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Yadav S, Singh N, Shah PP, Rowbotham DA, Malik D, Srivastav A, Shankar J, Lam WL, Lockwood WW, Beverly LJ. MIR155 Regulation of Ubiquilin1 and Ubiquilin2: Implications in Cellular Protection and Tumorigenesis. Neoplasia 2017; 19:321-332. [PMID: 28315615 PMCID: PMC5361868 DOI: 10.1016/j.neo.2017.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/31/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022] Open
Abstract
Ubiquilin (UBQLN) proteins are adaptors thought to link ubiquitinated proteins to the proteasome. However, our lab has recently reported a previously unappreciated role for loss of UBQLN in lung cancer progression. In fact, UBQLN genes are lost in over 50% of lung cancer samples examined. However, a reason for the loss of UBQLN has not been proposed, nor has a selective pressure that could lead to deletion of UBQLN been reported. Diesel Exhaust Particles (DEP) are a major concern in the large cities of developing nations and DEP exposed populations are at an increased risk of developing a number of illnesses, including lung cancer. A connection between DEP and UBQLN has never been examined. In the present study, we determined the effect of DEP on lung cell lines and were interested to determine if UBQLN proteins could potentially play a protective role following treatment with DEP. Interestingly, we found that DEP treated cells have increased expression of UBQLN proteins. In fact, over-expression of UBQLN was capable of protecting cells from DEP toxicity. To investigate the mechanism by which DEP leads to increased UBQLN protein levels, we identified and interrogated microRNAs that were predicted to regulate UBQLN mRNA. We found that DEP decreases the oncogenic microRNA, MIR155. Further, we showed that MIR155 regulates the mRNA of UBQLN1 and UBQLN2 in cells, such that increased MIR155 expression increased cell invasion, migration, wound formation and clonogenicity in UBQLN-loss dependent manner. This is the first report of an environmental carcinogen regulating expression of UBQLN proteins. We show that exposure of cells to DEP causes an increase in UBQLN levels and that MIR155 regulates mRNA of UBQLN. Thus, we propose that DEP-induced repression of MIR155 leads to increased UBQLN levels, which in turn may be a selective pressure on lung cells to lose UBQLN1.
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Affiliation(s)
- Sanjay Yadav
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202; CSIR-Indian Institute of Toxicology Research, Lucknow, UP 226001, India.
| | - Nishant Singh
- CSIR-Indian Institute of Toxicology Research, Lucknow, UP 226001, India.
| | - Parag P Shah
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202.
| | - David A Rowbotham
- Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C., Canada V5Z 1L3.
| | - Danial Malik
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202.
| | - Ankita Srivastav
- CSIR-Indian Institute of Toxicology Research, Lucknow, UP 226001, India.
| | - Jai Shankar
- CSIR-Indian Institute of Toxicology Research, Lucknow, UP 226001, India.
| | - Wan L Lam
- Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C., Canada V5Z 1L3; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, B.C., Canada V6T 2B5.
| | - William W Lockwood
- Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C., Canada V5Z 1L3; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, B.C., Canada V6T 2B5.
| | - Levi J Beverly
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202; Department of Medicine, Division of Hematology and Oncology, University of Louisville School of Medicine, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202.
