Frontiers in oncology, 2020
Authors
Amy Moore, Eleanor Kane, Zhaoming Wang, Orestis A Panagiotou, Lauren R Teras, Alain Monnereau, Nicole Wong Doo, Mitchell J Machiela, Christine F Skibola, Susan L Slager, Gilles Salles, Nicola J Camp, Paige M Bracci, Alexandra Nieters, Roel C H Vermeulen, Joseph Vijai, Karin E Smedby, Yawei Zhang, Claire M Vajdic, Wendy Cozen, John J Spinelli, Henrik Hjalgrim, Graham G Giles, Brian K Link, Jacqueline Clavel, Alan A Arslan, Mark P Purdue, Lesley F Tinker, Demetrius Albanes, Giovanni M Ferri, Thomas M Habermann, Hans-Olov Adami, Nikolaus Becker, Yolanda Benavente, Simonetta Bisanzi, Paolo Boffetta, Paul Brennan, Angela R Brooks-Wilson, Federico Canzian, Lucia Conde, David G Cox, Karen Curtin, Lenka Foretova, Susan M Gapstur, Hervé Ghesquières, Martha Glenn, Bengt Glimelius, Rebecca D Jackson, Qing Lan, Mark Liebow, Marc Maynadie, James McKay, Mads Melbye, Lucia Miligi, Roger L Milne, Thierry J Molina, Lindsay M Morton, Kari E North, Kenneth Offit, Marina Padoan, Alpa V Patel, Sara Piro, Vignesh Ravichandran, Elio Riboli, Silvia de Sanjose, Richard K Severson, Melissa C Southey, Anthony Staines, Carolyn Stewart, Ruth C Travis, Elisabete Weiderpass, Stephanie Weinstein, Tongzhang Zheng, Stephen J Chanock, Nilanjan Chatterjee, Nathaniel Rothman, Brenda M Birmann, James R Cerhan, Sonja I Berndt
Publication Abstract

Although the evidence is not consistent, epidemiologic studies have suggested that taller adult height may be associated with an increased risk of some non-Hodgkin lymphoma (NHL) subtypes. Height is largely determined by genetic factors, but how these genetic factors may contribute to NHL risk is unknown. We investigated the relationship between genetic determinants of height and NHL risk using data from eight genome-wide association studies (GWAS) comprising 10,629 NHL cases, including 3,857 diffuse large B-cell lymphoma (DLBCL), 2,847 follicular lymphoma (FL), 3,100 chronic lymphocytic leukemia (CLL), and 825 marginal zone lymphoma (MZL) cases, and 9,505 controls of European ancestry. We evaluated genetically predicted height by constructing polygenic risk scores using 833 height-associated SNPs. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for association between genetically determined height and the risk of four NHL subtypes in each GWAS and then used fixed-effect meta-analysis to combine subtype results across studies. We found suggestive evidence between taller genetically determined height and increased CLL risk (OR = 1.08, 95% CI = 1.00–1.17, p = 0.049), which was slightly stronger among women (OR = 1.15, 95% CI: 1.01–1.31, p = 0.036). No significant associations were observed with DLBCL, FL, or MZL. Our findings suggest that there may be some shared genetic factors between CLL and height, but other endogenous or environmental factors may underlie reported epidemiologic height associations with other subtypes.

Electrophoresis, 2020
Authors
Jianhui Cheng, Gregg B Morin, David D Y Chen
Publication Abstract

A high organic content CE‐MS/MS (HOCE‐MS/MS) method was developed for the proteomic analysis of envelope proteins extracted from spinach leaves. Separation was performed in a 1‐m long hydroxypropyl cellulose coated capillary, using 8% (v/v) formic acid in 70% (v/v) methanol and 22% water as the BGE. A flow‐through microvial interface was used to couple the CE system with an Orbitrap Fusion Lumos mass spectrometer, and field‐amplified sample stacking was used to improve the concentration sensitivity. Using this optimized method, 3579 peptides and 1141 proteins were identified using the Proteome Discoverer software with a 1% false discovery rate at the protein level. Relative to conventional aqueous CE, HOCE‐MS did a better job of discovering hydrophobic peptides and provided more peptide and protein identifications. Relative to nano‐LC‐MS, it achieved comparable peptide and protein identification performance and detected peptides not identified by LC‐MS: of the full set of peptides identified using the two techniques, 19% were identified only using HOCE‐MS. It also outperformed nano‐LC‐MS with respect to the detection of low molecular weight peptides.

