Medical Biology - Research Publications

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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)
    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: 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.htmlIt has been released under a GPL license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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    Women with type 1 diabetes exhibit a progressive increase in gut Saccharomyces cerevisiae in pregnancy associated with evidence of gut inflammation
    Bandala-Sanchez, E ; Roth-Schulze, AJ ; Oakey, H ; Penno, MAS ; Bediaga, NG ; Naselli, G ; Ngui, KM ; Smith, AD ; Huang, D ; Zozaya-Valdes, E ; Thomson, RL ; Brown, JD ; Vuillermin, PJ ; Barry, SC ; Craig, ME ; Rawlinson, WD ; Davis, EA ; Harris, M ; Soldatos, G ; Colman, PG ; Wentworth, JM ; Haynes, A ; Morahan, G ; Sinnott, RO ; Papenfuss, AT ; Couper, JJ ; Harrison, LC (ELSEVIER IRELAND LTD, 2022-02-01)
    AIMS: Studies of the gut microbiome have focused on its bacterial composition. We aimed to characterize the gut fungal microbiome (mycobiome) across pregnancy in women with and without type 1 diabetes. METHODS: Faecal samples (n = 162) were collected from 70 pregnant women (45 with and 25 without type 1 diabetes) across all trimesters. Fungi were analysed by internal transcribed spacer 1 amplicon sequencing. Markers of intestinal inflammation (faecal calprotectin) and intestinal epithelial integrity (serum intestinal fatty acid binding protein; I-FABP), and serum antibodies to Saccharomyces cerevisiae (ASCA) were measured. RESULTS: Women with type 1 diabetes had decreased fungal alpha diversity by the third trimester, associated with an increased abundance of Saccharomyces cerevisiae that was inversely related to the abundance of the anti-inflammatory butyrate-producing bacterium Faecalibacterium prausnitzii. Women with type 1 diabetes had higher concentrations of calprotectin, I-FABP and ASCA. CONCLUSIONS: Women with type 1 diabetes exhibit a shift in the gut mycobiome across pregnancy associated with evidence of gut inflammation and impaired intestinal barrier function. The relevance of these findings to the higher rate of pregnancy complications in type 1 diabetes warrants further study.
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    Melanoma brain metastases that progress on BRAF-MEK inhibitors demonstrate resistance to ipilimumab-nivolumab that is associated with the Innate PD-1 Resistance Signature (IPRES)
    Lau, PKH ; Feran, B ; Smith, L ; Lasocki, A ; Molania, R ; Smith, K ; Weppler, A ; Angel, C ; Kee, D ; Bhave, P ; Lee, B ; Young, RJ ; Iravani, A ; Yeang, HA ; Vergara, IA ; Kok, D ; Drummond, K ; Neeson, PJ ; Sheppard, KE ; Papenfuss, T ; Solomon, BJ ; Sandhu, S ; McArthur, GA (BMJ PUBLISHING GROUP, 2021-10-01)
    BACKGROUND: Melanoma brain metastases (MBMs) are a challenging clinical problem with high morbidity and mortality. Although first-line dabrafenib-trametinib and ipilimumab-nivolumab have similar intracranial response rates (50%-55%), central nervous system (CNS) resistance to BRAF-MEK inhibitors (BRAF-MEKi) usually occurs around 6 months, and durable responses are only seen with combination immunotherapy. We sought to investigate the utility of ipilimumab-nivolumab after MBM progression on BRAF-MEKi and identify mechanisms of resistance. METHODS: Patients who received first-line ipilimumab-nivolumab for MBMs or second/third line ipilimumab-nivolumab for intracranial metastases with BRAFV600 mutations with prior progression on BRAF-MEKi and MRI brain staging from March 1, 2015 to June 30, 2018 were included. Modified intracranial RECIST was used to assess response. Formalin-fixed paraffin-embedded samples of BRAFV600 mutant MBMs that were naïve to systemic treatment (n=18) or excised after progression on BRAF-MEKi (n=14) underwent whole transcriptome sequencing. Comparative analyses of MBMs naïve to systemic treatment versus BRAF-MEKi progression were performed. RESULTS: Twenty-five and 30 patients who received first and second/third line ipilimumab-nivolumab, were included respectively. Median sum of MBM diameters was 13 and 20.5 mm for the first and second/third line ipilimumab-nivolumab groups, respectively. Intracranial response rate was 75.0% (12/16), and median progression-free survival (PFS) was 41.6 months for first-line ipilimumab-nivolumab. Efficacy of second/third line ipilimumab-nivolumab after BRAF-MEKi progression was poor with an intracranial response rate of 4.8% (1/21) and median PFS of 1.3 months. Given the poor activity of ipilimumab-nivolumab after BRAF-MEKi MBM progression, we performed whole transcriptome sequencing to identify mechanisms of drug resistance. We identified a set of 178 differentially expressed genes (DEGs) between naïve and MBMs with progression on BRAF-MEKi treatment (p value <0.05, false discovery rate (FDR) <0.1). No distinct pathways were identified from gene set enrichment analyses using Kyoto Encyclopedia of Genes and Genomes, Gene Ontogeny or Hallmark libraries; however, enrichment of DEG from the Innate Anti-PD1 Resistance Signature (IPRES) was identified (p value=0.007, FDR=0.03). CONCLUSIONS: Second-line ipilimumab-nivolumab for MBMs after BRAF-MEKi progression has poor activity. MBMs that are resistant to BRAF-MEKi that also conferred resistance to second-line ipilimumab-nivolumab showed enrichment of the IPRES gene signature.