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Marshall EA, Ng KW, Kung SHY, Conway EM, Martinez VD, Halvorsen EC, Rowbotham DA, Vucic EA, Plumb AW, Becker-Santos DD, Enfield KSS, Kennett JY, Bennewith KL, Lockwood WW, Lam S, English JC, Abraham N, Lam WL. Emerging roles of T helper 17 and regulatory T cells in lung cancer progression and metastasis. Mol Cancer 2016; 15:67. [PMID: 27784305 PMCID: PMC5082389 DOI: 10.1186/s12943-016-0551-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is a leading cause of cancer-related deaths worldwide. Lung cancer risk factors, including smoking and exposure to environmental carcinogens, have been linked to chronic inflammation. An integral feature of inflammation is the activation, expansion and infiltration of diverse immune cell types, including CD4+ T cells. Within this T cell subset are immunosuppressive regulatory T (Treg) cells and pro-inflammatory T helper 17 (Th17) cells that act in a fine balance to regulate appropriate adaptive immune responses.In the context of lung cancer, evidence suggests that Tregs promote metastasis and metastatic tumor foci development. Additionally, Th17 cells have been shown to be an integral component of the inflammatory milieu in the tumor microenvironment, and potentially involved in promoting distinct lung tumor phenotypes. Studies have shown that the composition of Tregs and Th17 cells are altered in the tumor microenvironment, and that these two CD4+ T cell subsets play active roles in promoting lung cancer progression and metastasis.We review current knowledge on the influence of Treg and Th17 cells on lung cancer tumorigenesis, progression, metastasis and prognosis. Furthermore, we discuss the potential biological and clinical implications of the balance among Treg/Th17 cells in the context of the lung tumor microenvironment and highlight the potential prognostic function and relationship to metastasis in lung cancer.
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Affiliation(s)
- Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Sonia H Y Kung
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada. .,British Columbia Cancer Research Centre Centre, Vancouver, Canada.
| | - Emma M Conway
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Elizabeth C Halvorsen
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - David A Rowbotham
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Adam W Plumb
- Departments of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | | | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Jennifer Y Kennett
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Kevin L Bennewith
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - John C English
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ninan Abraham
- Departments of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada. .,British Columbia Cancer Research Centre Centre, Vancouver, Canada.
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Martinez VD, Enfield KSS, Rowbotham DA, Lam WL. An atlas of gastric PIWI-interacting RNA transcriptomes and their utility for identifying signatures of gastric cancer recurrence. Gastric Cancer 2016; 19:660-665. [PMID: 25779424 PMCID: PMC4573768 DOI: 10.1007/s10120-015-0487-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
Abstract
The poor survival and recurrence rate in gastric adenocarcinoma highlights the need for cancer gene discovery. Towards this end, we globally assessed the expression of an emerging class of small non-coding RNAs, called PIWI-interacting RNAs (piRNAs). We analysed the transcriptomes of 358 non-malignant stomach tissue and gastric adenocarcinoma samples, and found that nearly half of the expressed piRNAs were overexpressed in tumours. Our gastric piRNA atlas showed that most piRNAs were embedded in protein-coding sequences rather than known piRNA clusters. Furthermore, we identified a three-piRNA signature associated with recurrence-free survival. In this proof-of-principle study, we demonstrate the potential clinical utility of piRNAs in gastric cancer.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | - Katey SS Enfield
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | | | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
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Enfield KSS, Rowbotham DA, Holly A, Anderson C, Ng KW, Minatel BDC, Dellaire G, Pastrello C, Jurisica I, MacAulay C, Lam S, Lam WL. Abstract A21: MiR-106a and miR-106b affect growth and metastasis of lung adenocarcinoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-a21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: MiR-106a and miR-106b are paralogs of the oncogenic miR-17~92, and have been associated with poor outcome and metastasis in several solid tumors. Their role in lung cancer is relatively unexplored. We characterized the expression of miR-106a and miR-106b in a clinical cohort of lung adenocarcinoma (AC) tumors and assessed their ability to regulate growth and metastasis in cell models.
Methods: MicroRNA (miRNA) expression was deduced from small RNA sequencing data derived from clinical lung AC specimens (60 localized, 27 with lymph node invasion) and paired non-malignant tissues. MiR-106a and miR-106b overexpression vectors and controls were stably transfected into immortalized non-malignant Human Bronchial Epithelial Cells (HBECs) and stage I AC cell lines with epithelial expression patterns by lentiviral delivery. Migration and invasion was assessed by Boyden chamber assay, while cell proliferation was assessed by BrdU incorporation assay. Expression of epithelial-to-mesenchymal transition (EMT) markers and other proteins of interest were assessed by Western Blot. Clinical associations in an external cohort were derived using publically available TCGA data.
