Nature Communications, 2020
Authors
Constance H Li et al. & the PCAWG consortium
Publication Abstract

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.

Epigenomics, 2020
Authors
Madonna R Peter, Misha Bilenky, Ruth Isserlin, Gary D Bader, Shu Yi Shen, Daniel D De Carvalho, Aaron R Hansen, Pingzhao Hu, Neil E Fleshner, Anthony M Joshua, Martin Hirst, Bharati Bapat
Publication Abstract

Aim: We examined methylation changes in cell-free DNA (cfDNA) in metastatic castration-resistant prostate cancer (mCRPC) during treatment. Patients & methods: Genome-wide methylation analysis of sequentially collected cfDNA samples derived from mCRPC patients undergoing androgen-targeting therapy was performed. Results: Alterations in methylation states of genes previously implicated in prostate cancer progression were observed and patients that maintained methylation changes throughout therapy tended to have a longer time to clinical progression. Importantly, we also report that markers associated with a highly aggressive form of the disease, neuroendocrine-CRPC, were associated with a faster time to clinical progression. Conclusion: Our findings highlight the potential of monitoring the cfDNA methylome during therapy in mCRPC, which may serve as predictive markers of response to androgen-targeting agents.

Genome Research, 2020
Authors
Readman Chiu, Chen Yang, Justin Chu, Hamid Mohamadi, René L Warren, Inanc Birol
Publication Abstract

Despite the rapid advance in single-cell RNA sequencing (scRNA-seq) technologies within the last decade, single-cell transcriptome analysis workflows have primarily used gene expression data while isoform sequence analysis at the single-cell level still remains fairly limited. Detection and discovery of isoforms in single cells is difficult because of the inherent technical shortcomings of scRNA-seq data, and existing transcriptome assembly methods are mainly designed for bulk RNA samples. To address this challenge, we developed RNA-Bloom, an assembly algorithm that leverages the rich information content aggregated from multiple single-cell transcriptomes to reconstruct cell-specific isoforms. Assembly with RNA-Bloom can be either reference-guided or reference-free, thus enabling unbiased discovery of novel isoforms or foreign transcripts. We compared both assembly strategies of RNA-Bloom against five state-of-the-art reference-free and reference-based transcriptome assembly methods. In our benchmarks on a simulated 384-cell data set, reference-free RNA-Bloom reconstructed 37.9%-38.3% more isoforms than the best reference-free assembler, whereas reference-guided RNA-Bloom reconstructed 4.1%-11.6% more isoforms than reference-based assemblers. When applied to a real 3840-cell data set consisting of more than 4 billion reads, RNA-Bloom reconstructed 9.7%-25.0% more isoforms than the best competing reference-based and reference-free approaches evaluated. We expect RNA-Bloom to boost the utility of scRNA-seq data beyond gene expression analysis, expanding what is informatically accessible now.

Haematologica, 2020
Authors
Keren Isaev, Daisuke Ennishi, Laura Hilton, Brian Skinnider, Karen L Mungall, Andrew J Mungall, Mehran Bakhtiari, Rosemarie Tremblay-LeMay, Anjali Silva, Susana Ben-Neriah, Merrill Boyle, Diego Villa, Marco A Marra, Christian Steidl, Randy D Gascoyne, Ryan Morin, Kerry J Savage, David W Scott, Robert Kridel.

Nature Methods, 2020
Authors
Katriona Shea, Ottar N Bjørnstad, Martin Krzywinski, Naomi Altman

Nature Genetics, 2020
Authors
Alessia Gagliardi, Vanessa L Porter, Zusheng Zong, Reanne Bowlby, Emma Titmuss, Constance Namirembe, Nicholas B Griner, Hilary Petrello, Jay Bowen, Simon K Chan, Luka Culibrk, Teresa M Darragh, Mark H Stoler, Thomas C Wright, Patee Gesuwan, Maureen A Dyer, Yussanne Ma, Karen L Mungall, Steven J M Jones, Carolyn Nakisige, Karen Novik, Jackson Orem, Martin Origa, Julie M Gastier-Foster, Robert Yarchoan, Corey Casper, Gordon B Mills, Janet S Rader, Akinyemi I Ojesina, Daniela S Gerhard, Andrew J Mungall, Marco A Marra
Publication Abstract

Cervical cancer is the most common cancer affecting sub-Saharan African women and is prevalent among HIV-positive (HIV+) individuals. No comprehensive profiling of cancer genomes, transcriptomes or epigenomes has been performed in this population thus far. We characterized 118 tumors from Ugandan patients, of whom 72 were HIV+, and performed extended mutation analysis on an additional 89 tumors. We detected human papillomavirus (HPV)-clade-specific differences in tumor DNA methylation, promoter- and enhancer-associated histone marks, gene expression and pathway dysregulation. Changes in histone modification at HPV integration events were correlated with upregulation of nearby genes and endogenous retroviruses.