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    Safety, infectivity and immunogenicity of a Chick for genetically attenuated blood-stage malaria updates vaccine
    Webster, R ; Sekuloski, S ; Odedra, A ; Woolley, S ; Jennings, H ; Amante, F ; Trenholme, KR ; Healer, J ; Cowman, AF ; Eriksson, EM ; Sathe, P ; Penington, J ; Blanch, AJ ; Dixon, MWA ; Tilley, L ; Duffy, MF ; Craig, A ; Storm, J ; Chan, J-A ; Evans, K ; Papenfuss, AT ; Schofield, L ; Griffin, P ; Barber, BE ; Andrew, D ; Boyle, MJ ; Rivera, FDL ; Engwerda, C ; McCarthy, JS (BMC, 2021-11-22)
    BACKGROUND: There is a clear need for novel approaches to malaria vaccine development. We aimed to develop a genetically attenuated blood-stage vaccine and test its safety, infectivity, and immunogenicity in healthy volunteers. Our approach was to target the gene encoding the knob-associated histidine-rich protein (KAHRP), which is responsible for the assembly of knob structures at the infected erythrocyte surface. Knobs are required for correct display of the polymorphic adhesion ligand P. falciparum erythrocyte membrane protein 1 (PfEMP1), a key virulence determinant encoded by a repertoire of var genes. METHODS: The gene encoding KAHRP was deleted from P. falciparum 3D7 and a master cell bank was produced in accordance with Good Manufacturing Practice. Eight malaria naïve males were intravenously inoculated (day 0) with 1800 (2 subjects), 1.8 × 105 (2 subjects), or 3 × 106 viable parasites (4 subjects). Parasitemia was measured using qPCR; immunogenicity was determined using standard assays. Parasites were rescued into culture for in vitro analyses (genome sequencing, cytoadhesion assays, scanning electron microscopy, var gene expression). RESULTS: None of the subjects who were administered with 1800 or 1.8 × 105 parasites developed parasitemia; 3/4 subjects administered 3× 106 parasites developed significant parasitemia, first detected on days 13, 18, and 22. One of these three subjects developed symptoms of malaria simultaneously with influenza B (day 17; 14,022 parasites/mL); one subject developed mild symptoms on day 28 (19,956 parasites/mL); and one subject remained asymptomatic up to day 35 (5046 parasites/mL). Parasitemia rapidly cleared with artemether/lumefantrine. Parasitemia induced a parasite-specific antibody and cell-mediated immune response. Parasites cultured ex vivo exhibited genotypic and phenotypic properties similar to inoculated parasites, although the var gene expression profile changed during growth in vivo. CONCLUSIONS: This study represents the first clinical investigation of a genetically attenuated blood-stage human malaria vaccine. A P. falciparum 3D7 kahrp- strain was tested in vivo and found to be immunogenic but can lead to patent parasitemia at high doses. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (number: ACTRN12617000824369 ; date: 06 June 2017).
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    Detection of clinically relevant early genomic lesions in B-cell malignancies from circulating tumour DNA using a single hybridisation-based next generation sequencing assay
    Blombery, PA ; Ryland, GL ; Markham, J ; Guinto, J ; Wall, M ; McBean, M ; Jones, K ; Thompson, ER ; Cameron, DL ; Papenfuss, AT ; Prince, MH ; Dickinson, M ; Westerman, DA (WILEY, 2018-10-01)
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    Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome
    Roth-Schulze, AJ ; Penno, MAS ; Ngui, KM ; Oakey, H ; Bandala-Sanchez, E ; Smith, AD ; Allnutt, TR ; Thomson, RL ; Vuillermin, PJ ; Craig, ME ; Rawlinson, WD ; Davis, EA ; Harris, M ; Soldatos, G ; Colman, PG ; Wentworth, JM ; Haynes, A ; Barry, SC ; Sinnott, RO ; Morahan, G ; Bediaga, NG ; Smyth, GK ; Papenfuss, AT ; Couper, JJ ; Harrison, LC (BMC, 2021-08-06)
    BACKGROUND: The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D. RESULTS: Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage. CONCLUSIONS: Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means. Video abstract.