PloS one, 2018
Authors
Halaschek-Wiener, Julius, Tindale, Lauren C, Collins, Jennifer A, Leach, Stephen, McManus, Bruce, Madden, Kenneth, Meneilly, Graydon, Le, Nhu D, Connors, Joseph M, Brooks-Wilson, Angela R
Publication Abstract
To understand why some people live to advanced age in good health and others do not, it is important to study not only disease, but also long-term good health. The Super-Seniors Study aims to identify factors associated with healthy aging.

Frontiers in genetics, 2018
Authors
Lussier, Alexandre A, Bodnar, Tamara S, Mingay, Matthew, Morin, Alexandre M, Hirst, Martin, Kobor, Michael S, Weinberg, Joanne
Publication Abstract
Prenatal alcohol exposure (PAE) can alter the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE resulted in blood alcohol levels of ~80-150 mg/dl throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal days (P) 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing. PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental period at a false-discovery rate (FDR) < 0.05. In addition, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR < 0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses. Persistent DNA methylation changes in the hypothalamus may be associated with the long-term physiological and neurobehavioral alterations in observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology of neurodevelopmental and mental health disorders, as they share numerous phenotypes and comorbidities.

Source code for biology and medicine, 2018
Authors
Nieuwoudt, Christina, Jones, Samantha J, Brooks-Wilson, Angela, Graham, Jinko
Publication Abstract
Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, rare variants from next-generation sequencing data.

Research and reports in urology, 2018
Authors
Ito, Yusuke, Sadar, Marianne D
Publication Abstract
Enzalutamide is a nonsteroidal antiandrogen for the treatment of metastatic castration-resistant prostate cancer (mCRPC) both before and after chemotherapy. Enzalutamide is more effective than its predecessor bicalutamide, which was analyzed in head-to-head studies of patients with CRPC. This family of nonsteroidal antiandrogens is now comprised of four drugs approved by the US Food and Drug Administration with two investigational drugs in clinical trials. Antiandrogens have been employed clinically for more than five decades to provide a rich resource of information. Steady-state concentration minimums (C{{sub}}min{{/sub}} or trough) in the range of ~1-13 μg/mL are measured in patients at therapeutic doses. Interestingly, enzalutamide which is considered to have strong affinity for the androgen receptor (AR) requires C{{sub}}min{{/sub}} levels >10 μg/mL. The sequence of antiandrogens and the clinical order of application in regard to other drugs that target the androgen axis remain of high interest. One novel first-in-class drug, called ralaniten, which binds to a unique region in the N-terminus domain of both the full-length and the truncated constitutively active splice variants of the AR, is currently in clinical trials for patients who previously received abiraterone, enzalutamide, or both. This highlights the trend to develop drugs with novel mechanisms of action and potentially differing mechanisms of resistance compared with antiandrogens. Better and more complete inhibition of the transcriptional activity of the AR appears to continue to provide improvements in the clinical management of mCRPC.

Journal of visualized experiments : JoVE, 2017
Authors
Lorzadeh, Alireza, Lopez Gutierrez, Rodrigo, Jackson, Linda, Moksa, Michelle, Hirst, Martin
Publication Abstract
We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states. Combinatorial measurements of nucleosome accessibility with histone modification generated by ndChIP-seq allows for the simultaneous interrogation of these features. The ndChIP-seq methodology is applicable to small numbers of primary cells inaccessible to cross-linking based ChIP-seq protocols. Taken together, ndChIP-seq enables the measurement of histone modification in combination with local nucleosome density to obtain new insights into shared mechanisms that regulate RNA transcription within rare primary cell populations.

Genes, 2017
Authors
Jones, Steven J M, Taylor, Gregory A, Chan, Simon, Warren, René L, Hammond, S Austin, Bilobram, Steven, Mordecai, Gideon, Suttle, Curtis A, Miller, Kristina M, Schulze, Angela, Chan, Amy M, Jones, Samantha J, Tse, Kane, Li, Irene, Cheung, Dorothy, Mungall, Karen L, Choo, Caleb, Ally, Adrian, Dhalla, Noreen, Tam, Angela K Y, Troussard, Armelle, Kirk, Heather, Pandoh, Pawan, Paulino, Daniel, Coope, Robin J N, Mungall, Andrew J, Moore, Richard, Zhao, Yongjun, Birol, Inanc, Ma, Yussanne, Marra, Marco, Haulena, Martin
Publication Abstract
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus . The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

