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Li MY, Chong LC, Duns G, Lytle A, Woolcock B, Jiang A, Telenius A, Ben-Neriah S, Nawaz W, Slack GW, Elisia I, Viganò E, Aoki T, Healy S, Krystal G, Venturutti L, Scott DW, Steidl C. TRAF3 loss-of-function reveals the noncanonical NF-κB pathway as a therapeutic target in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2024; 121:e2320421121. [PMID: 38662551 PMCID: PMC11067025 DOI: 10.1073/pnas.2320421121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/29/2024] [Indexed: 05/05/2024] Open
Abstract
Here, we report recurrent focal deletions of the chr14q32.31-32 locus, including TRAF3, a negative regulator of NF-κB signaling, in de novo diffuse large B cell lymphoma (DLBCL) (24/324 cases). Integrative analysis revealed an association between TRAF3 copy number loss with accumulation of NIK, the central noncanonical (NC) NF-κB kinase, and increased NC NF-κB pathway activity. Accordingly, TRAF3 genetic ablation in isogenic DLBCL model systems caused upregulation of NIK and enhanced NC NF-κB downstream signaling. Knockdown or pharmacological inhibition of NIK in TRAF3-deficient cells differentially impaired their proliferation and survival, suggesting an acquired onco-addiction to NC NF-κB. TRAF3 ablation also led to exacerbated secretion of the immunosuppressive cytokine IL-10. Coculturing of TRAF3-deficient DLBCL cells with CD8+ T cells impaired the induction of Granzyme B and interferon (IFN) γ, which were restored following neutralization of IL-10. Our findings corroborate a direct relationship between TRAF3 genetic alterations and NC NF-κB activation, and highlight NIK as a potential therapeutic target in a defined subset of DLBCL.
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Affiliation(s)
- Michael Y. Li
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BCV6T 2B5, Canada
| | - Lauren C. Chong
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Andrew Lytle
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Bruce Woolcock
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Aixiang Jiang
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BCV6T 2B5, Canada
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Waqas Nawaz
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BCV6T 2B5, Canada
| | - Ingrid Elisia
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Elena Viganò
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Tomohiro Aoki
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Shannon Healy
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Gerald Krystal
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - Leandro Venturutti
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BCV6T 2B5, Canada
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BCV6T 2B5, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BCV5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BCV6T 2B5, Canada
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2
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Aoki T, Jiang A, Xu A, Yin Y, Gamboa A, Milne K, Takata K, Miyata-Takata T, Chung S, Rai S, Wu S, Warren M, Strong C, Goodyear T, Morris K, Chong LC, Hav M, Colombo AR, Telenius A, Boyle M, Ben-Neriah S, Power M, Gerrie AS, Weng AP, Karsan A, Roth A, Farinha P, Scott DW, Savage KJ, Nelson BH, Merchant A, Steidl C. Spatially Resolved Tumor Microenvironment Predicts Treatment Outcomes in Relapsed/Refractory Hodgkin Lymphoma. J Clin Oncol 2024; 42:1077-1087. [PMID: 38113419 PMCID: PMC10950131 DOI: 10.1200/jco.23.01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/21/2023] Open
Abstract
PURPOSE About a third of patients with relapsed or refractory classic Hodgkin lymphoma (r/r CHL) succumb to their disease after high-dose chemotherapy followed by autologous stem-cell transplantation (HDC/ASCT). Here, we aimed to describe spatially resolved tumor microenvironment (TME) ecosystems to establish novel biomarkers associated with treatment failure in r/r CHL. PATIENTS AND METHODS We performed imaging mass cytometry (IMC) on 71 paired primary diagnostic and relapse biopsies using a marker panel specific to CHL biology. For each cell type in the TME, we calculated a spatial score measuring the distance of nearest neighbor cells to the malignant Hodgkin Reed Sternberg cells within the close interaction range. Spatial scores were used as features in prognostic model development for post-ASCT outcomes. RESULTS Highly multiplexed IMC data revealed shared TME patterns in paired diagnostic and early r/r CHL samples, whereas TME patterns were more divergent in pairs of diagnostic and late relapse samples. Integrated analysis of IMC and single-cell RNA sequencing data identified unique architecture defined by CXCR5+ Hodgkin and Reed Sternberg (HRS) cells and their strong spatial relationship with CXCL13+ macrophages in the TME. We developed a prognostic assay (RHL4S) using four spatially resolved parameters, CXCR5+ HRS cells, PD1+CD4+ T cells, CD68+ tumor-associated macrophages, and CXCR5+ B cells, which effectively separated patients into high-risk versus low-risk groups with significantly different post-ASCT outcomes. The RHL4S assay was validated in an independent r/r CHL cohort using a multicolor immunofluorescence assay. CONCLUSION We identified the interaction of CXCR5+ HRS cells with ligand-expressing CXCL13+ macrophages as a prominent crosstalk axis in relapsed CHL. Harnessing this TME biology, we developed a novel prognostic model applicable to r/r CHL biopsies, RHL4S, opening new avenues for spatial biomarker development.