Cancers, 2020
Authors
Matthew Richardson, Hae Jung Min, Quan Hong, Katie Compton, Sze Wing Mung, Zoe Lohn, Jennifer Nuk, Mary McCullum, Cheryl Portigal-Todd, Aly Karsan, Dean Regier, Lori A Brotto, Sophie Sun, Kasmintan A Schrader
Publication Abstract

New streamlined models for genetic counseling and genetic testing have recently been developed in response to increasing demand for cancer genetic services. To improve access and decrease wait times, we implemented an oncology clinic-based genetic testing model for breast and ovarian cancer patients in a publicly funded population-based health care setting in British Columbia, Canada. This observational study evaluated the oncology clinic-based model as compared to a traditional one-on-one approach with a genetic counsellor using a multi-gene panel testing approach. The primary objectives were to evaluate wait times and patient reported outcome measures between the oncology clinic-based and traditional genetic counselling models. Secondary objectives were to describe oncologist and genetic counsellor acceptability and experience. Wait times from referral to return of genetic testing results were assessed for 400 patients with breast and/or ovarian cancer undergoing genetic testing for hereditary breast and ovarian cancer from June 2015 to August 2017. Patient wait times from referral to return of results were significantly shorter with the oncology clinic-based model as compared to the traditional model (403 vs. 191 days; p < 0.001). A subset of 148 patients (traditional n = 99; oncology clinic-based n = 49) completed study surveys to assess uncertainty, distress, and patient experience. Responses were similar between both models. Healthcare providers survey responses indicated they believed the oncology clinic-based model was acceptable and a positive experience. Oncology clinic-based genetic testing using a multi-gene panel approach and post-test counselling with a genetic counsellor significantly reduced wait times and is acceptable for patients and health care providers.

Nature, 2020
Authors
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Publication Abstract

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

Clinical colorectal cancer, 2020
Authors
Shehara Mendis, Miguel Alcaide, James T Topham, Benny Johnson, Ryan D Morin, Jenny Chu, Ian Bosdet, Scott Kopetz, Aly Karsan, Sharlene Gill, Janessa Laskin, Steven J M Jones, Marco A Marra, David F Schaeffer, Daniel J Renouf, Jonathan M Loree
Publication Abstract

Clinical Practice Points

Non-V600 B-Raf Proto-Oncogene, Serine/Threonine Kinase (BRAF) mutated metastatic colorectal cancer (mCRC) has a better prognosis than V600 BRAF mCRC Non-V600 mutations can be further subdivided into class II or III variants; class III variants might respond to anti-epidermal growth factor receptor (EGFR) therapy.

We describe an mCRC patient with a G466V (class III) BRAF variant found in the primary tumor before anti-EGFR therapy, but not in a liver metastasis after anti-EGFR exposure. A reduction in the BRAF variant between pre- and post-treatment plasma samples was discordant with a concomitant increase in circulating tumor DNA (ctDNA) levels of comutations and radiologic progression in metastatic lesions.

There was copy number neutral loss of heterozygosity (CN-LOH) at the BRAF coding region in the liver biopsy. The CN-LOH might have resulted in loss of the class III BRAF variant that chronologically corresponded with a decrease of this variant in ctDNA.

In a retrospective cohort from 2 institutions, we show that the relative variant allele frequency (rVAF) of non-V600 BRAF mutations (0.74) is lower than for rVAF of V600 (class I) BRAF mutations (1.00; P < .0001). Among non-V600 mutations, class III (P < .0001) but not class II mutations (P = .10) had statistically lower allele frequencies than V600 mutations.

Discordant responses between ctDNA levels of comutations can occur because of tumor heterogeneity and evolutionary pressures.

The CN-LOH described might be a novel mechanism of resistance to anti-EGFR therapy because wild type BRAF is less RAS signaling-dependent than class III variants. Non-V600 BRAF occurs at a lower rVAF than V600 BRAF mutations and may undergo clonal selection.

