Blood, 2020
Authors
Hanyang Lin, Katharina Rothe, Min Chen, Andrew Wu, Artem Babaian, Ryan Yen, Jonathan Zeng, Jens Ruschmann, Oleh I Petriv, Kieran O'Neill, Tobias Maetzig, David J H F Knapp, Naoto Nakamichi, Ryan Brinkman, Inanc Birol, Donna L Forrest, Carl Hansen, Keith Keith Humphries, Connie J Eaves, Xiaoyan Jiang
Publication Abstract

Overcoming drug resistance and targeting cancer stem cells remain challenges for curative cancer treatment. To investigate the role of miRNAs in regulating drug resistance and leukemic stem cell (LSCs) fate, we performed global transcriptome profiling in treatment-naïve chronic myeloid leukemia (CML) stem/progenitor cells and identified that miR-185 levels anticipate their response to ABL tyrosine kinase inhibitors (TKIs). miR-185 functions as a tumor suppressor; its restored expression impaired survival of drug-resistant cells, sensitized them to TKIs in vitro, and markedly eliminated long-term repopulating LSCs and infiltrating blast cells, conferring a survival advantage in pre-clinical xenotransplantation models. Integrative analysis with mRNA profiles uncovered PAK6 as a crucial target of miR-185 and pharmacological inhibition of PAK6 perturbed the RAS/MAPK pathway and mitochondrial activity, sensitizing therapy-resistant cells to TKIs. Thus, miR-185 presents as a potential predictive biomarker, and dual targeting of miR-185-mediated PAK6 activity and BCR-ABL may provide a valuable strategy for overcoming drug resistance in patients.

ACS Pharmacology & Translational Science, 2019
Authors
Jon K Obst, Jun Wang, Kunzhong Jian, David E Williams, Amy H Tien, Nasrin Mawji, Teresa Tam, Yu Chi Yang, Raymond J Andersen, Kim N Chi, Bruce Montgomery, Marianne D Sadar
Publication Abstract

Inhibition of the androgen receptor (AR) is the mainstay treatment for advanced prostate cancer. Ralaniten (formally EPI-002) prevents AR transcriptional activity by binding to its N-terminal domain (NTD) which is essential for transcriptional activity. Ralaniten acetate (EPI-506) the triacetate pro-drug of ralaniten, remains the only AR-NTD inhibitor to have entered clinical trials (NCT02606123). While well tolerated, the trial was ultimately terminated due to poor pharmacokinetic properties and resulting pill burden. Here we discovered that ralaniten was glucuronidated which resulted in decreased potency. Long-term treatment of prostate cancer cells with ralaniten results in upregulation of UGT2B enzymes with concomitant loss of potency. This has proven to be a useful model with which to facilitate the development of more potent second-generation AR-NTD inhibitors. Glucuronidated metabolites of ralaniten were also detected in the serum of patients in Phase 1 clinical trials. Therefore, we tested an analogue of ralaniten (EPI-045) which was resistant to glucuronidation and demonstrated superiority to ralaniten in our resistant model. These data support that analogues of ralaniten designed to mitigate glucuronidation may optimize clinical responses to AR-NTD inhibitors.

Nature Reviews Genetics, 2020
Authors
Maui Hudson, Nanibaa' A Garrison, Rogena Sterling, Nadine R Caron, Keolu Fox, Joseph Yracheta, Jane Anderson, Phil Wilcox, Laura Arbour, Alex Brown, Maile Taualii, Tahu Kukutai, Rodney Haring, Ben Te Aika, Gareth S Baynam, Peter K Dearden, David Chagné, Ripan S Malhi, Ibrahim Garba, Nicki Tiffin, Deborah Bolnick, Matthew Stott, Anna K Rolleston, Leah L Ballantyne, Ray Lovett, Dominique David-Chavez, Andrew Martinez, Andrew Sporle, Maggie Walter, Jeff Reading, Stephanie Russo Carroll
Publication Abstract

Addressing Indigenous rights and interests in genetic resources has become increasingly challenging in an open science environment that promotes unrestricted access to genomic data. Although Indigenous experiences with genetic research have been shaped by a series of negative interactions, there is increasing recognition that equitable benefits can only be realized through greater participation of Indigenous communities. Issues of trust, accountability and equity underpin Indigenous critiques of genetic research and the sharing of genomic data. This Perspectives article highlights identified issues for Indigenous communities around the sharing of genomic data and suggests principles and actions that genomic researchers can adopt to recognize community rights and interests in data.

