Medical Biology - Research Publications

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    Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers
    Gong, T ; Jaratlerdsiri, W ; Jiang, J ; Willet, C ; Chew, T ; Patrick, SM ; Lyons, RJ ; Haynes, A-M ; Pasqualim, G ; Brum, IS ; Stricker, PD ; Mutambirwa, SBA ; Sadsad, R ; Papenfuss, AT ; Bornman, RMS ; Chan, EKF ; Hayes, VM (BMC, 2022-08-31)
    BACKGROUND: African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa genomic studies are still biased towards small variant interrogation. METHODS: Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity (African versus European), with a focus on African men from southern Africa. RESULTS: Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count) increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic implications for African patients. CONCLUSIONS: In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed ethnic disparity in advanced PCa presentation in men of African ancestry.
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    A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin
    Qiu, D ; Pei, JV ; Rosling, JEO ; Thathy, V ; Li, D ; Xue, Y ; Tanner, JD ; Penington, JS ; Aw, YTV ; Aw, JYH ; Xu, G ; Tripathi, AK ; Gnadig, NF ; Yeo, T ; Fairhurst, KJ ; Stokes, BH ; Murithi, JM ; Kumpornsin, K ; Hasemer, H ; Dennis, ASM ; Ridgway, MC ; Schmitt, EK ; Straimer, J ; Papenfuss, AT ; Lee, MCS ; Corry, B ; Sinnis, P ; Fidock, DA ; van Dooren, GG ; Kirk, K ; Lehane, AM (NATURE PORTFOLIO, 2022-09-30)
    Diverse compounds target the Plasmodium falciparum Na+ pump PfATP4, with cipargamin and (+)-SJ733 the most clinically-advanced. In a recent clinical trial for cipargamin, recrudescent parasites emerged, with most having a G358S mutation in PfATP4. Here, we show that PfATP4G358S parasites can withstand micromolar concentrations of cipargamin and (+)-SJ733, while remaining susceptible to antimalarials that do not target PfATP4. The G358S mutation in PfATP4, and the equivalent mutation in Toxoplasma gondii ATP4, decrease the sensitivity of ATP4 to inhibition by cipargamin and (+)-SJ733, thereby protecting parasites from disruption of Na+ regulation. The G358S mutation reduces the affinity of PfATP4 for Na+ and is associated with an increase in the parasite's resting cytosolic [Na+]. However, no defect in parasite growth or transmissibility is observed. Our findings suggest that PfATP4 inhibitors in clinical development should be tested against PfATP4G358S parasites, and that their combination with unrelated antimalarials may mitigate against resistance development.
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    Epithelial-to-Mesenchymal Transition Supports Ovarian Carcinosarcoma Tumorigenesis and Confers Sensitivity to Microtubule Targeting with Eribulin.
    Ho, GY ; Kyran, EL ; Bedo, J ; Wakefield, MJ ; Ennis, DP ; Mirza, HB ; Vandenberg, CJ ; Lieschke, E ; Farrell, A ; Hadla, A ; Lim, R ; Dall, G ; Vince, JE ; Chua, NK ; Kondrashova, O ; Upstill-Goddard, R ; Bailey, U-M ; Dowson, S ; Roxburgh, P ; Glasspool, RM ; Bryson, G ; Biankin, AV ; Scottish Genomes Partnership, ; Cooke, SL ; Ratnayake, G ; McNally, O ; Traficante, N ; Australian Ovarian Cancer Study12,13, ; DeFazio, A ; Weroha, SJ ; Bowtell, DD ; McNeish, IA ; Papenfuss, AT ; Scott, CL ; Barker, HE (American Association for Cancer Research (AACR), 2022-12-02)
    UNLABELLED: Ovarian carcinosarcoma (OCS) is an aggressive and rare tumor type with limited treatment options. OCS is hypothesized to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analyzed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated that the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumors. Preclinical OCS models were used to test the efficacy of microtubule-targeting drugs, including eribulin, which has previously been shown to reverse EMT characteristics in breast cancers and induce differentiation in sarcomas. Vinorelbine and eribulin more effectively inhibited OCS growth than standard-of-care platinum-based chemotherapy, and treatment with eribulin reduced mesenchymal characteristics and N-MYC expression in OCS patient-derived xenografts. Eribulin treatment resulted in an accumulation of intracellular cholesterol in OCS cells, which triggered a downregulation of the mevalonate pathway and prevented further cholesterol biosynthesis. Finally, eribulin increased expression of genes related to immune activation and increased the intratumoral accumulation of CD8+ T cells, supporting exploration of immunotherapy combinations in the clinic. Together, these data indicate that EMT plays a key role in OCS tumorigenesis and support the conversion theory for OCS histogenesis. Targeting EMT using eribulin could help improve OCS patient outcomes. SIGNIFICANCE: Genomic analyses and preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate antitumor immunity.