Nature Medicine, 2020
Authors
Daisuke Ennishi, Shannon Healy, Ali Bashashati, Saeed Saberi, Christoffer Hother, Anja Mottok, Fong Chun Chan, Lauren Chong, Libin Abraham, Robert Kridel, Merrill Boyle, Barbara Meissner, Tomohiro Aoki, Katsuyoshi Takata, Bruce W Woolcock, Elena Viganò, Michael Gold, Laurie L Molday, Robert S Molday, Adele Telenius, Michael Y Li, Nicole Wretham, Nancy Dos Santos, Mark Wong, Natasja N Viller, Robert A Uger, Gerben Duns, Abigail Baticados, Angel Madero, Brianna N Bristow, Pedro Farinha, Graham W Slack, Susana Ben-Neriah, Daniel Lai, Allen W Zhang, Sohrab Salehi, Hennady P Shulha, Derek S Chiu, Sara Mostafavi, Alina S Gerrie, Da Wei Huang, Christopher Rushton, Diego Villa, Laurie H Sehn, Kerry J Savage, Andrew J Mungall, Andrew P Weng, Marcel B Bally, Ryan D Morin, Gabriela V Cohen Freue, Louis M Staudt, Joseph M Connors, Marco A Marra, Sohrab P Shah, Randy D Gascoyne, David W Scott, Christian Steidl
Publication Abstract

Transmembrane protein 30A (TMEM30A) maintains the asymmetric distribution of phosphatidylserine, an integral component of the cell membrane and ‘eat-me’ signal recognized by macrophages. Integrative genomic and transcriptomic analysis of diffuse large B-cell lymphoma (DLBCL) from the British Columbia population-based registry uncovered recurrent biallelic TMEM30A loss-of-function mutations, which were associated with a favorable outcome and uniquely observed in DLBCL. Using TMEM30A-knockout systems, increased accumulation of chemotherapy drugs was observed in TMEM30A-knockout cell lines and TMEM30A-mutated primary cells, explaining the improved treatment outcome. Furthermore, we found increased tumor-associated macrophages and an enhanced effect of anti-CD47 blockade limiting tumor growth in TMEM30A-knockout models. By contrast, we show that TMEM30A loss-of-function increases B-cell signaling following antigen stimulation—a mechanism conferring selective advantage during B-cell lymphoma development. Our data highlight a multifaceted role for TMEM30A in B-cell lymphomagenesis, and characterize intrinsic and extrinsic vulnerabilities of cancer cells that can be therapeutically exploited.

Expert opinion on drug discovery, 2020
Authors
Marianne D Sadar
Publication Abstract

Introduction: Intrinsically disordered proteins (IDPs) and regions (IDRs) lack stable three-dimensional structure making drug discovery challenging. A validated therapeutic target for diseases such as prostate cancer is the androgen receptor (AR) which has a disordered amino-terminal domain (NTD) that contains all of its transcriptional activity. Drug discovery against the AR-NTD is of intense interest as a potential treatment for disease such as advanced prostate cancer that is driven by truncated constitutively active splice variants of AR that lack the C-terminal ligand-binding domain (LBD).

Areas covered: This article presents an overview of the relevance of AR and its intrinsically disordered NTD as a drug target. AR structure and approaches to blocking AR transcriptional activity are discussed. The discovery of small molecules, including the libraries used, proven binders to the AR-NTD, and site of interaction of these small molecules in the AR-NTD are presented along with discussion of the Phase I clinical trial.

Expert opinion: The lack of drugs in the clinic that directly bind IDPs/IDRs reflects the difficulty of targeting these proteins and obtaining specificity. However, it may also point to an inappropriateness of too closely borrowing concepts and resources from drug discovery to folded proteins.