Bioinformatics (Oxford, England), 2020
Authors
Nieuwoudt, Christina, Brooks-Wilson, Angela, Graham, Jinko
Publication Abstract
We present the R package SimRVSequences to simulate sequence data for pedigrees. SimRVSequences allows for simulations of large numbers of single-nucleotide variants (SNVs) and scales well with increasing numbers of pedigrees. Users provide a sample of pedigrees and SNV data from a sample of unrelated individuals.

Cancer Epidemiology, Biomarkers & Prevention
Authors
Samantha Jean Jones, Sumara Stroshein, Amy M Williams, Dongmeng Liu, John J Spinelli, Joseph M Connors, Angela R Brooks-Wilson
Publication Abstract

Familial aggregation of lymphoid cancers and immune-related disorders suggests a role for genetic susceptibility; however, few studies examine environmental factors. According to the hygiene hypothesis, adult-onset-immune-related diseases may be a consequence of reduced childhood infectious exposures and aberrant immune development. In a cohort of 196 multiple-case lymphoid cancer families, we analyzed environmental factors related to the hygiene hypothesis.

BMC Geriatrics, 2020
Authors
Qianqian Gu, Carly M Sable, Angela Brooks-Wilson, Rachel A Murphy
Publication Abstract

Very few people live to eighty-five years and older (the 'oldest old'), and even fewer live to this age without developing chronic diseases. It is important to understand the relationship, if any, of modifiable factors such as diet on healthy aging. However, there are few studies of diet among healthy oldest old, especially in North American populations. We aimed to characterize dietary patterns among 'super-seniors' (SS) within the Canadian Healthy Aging Study.

Investigational New Drugs, 2020
Authors
Jean-Michel Lavoie, Teresa Mitchell, Sung-Eun Lee, Balvir Deol, Stephen K Chia, Karen A Gelmon, Christian K Kollmannsberger, Anna V Tinker, Steven J M Jones, Marco Marra, Janessa Laskin, Daniel J Renouf
Publication Abstract

Introduction Given the high level of uncertainty surrounding the outcomes of early phase clinical trials, whole genome and transcriptome analysis (WGTA) can be used to optimize patient selection and study assignment. In this retrospective analysis, we reviewed the impact of this approach on one such program. Methods Patients with advanced malignancies underwent fresh tumor biopsies as part of our personalized medicine program (NCT02155621). Tumour molecular data were reviewed for potentially clinically actionable findings and patients were referred to the developmental therapeutics program. Outcomes were reviewed in all patients, including those where trial selection was driven by molecular data (matched) and those where there was no clear molecular rationale (unmatched). Results From January 2014 to January 2018, 28 patients underwent WGTA and enrolled in clinical trials, including 2 patients enrolled in two trials. Fifteen patients were matched to a treatment based on a molecular target. Five patients were matched to a trial based upon single-gene DNA changes, all supported by RNA data. Ten cases were matched on the basis of genome-wide data (n = 4) or RNA gene expression only (n = 6). With a median follow-up of 6.7 months, the median time on treatment was 8.2 weeks. Discussion When compared to single-gene DNA-based data alone, WGTA led to a 3-fold increase in treatment matching. In a setting where there is a high level of uncertainty around both the investigational agents and the biomarkers, more data are needed to fully evaluate the impact of routine use of WGTA.

Nature Genetics, 2020
Authors
Laura Fachal, Hugues Aschard, Jonathan Beesley, Daniel R Barnes, Jamie Allen, Siddhartha Kar, Karen A Pooley, Joe Dennis, Kyriaki Michailidou, Constance Turman, Penny Soucy, Audrey Lemaçon, Michael Lush, Jonathan P Tyrer, Maya Ghoussaini, Mahdi Moradi Marjaneh, Xia Jiang, Simona Agata, Kristiina Aittomäki, M Rosario Alonso, Irene L Andrulis, Hoda Anton-Culver, Natalia N Antonenkova, Adalgeir Arason, Volker Arndt, Kristan J Aronson, Banu K Arun, Bernd Auber, Paul L Auer, Jacopo Azzollini, Judith Balmaña, Rosa B Barkardottir, Daniel Barrowdale, Alicia Beeghly-Fadiel, Javier Benitez, Marina Bermisheva, Katarzyna Białkowska, Amie M Blanco, Carl Blomqvist, William Blot, Natalia V Bogdanova, Stig E Bojesen, Manjeet K Bolla, Bernardo Bonanni, Ake Borg, Kristin Bosse, Hiltrud Brauch, Hermann Brenner, Ignacio Briceno, Ian W Brock, Angela Brooks-Wilson et al.
Publication Abstract

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.

