 acute myeloid leukemia patients reveals multiple prognostic gene signatures', Haematologica, pp. 208-209.