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Affiliation(s)
- Tomohiro Aoki
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Princess Margaret Cancer Centre—University Health Network, Toronto, Ontario, Canada
| | - Aixiang Jiang
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Yifan Yin
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | | | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Shanee Chung
- Leukemia/Bone Marrow Transplant Program of BC, BC Cancer, Vancouver, British Columbia, Canada
| | - Shinya Rai
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Shaocheng Wu
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Mary Warren
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Celia Strong
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Talia Goodyear
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Kayleigh Morris
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Lauren C. Chong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | | | | | - Adele Telenius
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Maryse Power
- Leukemia/Bone Marrow Transplant Program of BC, BC Cancer, Vancouver, British Columbia, Canada
| | - Alina S. Gerrie
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Brad H. Nelson
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | | | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Tengku Kamalden TMI, Azali MZ, Chong LC, Ali A, Abdul Wahid SNH, Norazman N, Abdul Rahman N, Bhaskran F, Misron K. Evaluating factors associated with paediatric cochlear implant outcome in four cochlear implant satellite centres in Malaysia. Med J Malaysia 2022; 77:521-525. [PMID: 36169061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Many factors are associated with cochlear implant (CI) outcomes and various methods of assessment for auditory and speech performance outcomes in CI are available globally. The objective of this study is to identify factors relating to CI outcomes in paediatric population that suits local context. MATERIALS AND METHODS A total of 18 factors consisted of variables which emphasise on audiological, CI service team, speech therapy, and family-related factors. These factors were then retrospectively analyzed among CI recipients. The outcome measurements of categorical auditory performance II (CAP-II) and speech intelligibility rating (SIR) were used to individually study each factor. Kruskal-Wallis H Test and Fisher Exact Test used with p-value <0.05 were considered significant. RESULTS There were significant associations between post- CI CAP-II with type of hearing loss, hearing aid usage per day and mode of communication, attention, attending audiology and speech session, and siblings. For post-CI SIR, hearing aid usage per day, attention, mode of communication, attending audiology and speech session, initiatives, and siblings were statistically significant. CONCLUSION The factors affecting the outcome of CI are dynamic. Some of the factors have demonstrated to be associated with the auditory and speech outcome in CI recipients while some factors failed to replicate similar findings. Further prospective research may refine the outcome of individual factors.
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Affiliation(s)
- T M I Tengku Kamalden
- Hospital Sultan Ismail, Department of Otorhinolaryngology, Johor Bahru, Johor, Malaysia
| | - M Z Azali
- Hospital Sultan Ismail, Audiology Unit, Johor Bahru, Johor, Malaysia
| | - L C Chong
- Hospital Sultan Ismail, Speech and Language Pathology Unit, Johor Bahru, Johor, Malaysia
| | - A Ali
- Hospital Sultan Ismail, Clinical Research Centre, Johor Bahru, Johor, Malaysia
| | - S N H Abdul Wahid
- Hospital Sultan Ismail, Audiology Unit, Johor Bahru, Johor, Malaysia
| | - N Norazman
- Hospital Sultan Ismail, Audiology Unit, Johor Bahru, Johor, Malaysia
| | - N Abdul Rahman
- Hospital Sultan Ismail, Speech and Language Pathology Unit, Johor Bahru, Johor, Malaysia
| | - F Bhaskran
- Hospital Sultan Ismail, Speech and Language Pathology Unit, Johor Bahru, Johor, Malaysia
| | - K Misron
- Hospital Sultan Ismail, Department of Otorhinolaryngology, Johor Bahru, Johor, Malaysia.