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    Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass
    Duffy, MF ; Tonkin-Hill, GQ ; Trianty, L ; Noviyanti, R ; Nguyen, HHT ; Rambhatla, JS ; McConville, MJ ; Rogerson, SJ ; Brown, GV ; Price, RN ; Anstey, NM ; Day, KP ; Papenfuss, AT (NATURE PORTFOLIO, 2022-09-23)
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    Removing unwanted variation from large-scale RNA sequencing data with PRPS
    Molania, R ; Foroutan, M ; Gagnon-Bartsch, JA ; Gandolfo, LC ; Jain, A ; Sinha, A ; Olshansky, G ; Dobrovic, A ; Papenfuss, AT ; Speed, TP (NATURE PORTFOLIO, 2022-09-15)
    Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing (RNA-seq) data, especially when the data come from large and complex studies. Using RNA-seq data from The Cancer Genome Atlas (TCGA), we examined several sources of unwanted variation and demonstrate here how these can significantly compromise various downstream analyses, including cancer subtype identification, association between gene expression and survival outcomes and gene co-expression analysis. We propose a strategy, called pseudo-replicates of pseudo-samples (PRPS), for deploying our recently developed normalization method, called removing unwanted variation III (RUV-III), to remove the variation caused by library size, tumor purity and batch effects in TCGA RNA-seq data. We illustrate the value of our approach by comparing it to the standard TCGA normalizations on several TCGA RNA-seq datasets. RUV-III with PRPS can be used to integrate and normalize other large transcriptomic datasets coming from multiple laboratories or platforms.
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    Unscrambling cancer genomes via integrated analysis of structural variation and copy number
    Shale, C ; Cameron, DL ; Baber, J ; Wong, M ; Cowley, MJ ; Papenfuss, AT ; Cuppen, E ; Priestley, P (Elsevier BV, 2022-04)
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    Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition
    Hogg, SJ ; Motorna, O ; Cluse, LA ; Johanson, TM ; Coughlan, HD ; Raviram, R ; Myers, RM ; Costacurta, M ; Todorovski, I ; Pijpers, L ; Bjelosevic, S ; Williams, T ; Huskins, SN ; Kearney, CJ ; Devlin, JR ; Fan, Z ; Jabbari, JS ; Martin, BP ; Fareh, M ; Kelly, MJ ; Dupere-Richer, D ; Sandow, JJ ; Feran, B ; Knight, D ; Khong, T ; Spencer, A ; Harrison, SJ ; Gregory, G ; Wickramasinghe, VO ; Webb, A ; Taberlay, PC ; Bromberg, KD ; Lai, A ; Papenfuss, AT ; Smyth, GK ; Allan, RS ; Licht, JD ; Landau, DA ; Abdel-Wahab, O ; Shortt, J ; Vervoort, SJ ; Johnstone, RW (CELL PRESS, 2021-05-20)
    To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP in hematological malignancies. We found that catalytic P300/CBP inhibition dynamically perturbs steady-state acetylation kinetics and suppresses oncogenic transcriptional networks in the absence of changes to chromatin accessibility. CRISPR-Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principal antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300/CBP inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.