Molecular cancer therapeutics, 2017
Authors
Weiswald, Louis-Bastien, Hasan, Mohammad R, Wong, John C T, Pasiliao, Clarissa C, Rahman, Mahbuba, Ren, Jianhua, Yin, Yaling, Gusscott, Samuel, Vacher, Sophie, Weng, Andrew P, Kennecke, Hagen F, Bièche, Ivan, Schaeffer, David F, Yapp, Donald T, Tai, Isabella T
Publication Abstract
Cyclin-dependent kinase 10 (CDK10), a CDC2-related kinase, is highly expressed in colorectal cancer. Its role in the pathogenesis of colorectal cancer is unknown. This study examines the function of CDK10 in colorectal cancer, and demonstrates its role in suppressing apoptosis and in promoting tumor growth and Modulation of CDK10 expression in colorectal cancer cell lines demonstrates that CDK10 promotes cell growth, reduces chemosensitivity and inhibits apoptosis by upregulating the expression of Bcl-2. This effect appears to depend on its kinase activity, as kinase-defective mutant colorectal cancer cell lines have an exaggerated apoptotic response and reduced proliferative capacity. , inhibiting CDK10 in colorectal cancer following intratumoral injections of lentivirus-mediated CDK10 siRNA in a patient-derived xenograft mouse model demonstrated its efficacy in suppressing tumor growth. Furthermore, using a tissue microarray of human colorectal cancer tissues, the potential for CDK10 to be a prognostic biomarker in colorectal cancer was explored. In tumors of individuals with colorectal cancer, high expression of CDK10 correlates with earlier relapse and shorter overall survival. The findings of this study indicate that CDK10 plays a role in the pathogenesis in colorectal cancer and may be a potential therapeutic target for treatment. .

Cancer causes & control : CCC, 2017
Authors
McGahan, Colleen E, Linn, Kevin, Guno, Preston, Johnson, Harmony, Coldman, Andrew J, Spinelli, John J, Caron, Nadine R
Publication Abstract
For First Nations (FN) peoples living in British Columbia (BC), little is known regarding cancer in the population. The aim of this study was to explore cancer incidence and survival in the FN population of BC and compare it to the non-FN population.

Leukemia & lymphoma, 2017
Authors
Jones, Samantha J, Voong, Jackson, Thomas, Ruth, English, Amy, Schuetz, Johanna, Slack, Graham W, Graham, Jinko, Connors, Joseph M, Brooks-Wilson, Angela
Publication Abstract
We studied 140 families with two or more lymphoid cancers, including non-Hodgkin lymphoma (NHL), Hodgkin lymphoma (HL), chronic lymphocytic leukemia (CLL), and multiple myeloma (MM), for deviation from the population age of onset and lymphoid cancer co-occurrence patterns. Median familial NHL, HL, CLL and MM ages of onset are substantially earlier than comparable population data. NHL, HL and CLL (but not MM) also show earlier age of onset in later generations, known as anticipation. The co-occurrence of lymphoid cancers is significantly different from that expected based on population frequencies (p < .0001), and the pattern differs more in families with more affected members (p < .0001), suggesting specific lymphoid cancer combinations have a shared genetic basis. These families provide evidence for inherited factors that increase the risk of multiple lymphoid cancers. This study was approved by the BC Cancer Agency - University of British Columbia Clinical Research Ethics Board.

Nature, 2017
Authors
Lan, Xiaoyang, Jörg, David J, Cavalli, Florence M G, Richards, Laura M, Nguyen, Long V, Vanner, Robert J, Guilhamon, Paul, Lee, Lilian, Kushida, Michelle M, Pellacani, Davide, Park, Nicole I, Coutinho, Fiona J, Whetstone, Heather, Selvadurai, Hayden J, Che, Clare, Luu, Betty, Carles, Annaick, Moksa, Michelle, Rastegar, Naghmeh, Head, Renee, Dolma, Sonam, Prinos, Panagiotis, Cusimano, Michael D, Das, Sunit, Bernstein, Mark, Arrowsmith, Cheryl H, Mungall, Andrew J, Moore, Richard A, Ma, Yussanne, Gallo, Marco, Lupien, Mathieu, Pugh, Trevor J, Taylor, Michael D, Hirst, Martin, Eaves, Connie J, Simons, Benjamin D, Dirks, Peter B
Publication Abstract
Human glioblastomas harbour a subpopulation of glioblastoma stem cells that drive tumorigenesis. However, the origin of intratumoural functional heterogeneity between glioblastoma cells remains poorly understood. Here we study the clonal evolution of barcoded glioblastoma cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of glioblastoma clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in glioblastoma stem cells. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, which in turn generates non-proliferative cells. We also identify rare 'outlier' clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant glioblastoma stem cells. Finally, we show that functionally distinct glioblastoma stem cells can be separately targeted using epigenetic compounds, suggesting new avenues for glioblastoma-targeted therapy.
Back to top