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Stanwood SR, Chong LC, Steidl C, Jefferies WA. Distinct Gene Expression Patterns of Calcium Channels and Related Signaling Pathways Discovered in Lymphomas. Front Pharmacol 2022; 13:795176. [PMID: 35685639 PMCID: PMC9172636 DOI: 10.3389/fphar.2022.795176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/24/2022] [Indexed: 01/14/2023] Open
Abstract
Cell surface calcium (Ca2+) channels permit Ca2+ ion influx, with Ca2+ taking part in cellular functions such as proliferation, survival, and activation. The expression of voltage-dependent Ca2+ (CaV) channels may modulate the growth of hematologic cancers. Profile analysis of Ca2+ channels, with a focus on the Ca2+ release-activated Ca2+ (CRAC) and L-type CaV channels, was performed on RNA sequencing data from lymphoma cell lines and samples derived from patients with diffuse large B cell lymphoma (DLBCL). CaV1.2 expression was found to be elevated in classical Hodgkin lymphoma (CHL) cell lines when compared to other B cell lymphoma cell lines. In contrast, CHL exhibited reduced expression of ORAI2 and STIM2. In our differential expression analysis comparing activated B cell-like DLBCL (ABC-DLBCL) and germinal centre B cell-like DLBCL (GCB-DLBCL) patient samples, ABC-DLBCL revealed stronger expression of CaV1.3, whereas CaV1.1, CaV1.2, and CaV1.4 showed greater expression levels in GCB-DLBCL. Interestingly, no differences in ORAI/STIM expression were noted in the patient samples. As Ca2+ is known to bind to calmodulin, leading to calcineurin activation and the passage of nuclear factor of activated T cells (NFAT) to the cell nucleus, pathways for calcineurin, calmodulin, NFAT, and Ca2+ signaling were also analyzed by gene set enrichment analysis. The NFAT and Ca2+ signaling pathways were found to be upregulated in the CHL cell lines relative to other B cell lymphoma cell lines. Furthermore, the calmodulin and Ca2+ signaling pathways were shown to be downregulated in the ABC-DLBCL patient samples. The findings of this study suggest that L-type CaV channels and Ca2+-related pathways could serve as differentiating components for biologic therapies in targeted lymphoma treatments.
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Affiliation(s)
- Shawna R. Stanwood
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, BC, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Lauren C. Chong
- Centre for Lymphoid Cancer, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Christian Steidl
- Lymphoid Cancer Research, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wilfred A. Jefferies
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, BC, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Wilfred A. Jefferies,
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Takata K, Chong LC, Ennishi D, Aoki T, Li MY, Thakur A, Healy S, Viganò E, Dao T, Kwon D, Duns G, Nielsen JS, Ben-Neriah S, Tse E, Hung SS, Boyle M, Mun SS, Bourne CM, Woolcock B, Telenius AH, Kishida M, Rai S, Zhang AW, Bashashati A, Saberi S, D' Antonio G, Nelson BH, Shah SP, Hoodless PA, Melnick AM, Gascoyne RD, Connors JM, Scheinberg DA, Béguelin W, Scott DW, Steidl C. Tumor associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B-cell lymphoma. J Clin Invest 2022; 132:145343. [PMID: 35380993 PMCID: PMC9106353 DOI: 10.1172/jci145343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/29/2022] [Indexed: 11/26/2022] Open
Abstract
PRAME is a prominent member of the cancer testis antigen family of proteins, which triggers autologous T cell–mediated immune responses. Integrative genomic analysis in diffuse large B cell lymphoma (DLBCL) uncovered recurrent and highly focal deletions of 22q11.22, including the PRAME gene, which were associated with poor outcome. PRAME-deleted tumors showed cytotoxic T cell immune escape and were associated with cold tumor microenvironments. In addition, PRAME downmodulation was strongly associated with somatic EZH2 Y641 mutations in DLBCL. In turn, PRC2-regulated genes were repressed in isogenic PRAME-KO lymphoma cell lines, and PRAME was found to directly interact with EZH2 as a negative regulator. EZH2 inhibition with EPZ-6438 abrogated these extrinsic and intrinsic effects, leading to PRAME expression and microenvironment restoration in vivo. Our data highlight multiple functions of PRAME during lymphomagenesis and provide a preclinical rationale for synergistic therapies combining epigenetic reprogramming with PRAME-targeted therapies.