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    Tissue-resident memory T cells from a metastatic vaginal melanoma patient are tumor-responsive T cells and increase after anti-PD-1 treatment
    Pizzolla, A ; Keam, SP ; Vergara, IA ; Caramia, F ; Thio, N ; Wang, M ; Kocovski, N ; Tantalo, D ; Jabbari, J ; Au-Yeung, G ; Sandhu, S ; Gyorki, DE ; Weppler, A ; Perdicchio, M ; McArthur, GA ; Papenfuss, AT ; Neeson, PJ (BMJ PUBLISHING GROUP, 2022-05-01)
    BACKGROUND: Vaginal melanoma (VM) is a rare cancer and has a poor response to immune checkpoint blockade (ICB). CD8+Tissue Resident Memory (TRM) T cells proliferate in response to ICB and correlate with longer survival in metastatic cutaneous melanoma. However, their capacity to respond to VM and their neoantigens is not known. METHODS: Using longitudinal samples, we explored the evolution of VM mutations by whole-exome sequencing and RNAseq, we also defined the immune context using multiplex immunohistochemistry and nanostring pan cancer immune profile. Then using fresh single cell suspensions of the metastatic samples, we explored VM T cells via mass cytometry and single cell RNAseq and T cell receptor sequencing (TCRseq). Finally, we investigated TRM, pre-TRM and exhausted T cell function against melanoma neo-antigens and melanoma differentiation antigens in vitro. RESULTS: Primary VM was non-inflamed and devoid of CD8+ TRM cells. In contrast, both metastases showed proliferating CD8+ TRM were clustered at the tumor margin, with increased numbers in the second ICB-refractory metastasis. The first metastasis showed dense infiltration of CD8+ T cells, the second showed immune exclusion with loss of melanoma cell Major histocompatibility complex (MHC)-I expression associated with downregulation of antigen presentation pathway gene expression. CD8+ TRM from both metastases responded to autologous melanoma cells more robustly than all other CD8+ T cell subsets. In addition, CD8+ TRM shared TCR clones across metastases, suggesting a response to common antigens, which was supported by recognition of the same neoantigen by expanded tumor infiltrating lymphocytes. CONCLUSIONS: In this study, we identified TRM clusters in VM metastases from a patient, but not primary disease. We showed TRM location at the tumor margin, and their superior functional response to autologous tumor cells, predicted neoantigens and melanoma differentiation antigens. These CD8+ TRM exhibited the highest tumor-responsive potential and shared their TCR with tumor-infiltrating effector memory T cells. This suggests VM metastases from this patient retain strong antitumor T cell functional responses; however, this response is suppressed in vivo. The loss of VG MHC-I expression is a common immune escape mechanism which was not addressed by anti-PD-1 monotherapy; rather an additional targeted approach to upregulate MHC-I expression is required.
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    TERT structural rearrangements in metastatic pheochromocytomas
    Dwight, T ; Flynn, A ; Amarasinghe, K ; Benn, DE ; Lupat, R ; Li, J ; Cameron, DL ; Hogg, A ; Balachander, S ; Candiloro, ILM ; Wong, SQ ; Robinson, BG ; Papenfuss, AT ; Gill, AJ ; Dobrovic, A ; Hicks, RJ ; Clifton-Bligh, RJ ; Tothill, RW (BIOSCIENTIFICA LTD, 2018-01-01)
    Pheochromocytomas (PC) and paragangliomas (PGL) are endocrine tumors for which the genetic and clinicopathological features of metastatic progression remain incompletely understood. As a result, the risk of metastasis from a primary tumor cannot be predicted. Early diagnosis of individuals at high risk of developing metastases is clinically important and the identification of new biomarkers that are predictive of metastatic potential is of high value. Activation of TERT has been associated with a number of malignant tumors, including PC/PGL. However, the mechanism of TERT activation in the majority of PC/PGL remains unclear. As TERT promoter mutations occur rarely in PC/PGL, we hypothesized that other mechanisms - such as structural variations - may underlie TERT activation in these tumors. From 35 PC and four PGL, we identified three primary PCs that developed metastases with elevated TERT expression, each of which lacked TERT promoter mutations and promoter DNA methylation. Using whole genome sequencing, we identified somatic structural alterations proximal to the TERT locus in two of these tumors. In both tumors, the genomic rearrangements led to the positioning of super-enhancers proximal to the TERT promoter, that are likely responsible for the activation of the normally tightly repressed TERT expression in chromaffin cells.
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    StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem
    Cameron, DL ; Dong, R ; Papenfuss, AT ; Alkan, C (OXFORD UNIV PRESS, 2022-03-28)
    SUMMARY: StructuralVariantAnnotation is an R/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the three different notations supported by VCF into a breakpoint GRanges data structure suitable for use by the wider Bioconductor ecosystem. It handles both transitive breakpoints and duplication/insertion notational differences of identical variants-both common scenarios when comparing short/long read-based call sets that confound downstream analysis. StructuralVariantAnnotation provides the caller-agnostic foundation needed for a R/Bioconductor ecosystem of structural variant annotation, classification and interpretation tools able to handle both simple and complex genomic rearrangements. AVAILABILITY AND IMPLEMENTATION: StructuralVariantAnnotation is implemented in R and available for download as the Bioconductor StructuralVariantAnnotation package. Details can be found at https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.html. It has been released under a GPL license.