Results: MiR-106a and miR-106b were significantly overexpressed in lung AC with lymph node invasion. Overexpression of miR-106a and miR-106b significantly increased proliferation of lung AC cell lines, and was associated with decreased levels of predicted target, p21. AC cell lines displayed a marked increase in metastatic phenotypes in vitro, and were associated with increased mesenchymal and decreased epithelial markers, characteristic of EMT. Importantly, tumors with high expression of both miR-106a and miR-106b and mesenchymal marker vimentin had significantly poorer outcome.
Conclusions: MiR-106a and miR-106b are overexpressed in metastatic lung AC. Lung AC cell models indicate these miRNAs are metastatic agonists, affecting the metastatic potential of cells at least in part via induction of EMT. A deeper characterization of this observation may reveal therapeutic intervention points, or, with the development of miRNA therapeutics, miR-106a/b may be promising targets to prevent or treat metastatic disease.
Citation Format: Katey SS Enfield, David A. Rowbotham, Alice Holly, Christine Anderson, Kevin W. Ng, Brenda de Carvalho Minatel, Graham Dellaire, Chiara Pastrello, Igor Jurisica, Calum MacAulay, Stephen Lam, Wan L. Lam. MiR-106a and miR-106b affect growth and metastasis of lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A21.
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Affiliation(s)
| | | | | | | | - Kevin W. Ng
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | | | | | | | - Igor Jurisica
- 3Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Stephen Lam
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Wan L. Lam
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
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Stewart GL, Enfield KSS, Rowbotham DA, Hubaux R, Martinez V, Lam S, Lam W. Abstract B26: OIP5-Antisense 1, a long noncoding RNA deregulated in non-small cell lung cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-b26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Lung cancer represents an enormous health burden, representing the most common cause of cancer death worldwide. The poor therapeutic outcome is largely due to a complex molecular background as well as late stage diagnosis, with most patients presenting unresectable local tumors, or metastatic disease. While mutations of driver genes is a well-known mechanism, approximately half of all non-small cell lung cancer (NSCLC) tumors harbor no known clinically relevant oncogenic drivers, emphasizing the need to explore alternative mechanisms such as non-coding RNAs (ncRNAs). Natural antisense transcripts (NATS) are ncRNAs that are expressed from the opposite strand of coding mRNAs. These genes overlap with, and are often involved in the regulation of their sense counterparts. NATs can recruit regulatory complexes to their transcriptional locus, leading to silencing of transcription and have recently been described in cancer to silence tumor suppressor genes. NATs are quite prevalent as it is estimated that 25-40% of genes display overlapping transcription, however only a few NATs have been characterized, emphasizing the need to explore these ncRNAs in the context of NSCLC.
Hypothesis: We hypothesize NATs of NSCLC-related genes are deregulated in NSCLC.
Methods: We performed RNAseq and miRNAseq on a set of 65 NSCLC tumors including 36 adenocarcinomas and 29 squamous cell carcinomas as well as matched non-malignant lung tissue. A sign rank test was used to identify NATs with significantly altered expression between tumor and matched normal. Survival analysis was done using a Cox Proportional hazard model, as well as the Kaplan-Meier method.
Results: We have identified a NAT of OIP5, a lung cancer oncogene required for chromatin segregation, to be significantly underexpressed, while its sense counterpart, OIP5 mRNA, is significantly overexpressed. We also find that expression of both OIP5 and OIP5-AS1 has a significant impact on 5 year survival. These findings suggest that deregulation of OIP5 through its antisense RNA may represent a novel mechanism regulating tumor phenotypes in NSCLC.
Citation Format: Greg L. Stewart, Katey SS Enfield, David A. Rowbotham, Roland Hubaux, Victor Martinez, Stephen Lam, Wan Lam. OIP5-Antisense 1, a long noncoding RNA deregulated in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B26.