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Affiliation(s)
| | - Lauren C Chong
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Daisuke Ennishi
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Tomohiro Aoki
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Michael Yu Li
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Avinash Thakur
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Shannon Healy
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Elena Viganò
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Daniel Kwon
- Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Gerben Duns
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Julie S Nielsen
- Trev and Joyce Deeley Research Centre, BC Cancer Research, Vancouver, Canada
| | | | - Ethan Tse
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Stacy S Hung
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Merrill Boyle
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Sung Soo Mun
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Christopher M Bourne
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Bruce Woolcock
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | | | - Makoto Kishida
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Shinya Rai
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Saeed Saberi
- Department of Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Gianluca D' Antonio
- Trev and Joyce Deeley Research Centre, BC Cancer Research, Vancouver, Canada
| | - Brad H Nelson
- Trev and Joyce Deeley Research Centre, BC Cancer Research, Vancouver, Canada
| | - Sohrab P Shah
- Department of Epidemiology and Biostatistics, Weill Cornell Medical College, New York, United States of America
| | | | - Ari M Melnick
- Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | | | | | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Wendy Béguelin
- Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, Canada
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6
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Tong KI, Yoon S, Isaev K, Bakhtiari M, Lackraj T, He MY, Joynt J, Silva A, Xu MC, Privé GG, He HH, Tiedemann RE, Chavez EA, Chong LC, Boyle M, Scott DW, Steidl C, Kridel R. Combined EZH2 Inhibition and IKAROS Degradation Leads to Enhanced Antitumor Activity in Diffuse Large B-cell Lymphoma. Clin Cancer Res 2021; 27:5401-5414. [PMID: 34168051 DOI: 10.1158/1078-0432.ccr-20-4027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/24/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The efficacy of EZH2 inhibition has been modest in the initial clinical exploration of diffuse large B-cell lymphoma (DLBCL), yet EZH2 inhibitors are well tolerated. Herein, we aimed to uncover genetic and pharmacologic opportunities to enhance the clinical efficacy of EZH2 inhibitors in DLBCL. EXPERIMENTAL DESIGN We conducted a genome-wide sensitizing CRISPR/Cas9 screen with tazemetostat, a catalytic inhibitor of EZH2. The sensitizing effect of IKZF1 loss of function was then validated and leveraged for combination treatment with lenalidomide. RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing analyses were performed to elucidate transcriptomic and epigenetic changes underlying synergy. RESULTS We identified IKZF1 knockout as the top candidate for sensitizing DLBCL cells to tazemetostat. Treating cells with tazemetostat and lenalidomide, an immunomodulatory drug that selectively degrades IKAROS and AIOLOS, phenocopied the effects of the CRISPR/Cas9 screen. The combined drug treatment triggered either cell-cycle arrest or apoptosis in a broad range of DLBCL cell lines, regardless of EZH2 mutational status. Cell-line-based xenografts also showed slower tumor growth and prolonged survival in the combination treatment group. RNA-seq analysis revealed strong upregulation of interferon signaling and antiviral immune response signatures. Gene expression of key immune response factors such as IRF7 and DDX58 were induced in cells treated with lenalidomide and tazemetostat, with a concomitant increase of H3K27 acetylation at their promoters. Furthermore, transcriptome analysis demonstrated derepression of endogenous retroviruses after combination treatment. CONCLUSIONS Our data underscore the synergistic interplay between IKAROS degradation and EZH2 inhibition on modulating epigenetic changes and ultimately enhancing antitumor effects in DLBCL.