Cancer epidemiology, biomarkers & prevention, 2020
Authors
Geffen Kleinstern, Nicola J Camp, Sonja I Berndt, Brenda M Birmann, Alexandra Nieters, Paige M Bracci, James D McKay, Hervé Ghesquières, Qing Lan, Henrik Hjalgrim, Yolanda Benavente, Alain Monnereau, Sophia S Wang, Yawei Zhang, Mark P Purdue, Anne Zeleniuch-Jacquotte, Graham G Giles, Roel Vermeulen, Pierluigi Cocco, Demetrius Albanes, Lauren R Teras, Angela R Brooks-Wilson, Claire M Vajdic, Eleanor Kane, Neil E Caporaso, Karin E Smedby, Gilles Salles, Joseph Vijai, Stephen J Chanock, Christine F Skibola, Nathaniel Rothman, Susan L Slager, James R Cerhan
Publication Abstract

Background: Lipid traits have been inconsistently linked to risk of non-Hodgkin lymphoma (NHL). We examined the association of genetically predicted lipid traits with risk of diffuse large B-cell lymphoma (DLBCL), chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and marginal zone lymphoma (MZL) using Mendelian randomization (MR) analysis.

Methods: Genome-wide association study data from the InterLymph Consortium were available for 2,661 DLBCLs, 2,179 CLLs, 2,142 FLs, 824 MZLs, and 6,221 controls. SNPs associated (P < 5 × 10−8) with high-density lipoprotein (HDL, n = 164), low-density lipoprotein (LDL, n = 137), total cholesterol (TC, n = 161), and triglycerides (TG, n = 123) were used as instrumental variables (IV), explaining 14.6%, 27.7%, 16.8%, and 12.8% of phenotypic variation, respectively. Associations between each lipid trait and NHL subtype were calculated using the MR inverse variance–weighted method, estimating odds ratios (OR) per standard deviation and 95% confidence intervals (CI).

Results: HDL was positively associated with DLBCL (OR = 1.14; 95% CI, 1.00–1.30) and MZL (OR = 1.09; 95% CI, 1.01–1.18), while TG was inversely associated with MZL risk (OR = 0.90; 95% CI, 0.83–0.99), all at nominal significance (P < 0.05). A positive trend was observed for HDL with FL risk (OR = 1.08; 95% CI, 0.99–1.19; P = 0.087). No associations were noteworthy after adjusting for multiple testing.

Conclusions: We did not find evidence of a clear or strong association of these lipid traits with the most common NHL subtypes. While these IVs have been previously linked to other cancers, our findings do not support any causal associations with these NHL subtypes.

Impact: Our results suggest that prior reported inverse associations of lipid traits are not likely to be causal and could represent reverse causality or confounding.

Blood, 2020
Authors
Prasath Pararajalingam, Krysta M Coyle, Sarah Arthur, Nicole Thomas, Miguel Alcaide, Barbara Meissner, Merrill Boyle, Quratulain Qureshi, Bruno M Grande, Christopher Rushton, Graham W Slack, Andrew Mungall, Constantine Tam, Rishu Agarwal, Sarah-Jane Dawson, Georg Lenz, Sriram Balasubramanian, Randy D Gascoyne, Christian Steidl, Joseph Connors, Diego Villa, Timothy E Audas, Marco A Marra, Nathalie A Johnson, David W Scott, Ryan D Morin
Publication Abstract

Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we re-sequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent non-coding mutations surrounding a single exon of the HNRNPH1 gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent non-coding mutations in disrupting an auto-regulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly implicate a role for aberrant regulation of mRNA processing in MCL pathobiology.

Methods & Clinical Development, 2020
Authors
Lisa Dreolini, Mark Cullen, Eric Yung, Lawrence Laird, John R. Webb, Brad H. Nelson, Kevin A. Hay, Miruna Balasundaram, Natasha Kekre, Robert A. Holt.
Publication Abstract

Mycoplasma species (spp.) bacteria can infect cell cultures, posing a potential threat to recipients of cell therapy products. Conventional Mycoplasma testing methods are highly sensitive but typically require a minimum of 28 days to produce results. This delay is problematic if rapid results are needed to inform treatment decisions. Nucleic acid amplification technique (NAT) methods have been gaining favor for Mycoplasma testing due to their speed and specificity; however, they must first be qualified as meeting or exceeding the sensitivity of the compendial method. We present herein a NAT method for the detection of Mycoplasma that circumvents the need for live Mycoplasma spp. in the test procedure by instead being qualified using Mycoplasma spp. genomic DNA. We have demonstrated a lower limit of detection that exceeds the regulatory requirements set by Health Canada. This assay is now being used to screen clinical cell therapy products manufactured at our center.

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