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Affiliation(s)
| | | | | | | | | | - Stephen Lam
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Wan Lam
- BC Cancer Research Centre, Vancouver, BC, Canada
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Firmino N, Martinez VD, Rowbotham DA, Enfield KSS, Bennewith KL, Lam WL. HPV status is associated with altered PIWI-interacting RNA expression pattern in head and neck cancer. Oral Oncol 2016; 55:43-48. [PMID: 26852287 DOI: 10.1016/j.oraloncology.2016.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/11/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVES As HPV-induced cases of oral malignancy increase, it is important to understand the molecular differences between HPV positive and negative head and neck squamous cell carcinoma (HNSCC). PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs aberrantly expressed in cancer. We analyzed global piRNA expression patterns to define the HNSCC piRNA transcriptome and assess whether HPV infection status associates with changes in piRNA levels. MATERIALS AND METHODS A total of 498 HNSCC small RNA sequencing libraries were acquired from the Cancer Genomics Hub (cgHUB) Data Repository and a custom sequence analysis pipeline was developed to deduce piRNA expression from raw sequencing data. Expression matrices were aligned to clinicopathological features in order to analyze piRNA expression patterns across different HNSCC groups. The association of a piRNA signature with HPV-positive patient survival was evaluated using a Cox proportional hazard model. RESULTS Analysis of piRNA levels between HNSCC and non-malignant tissues revealed distinct expression patterns, with 87 piRNAs exclusively expressed in tumor samples. HPV infection status affected the expression of 41 of these piRNAs. Eleven (26.8%) piRNAs were significantly downregulated in HPV16/18 tumors compared to other HPV types. Remarkably, expression of a combination of five-piRNAs in HPV-positive HNSCC tumors was associated with worse overall survival. CONCLUSION The expression of specific piRNAs is deregulated in HNSCC, and changes with both HPV status and type. Importantly, a five-piRNA signature is able to delineate a subset of HPV-positive HNSCC patients with poor outcome, highlighting the potential utility of piRNAs in patient management.
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Enfield KS, Anderson C, Marshall E, Ng KW, de Carvalho Minatel B, Rowbotham DA, Chari R, Fuller M, Milne K, Becker-Santos DD, MacAulay C, Karsan A, Lam S, Lam WL. ELF3 amplification at 1q32.1 promotes SMAD4-independent tumorigenesis. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2015.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Stewart GL, Enfield KSS, Rowbotham DA, Hubaux R, Lam S, Lam W. Natural antisense transcript deregulation in non-small cell lung cancer. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2015.12.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rowbotham DA, Enfield KSS, Martinez VD, Thu KL, Vucic EA, Stewart GL, Bennewith KL, Lam WL. Multiple Components of the VHL Tumor Suppressor Complex Are Frequently Affected by DNA Copy Number Loss in Pheochromocytoma. Int J Endocrinol 2014; 2014:546347. [PMID: 25298778 PMCID: PMC4178909 DOI: 10.1155/2014/546347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 02/06/2023] Open
Abstract
Pheochromocytomas (PCC) are rare tumors that arise in chromaffin tissue of the adrenal gland. PCC are frequently inherited through predisposing mutations in genes such as the von Hippel-Lindau (VHL) tumor suppressor. VHL is part of the VHL elongin BC protein complex that also includes CUL2/5, TCEB1, TCEB2, and RBX1; in normoxic conditions this complex targets hypoxia-inducible factor 1 alpha (HIF1A) for degradation, thus preventing a hypoxic response. VHL inactivation by genetic mechanisms, such as mutation and loss of heterozygosity, inhibits HIF1A degradation, even in the presence of oxygen, and induces a pseudohypoxic response. However, the described <10% VHL mutation rate cannot account for the high frequency of hypoxic response observed. Indeed, little is known about genetic mechanisms disrupting other complex component genes. Here, we show that, in a panel of 171 PCC tumors, 59.6% harbored gene copy number loss (CNL) of at least one complex component. CNL significantly reduced gene expression and was associated with enrichment of gene targets controlled by HIF1. Interestingly, we show that VHL-related renal clear cell carcinoma harbored disruption of VHL alone. Our results indicate that VHL elongin BC protein complex components other than VHL could be important for PCC tumorigenesis and merit further investigation.
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Affiliation(s)
- David A. Rowbotham
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | | | - Victor D. Martinez
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
- BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
- *Victor D. Martinez:
| | - Kelsie L. Thu
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Emily A. Vucic
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Greg L. Stewart
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Kevin L. Bennewith
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
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