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Affiliation(s)
- Kit I Tong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sharon Yoon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Ontario, Canada
| | - Keren Isaev
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mehran Bakhtiari
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tracy Lackraj
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Y He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jesse Joynt
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Ontario, Canada
| | - Anjali Silva
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Vector Institute, Toronto, Ontario, Canada
| | - Maria C Xu
- University of Toronto Schools, Ontario, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Rodger E Tiedemann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Lauren C Chong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Institute of Medical Science, University of Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Ontario, Canada
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7
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Laumont CM, Wouters MCA, Smazynski J, Gierc NS, Chavez EA, Chong LC, Thornton S, Milne K, Webb JR, Steidl C, Nelson BH. Single-cell Profiles and Prognostic Impact of Tumor-Infiltrating Lymphocytes Coexpressing CD39, CD103, and PD-1 in Ovarian Cancer. Clin Cancer Res 2021; 27:4089-4100. [PMID: 33963000 DOI: 10.1158/1078-0432.ccr-20-4394] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/27/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Tumor-infiltrating lymphocytes (TIL) are strongly associated with survival in most cancers; however, the tumor-reactive subset that drives this prognostic effect remains poorly defined. CD39, CD103, and PD-1 have been independently proposed as markers of tumor-reactive CD8+ TIL in various cancers. We evaluated the phenotype, clonality, and prognostic significance of TIL expressing various combinations of these markers in high-grade serous ovarian cancer (HGSC), a malignancy in need of more effective immunotherapeutic approaches. EXPERIMENTAL DESIGN Expression of CD39, CD103, PD-1, and other immune markers was assessed by high-dimensional flow cytometry, single-cell sequencing, and multiplex immunofluorescence of primary and matched pre/post-chemotherapy HGSC specimens. RESULTS Coexpression of CD39, CD103, and PD-1 ("triple-positive" phenotype) demarcated subsets of CD8+ TIL and CD4+ regulatory T cells (Treg) with a highly activated/exhausted phenotype. Triple-positive CD8+ TIL exhibited reduced T-cell receptor (TCR) diversity and expressed genes involved in both cytolytic and humoral immunity. Triple-positive Tregs exhibited higher TCR diversity and a tumor-resident phenotype. Triple-positive TIL showed superior prognostic impact relative to TIL expressing other combinations of these markers. TIGIT was uniquely upregulated on triple-positive CD8+ effector cells relative to their CD4+ Treg counterparts. CONCLUSIONS Coexpression of CD39, CD103, and PD-1 demarcates highly activated CD8+ and CD4+ TIL with inferred roles in cytolytic, humoral, and regulatory immune functions. Triple-positive TIL demonstrate exceptional prognostic significance and express compelling targets for combination immunotherapy, including PD-1, CD39, and TIGIT.
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Affiliation(s)
- Céline M Laumont
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Julian Smazynski
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Nicole S Gierc
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Lauren C Chong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Shelby Thornton
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - John R Webb
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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8
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Wong YC, Chan SY, Yuen KY, Chong LC. Locally invasive and obstructive colonic leiomyosarcoma: a diagnostic and therapeutic challenge. Hong Kong Med J 2021; 26:73-75. [PMID: 32077864 DOI: 10.12809/hkmj197873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Y C Wong
- Department of Surgery, Tseung Kwan O Hospital, Tseung Kwan O, Hong Kong
| | - S Y Chan
- Department of Surgery, Tseung Kwan O Hospital, Tseung Kwan O, Hong Kong
| | - K Y Yuen
- Department of Surgery, Tseung Kwan O Hospital, Tseung Kwan O, Hong Kong
| | - L C Chong
- Department of Surgery, Tseung Kwan O Hospital, Tseung Kwan O, Hong Kong
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9
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Aoki T, Chong LC, Takata K, Milne K, Hav M, Colombo A, Chavez EA, Nissen M, Wang X, Miyata-Takata T, Lam V, Viganò E, Woolcock BW, Telenius A, Li MY, Healy S, Ghesquiere C, Kos D, Goodyear T, Veldman J, Zhang AW, Kim J, Saberi S, Ding J, Farinha P, Weng AP, Savage KJ, Scott DW, Krystal G, Nelson BH, Mottok A, Merchant A, Shah SP, Steidl C. Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma. Cancer Discov 2019; 10:406-421. [PMID: 31857391 DOI: 10.1158/2159-8290.cd-19-0680] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Hodgkin lymphoma is characterized by an extensively dominant tumor microenvironment (TME) composed of different types of noncancerous immune cells with rare malignant cells. Characterization of the cellular components and their spatial relationship is crucial to understanding cross-talk and therapeutic targeting in the TME. We performed single-cell RNA sequencing of more than 127,000 cells from 22 Hodgkin lymphoma tissue specimens and 5 reactive lymph nodes, profiling for the first time the phenotype of the Hodgkin lymphoma-specific immune microenvironment at single-cell resolution. Single-cell expression profiling identified a novel Hodgkin lymphoma-associated subset of T cells with prominent expression of the inhibitory receptor LAG3, and functional analyses established this LAG3+ T-cell population as a mediator of immunosuppression. Multiplexed spatial assessment of immune cells in the microenvironment also revealed increased LAG3+ T cells in the direct vicinity of MHC class II-deficient tumor cells. Our findings provide novel insights into TME biology and suggest new approaches to immune-checkpoint targeting in Hodgkin lymphoma. SIGNIFICANCE: We provide detailed functional and spatial characteristics of immune cells in classic Hodgkin lymphoma at single-cell resolution. Specifically, we identified a regulatory T-cell-like immunosuppressive subset of LAG3+ T cells contributing to the immune-escape phenotype. Our insights aid in the development of novel biomarkers and combination treatment strategies targeting immune checkpoints.See related commentary by Fisher and Oh, p. 342.This article is highlighted in the In This Issue feature, p. 327.