Nature Genetics, 2020
Authors
Michelle Chan-Seng-Yue, Jaeseung C Kim, Gavin W Wilson, Karen Ng, Eugenia Flores Figueroa, Grainne M O'Kane, Ashton A Connor, Robert E Denroche, Robert C Grant, Jessica McLeod, Julie M Wilson, Gun Ho Jang, Amy Zhang, Sheng-Ben Liang, Ayelet Borgida, Dianne Chadwick, Sangeetha Kalimuthu, Ilinca Lungu, John M S Bartlett, Paul M Krzyzanowski, Vandana Sandhu, Hervé Tiriac, Fieke E M Froeling, Joanna M Karasinska, James T Topham, Daniel J Renouf, David F Schaeffer, Steven J M Jones, Marco A Marra, Janessa Laskin, Runjan Chetty, Lincoln D Stein, George Zogopoulos, Benjamin Haibe-Kains, Peter J Campbell, David A Tuveson, Jennifer J Knox, Sandra E Fischer, Steven Gallinger, Faiyaz Notta
Publication Abstract

Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor tumor cellularity and extensive genomic instability. To address this, a dataset of whole genomes and transcriptomes was generated from purified epithelium of primary and metastatic tumors. Transcriptome analysis demonstrated that molecular subtypes are a product of a gene expression continuum driven by a mixture of intratumoral subpopulations, which was confirmed by single-cell analysis. Integrated whole-genome analysis uncovered that molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and GATA6. By mapping tumor genetic histories, tetraploidization emerged as a key mutational process behind these events. Taken together, these data support the premise that the constellation of genomic aberrations in the tumor gives rise to the molecular subtype, and that disease heterogeneity is due to ongoing genomic instability during progression.

Leukemia, 2020
Authors
Alexander Pemov, Anand Pathak, Samantha J Jones, Ramita Dewan, Jessica Merberg, Sirisha Karra, Jung Kim, Evgeny Arons, Sarangan Ravichandran, Brian T Luke, Shalabh Suman, Meredith Yeager, Martin J S Dyer, Henry T Lynch, Mark H Greene, Neil E Caporaso, Robert J Kreitman, Lynn R Goldin, John J Spinelli, Angela Brooks-Wilson, Mary L McMaster, Douglas R Stewart
Publication Abstract

Hairy cell leukemia (HCL) is a rare chronic B-cell lymphoproliferative disorder named for its characteristic hair-like cytoplasmic projections from the malignant cells. HCL is classified as an indolent lymphoproliferative neoplasm, representing ~2% of all leukemias with ~1240 new cases diagnosed annually in the US; median age-at-onset is 55 years [1]. It affects males more than females (4:1), and whites more than African-Americans [1]. Although familial and sporadic HCL exhibit similar clinical features, no characteristic germline genetic variation has been found. Familial HCL is rare with fewer than 20 families reported in the literature. Thirteen of the 15 reported pedigrees had two affected individuals; the remaining two pedigrees harbored three, including the family reported here [2,3,4,5]. Investigators have speculated that HCL may be an HLA-linked disorder but, in aggregate, the data are inconclusive [3,4,5]. The discovery that a somatic BRAF mutation (V600E) was nearly universal in HCL (but absent in other B-cell neoplasms) provided major insight into disease biology, identifying a critical therapeutic target [6], but no germline genetic susceptibility variants have been identified. In this study we applied high-throughput sequencing technology to four multiplex HCL pedigrees, seeking to identify shared germline variants conferring HCL susceptibility. In addition, we used CRISPR/Cas9-based genome editing to introduce CASP9 p.H237P, one of the variants shared by all four affected members of the largest pedigree, into a model cell line, followed by measurements of cellular caspase-9 activity and apoptotic response.

Back to top