Molecular Oncology, 2020
Authors
Yukiyoshi Hirayama, Teresa Tam, Kunzhong Jian, Raymond J Andersen, Marianne D Sadar.
Publication Abstract

Resistance of castration‐recurrent prostate cancer (CRPC) to enzalutamide and abiraterone involves the expression of constitutively active, truncated androgen receptor (AR) splice variants (AR‐Vs) that lack a C‐terminal ligand‐binding domain (LBD). Both full‐length AR and truncated AR‐Vs require a functional N‐terminal domain (NTD) for transcriptional activity thereby providing rationale for development of ralaniten (EPI‐002) as a first‐in‐class antagonist of the AR‐NTD. Here we evaluated the antitumor effect of a next‐generation analog of ralaniten (EPI‐7170) as a monotherapy or in combination with enzalutamide in prostate cancer cells that express AR‐V7 that were resistant to enzalutamide. EPI‐7170 had 8‐9 times improved potency compared to ralaniten. Enzalutamide increased levels of AR‐V7 and expression of its target genes. Knockdown of AR‐V7 restored sensitivity to enzalutamide, indicating a role for AR‐V7 in the mechanism of resistance. EPI‐7170 inhibited expression of genes transcriptionally regulated by full‐length AR and AR‐V7. A combination of EPI‐7170 and enzalutamide resulted in synergistic inhibition of proliferation of enzalutamide resistant cells that was consistent with results from cell cycle and clonogenic assays. In addition, this drug enhanced the anti‐tumor effect of enzalutamide in enzalutamide‐resistant CRPC preclinical models. Thus, a combination therapy targeting both the NTD and LBD of AR, and thereby blocking both full‐length AR and AR‐Vs, has potential for the treatment of enzalutamide‐resistant CRPC.

Scientific Reports, 2020
Authors
Miguel Alcaide, Matthew Cheung, Jack Hillman, S Rod Rassekh, Rebecca J Deyell, Gerald Batist, Aly Karsan, Alexander W Wyatt, Nathalie Johnson, David W Scott, Ryan D Morin
Publication Abstract

Cell-free DNA (cfDNA) has become a comprehensive biomarker in the fields of non-invasive cancer detection and monitoring, organ transplantation, prenatal genetic testing and pathogen detection. While cfDNA samples can be obtained using a broad variety of approaches, there is an urgent need to standardize analytical tools aimed at assessing its basic properties. Typical methods to determine the yield and fragment size distribution of cfDNA samples are usually either blind to genomic DNA contamination or the presence of enzymatic inhibitors, which can confound and undermine downstream analyses. Here, we present a novel droplet digital PCR assay to identify suboptimal samples and aberrant cfDNA size distributions, the latter typically associated with high levels of circulating tumour DNA (ctDNA). Our assay was designed to promiscuously cross-amplify members of the human olfactory receptor (OR) gene family and includes a customizable diploid locus for the determination of absolute cfDNA concentrations. We demonstrate here the utility of our assay to estimate the yield and quality of cfDNA extracts and deduce fragment size distributions that correlate well with those inferred by capillary electrophoresis and high throughput sequencing. The assay described herein is a powerful tool to establish quality controls and stratify cfDNA samples based on presumed ctDNA levels, then facilitating the implementation of robust, cost-effective and standardized analytical workflows into clinical practice.

Cancers, 2020
Authors
Carmen A Banuelos, Yusuke Ito, Jon K Obst, Nasrin R Mawji, Jun Wang, Yukiyoshi Hirayama, Jacky K Leung, Teresa Tam, Amy H Tien, Raymond J Andersen, Marianne D Sadar
Publication Abstract

Blocking androgen receptor (AR) transcriptional activity by androgen deprivation therapy (ADT) improves the response to radiotherapy for intermediate and high risk prostate cancer. Unfortunately, ADT, antiandrogens, and abiraterone increase expression of constitutively active splice variants of AR (AR-Vs) which regulate DNA damage repair leading to resistance to radiotherapy. Here we investigate whether blocking the transcriptional activities of full-length AR and AR-Vs with ralaniten leads to enhanced sensitivity to radiotherapy. Combination therapies using ralaniten with ionizing radiation were evaluated for effects on proliferation, colony formation, cell cycle, DNA damage, and Western blot analyses in human prostate cancer cells that express both full-length AR and AR-Vs. Ralaniten and a potent next-generation analog (EPI-7170) decreased expression of DNA repair genes whereas enzalutamide had no effect. FACS analysis revealed a dose-dependent decrease of BrdU incorporation with increased accumulation of γH2AX with a combination of ionizing radiation with ralaniten. An additive inhibitory effect on proliferation of enzalutamide-resistant cells was achieved with a combination of ralaniten compounds with ionizing radiation. Ralaniten and EPI-7170 sensitized prostate cancer cells that express full-length AR and AR-Vs to radiotherapy whereas enzalutamide had no added benefit.

Bioinformatics, 2020
Authors
Sarah E I Perez, Aria S Hahn, Martin Krzywinski, Steven J Hallam
Publication Abstract

Motivation: Networks are used to relate topological structure to system dynamics and function, particularly in ecology and systems biology. Network analysis is often guided or complemented by data-driven visualization. Hive plots, one of many network visualizations, distinguish themselves as providing a general, consistent, and coherent rule-based representation to motivate hypothesis development and testing.

Results: Here, we present HyPE, Hive Panel Explorer, a software application that creates a panel of interactive hive plots. HyPE enables network exploration based on user-driven layout rules and parameter combinations for simultaneous rendering of multiple network views. We demonstrate HyPE's features by exploring a microbial co-occurrence network constructed from forest soil microbiomes.

Availability: HyPE is available under the GNU license: https://github.com/hallamlab/HivePanelExplorer. A wiki, including a tutorial, is available at https://github.com/hallamlab/HivePanelExplorer/wiki.

Supplementary information: Supplementary data are available at Bioinformatics online.

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