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Affiliation(s)
- Tomohiro Aoki
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lauren C Chong
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katy Milne
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Monirath Hav
- Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Michael Nissen
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Xuehai Wang
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Tomoko Miyata-Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Vivian Lam
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Elena Viganò
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce W Woolcock
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Michael Y Li
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shannon Healy
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Chanel Ghesquiere
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Daniel Kos
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Talia Goodyear
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Johanna Veldman
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Allen W Zhang
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jubin Kim
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Pedro Farinha
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Gerald Krystal
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Brad H Nelson
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anja Mottok
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Akil Merchant
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Sohrab P Shah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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10
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P'ng C, Green J, Chong LC, Waggott D, Prokopec SD, Shamsi M, Nguyen F, Mak DYF, Lam F, Albuquerque MA, Wu Y, Jung EH, Starmans MHW, Chan-Seng-Yue MA, Yao CQ, Liang B, Lalonde E, Haider S, Simone NA, Sendorek D, Chu KC, Moon NC, Fox NS, Grzadkowski MR, Harding NJ, Fung C, Murdoch AR, Houlahan KE, Wang J, Garcia DR, de Borja R, Sun RX, Lin X, Chen GM, Lu A, Shiah YJ, Zia A, Kearns R, Boutros PC. BPG: Seamless, automated and interactive visualization of scientific data. BMC Bioinformatics 2019; 20:42. [PMID: 30665349 PMCID: PMC6341661 DOI: 10.1186/s12859-019-2610-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/04/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment. RESULTS This open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines. CONCLUSION BPG provides a new approach for linking interactive and scripted data visualization and is available at http://labs.oicr.on.ca/boutros-lab/software/bpg or via CRAN at https://cran.r-project.org/web/packages/BoutrosLab.plotting.general.
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Affiliation(s)
| | - Jeffrey Green
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Daryl Waggott
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | | | | | | | - Felix Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Ying Wu
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Esther H Jung
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | | | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Bianca Liang
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Emilie Lalonde
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Syed Haider
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | | | - Kenneth C Chu
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Natalie S Fox
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | | | | | - Clement Fung
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, Canada.,Present address: Center for Computational Research, Buffalo Institute for Genomics and Data Analytics, NYS Center for Excellence in Bioinformatics & Life Science, University at Buffalo, Buffalo, USA
| | | | | | - Ren X Sun
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Xihui Lin
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Aileen Lu
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Amin Zia
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Ryan Kearns
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada. .,Department of Human Genetics, University of California, Los Angeles, USA. .,Department of Urology, University of California, Los Angeles, USA. .,Institute for Precision Health, University of California, Los Angeles, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA.
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11
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Prokopec SD, Houlahan KE, Sun RX, Watson JD, Yao CQ, Lee J, P'ng C, Pang R, Wu AH, Chong LC, Smith AB, Harding NJ, Moffat ID, Lindén J, Lensu S, Okey AB, Pohjanvirta R, Boutros PC. Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems. BMC Genomics 2017; 18:78. [PMID: 28086803 PMCID: PMC5237151 DOI: 10.1186/s12864-016-3446-z] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 12/20/2016] [Indexed: 02/04/2023] Open
Abstract
Background 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute lethality. The severity of toxicity is highly dependent on the aryl hydrocarbon receptor (AHR). Binding of TCDD to the AHR leads to changes in transcription of numerous genes. Studies evaluating the transcriptional changes brought on by TCDD may provide valuable insight into the role of the AHR in human health and disease. We therefore compiled a collection of transcriptomic datasets that can be used to aid the scientific community in better understanding the transcriptional effects of ligand-activated AHR. Results Specifically, we have created a datasets package – TCDD.Transcriptomics – for the R statistical environment, consisting of 63 unique experiments comprising 377 samples, including various combinations of 3 species (human derived cell lines, mouse and rat), 4 tissue types (liver, kidney, white adipose tissue and hypothalamus) and a wide range of TCDD exposure times and doses. These datasets have been fully standardized using consistent preprocessing and annotation packages (available as of September 14, 2015). To demonstrate the utility of this R package, a subset of “AHR-core” genes were evaluated across the included datasets. Ahrr, Nqo1 and members of the Cyp family were significantly induced following exposure to TCDD across the studies as expected while Aldh3a1 was induced specifically in rat liver. Inmt was altered only in liver tissue and primarily by rat-AHR. Conclusions Analysis of the “AHR-core” genes demonstrates a continued need for studies surrounding the impact of AHR-activity on the transcriptome; genes believed to be consistently regulated by ligand-activated AHR show surprisingly little overlap across species and tissues. Until now, a comprehensive assessment of the transcriptome across these studies was challenging due to differences in array platforms, processing methods and annotation versions. We believe that this package, which is freely available for download (http://labs.oicr.on.ca/boutros-lab/tcdd-transcriptomics) will prove to be a highly beneficial resource to the scientific community evaluating the effects of TCDD exposure as well as the variety of functions of the AHR. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3446-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephenie D Prokopec
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Kathleen E Houlahan
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Ren X Sun
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - John D Watson
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Cindy Q Yao
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Jamie Lee
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Christine P'ng
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Renee Pang
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Alexander H Wu
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Lauren C Chong
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Ashley B Smith
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Nicholas J Harding
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Ivy D Moffat
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Jere Lindén
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Sanna Lensu
- Department of Biology of Physical Activity, University of Jyväskylä, Jyväskylä, Finland.,Department of Environmental Health, National Institute for Health and Welfare, Kuopio, Finland
| | - Allan B Okey
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Raimo Pohjanvirta
- Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio, Finland.,Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Paul C Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada. .,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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12
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Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MHW, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet 2015; 47:736-45. [PMID: 26005866 DOI: 10.1038/ng.3315] [Citation(s) in RCA: 340] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/01/2015] [Indexed: 12/12/2022]
Abstract
Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer to delineate new oncogenes or tumor suppressors. We initially determined the copy number aberration (CNA) profiles of 74 patients with index tumors of Gleason score 7. Of these, 5 patients were subjected to whole-genome sequencing using DNA quantities achievable in diagnostic biopsies, with detailed spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity in focal genomics. Multifocal tumors are highly heterogeneous for single-nucleotide variants (SNVs), CNAs and genomic rearrangements. We identified and validated a new recurrent amplification of MYCL, which is associated with TP53 deletion and unique profiles of DNA damage and transcriptional dysregulation. Moreover, we demonstrate divergent tumor evolution in multifocal cancer and, in some cases, tumors of independent clonal origin. These data represent the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcome and inform the development of novel biomarkers that reflect individual prognosis.
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Affiliation(s)
- Paul C Boutros
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | - Dominique Trudel
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Emilie Lalonde
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alice Meng
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrew McPherson
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Amin Zia
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Natalie S Fox
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timothy A Beck
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Cherry L Have
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Taryne Chong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michelle Sam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeremy Johns
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Ada Wong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trent T Simmons
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christine P'ng
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gaetano Zafarana
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Francis Nguyen
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Xuemei Luo
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kenneth C Chu
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Jenna Sykes
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alan Dal Pra
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Alejandro Berlin
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Brown
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Fouad Yousif
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Lauren C Chong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gregory M Chen
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Esther Jung
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Clement Fung
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Hanbo Chen
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - James Hawley
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alister D'Costa
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Melania Pintilie
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Daryl Waggott
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faraz Hach
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Philippe Lambin
- Department of Radiotherapy, Maastricht University, Maastricht, the Netherlands
| | | | - Colin Cooper
- 1] Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK. [2] Department of Biological Sciences, University of East Anglia, Norwich, UK. [3] School of Medicine, University of East Anglia, Norwich, UK
| | - Rosalind Eeles
- 1] Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK. [2] Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK
| | - David Neal
- 1] Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK. [2] Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Bernard Tetu
- Department of Pathology, Laval University, Quebec City, Quebec, Canada
| | - Cenk Sahinalp
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Neil Fleshner
- Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sohrab P Shah
- 1] Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada. [2] Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada. [3] British Columbia Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - Colin C Collins
- 1] Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada. [2] Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Robert G Bristow
- 1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [3] Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
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13
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Sun RX, Chong LC, Simmons TT, Houlahan KE, Prokopec SD, Watson JD, Moffat ID, Lensu S, Lindén J, P'ng C, Okey AB, Pohjanvirta R, Boutros PC. Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity. BMC Genomics 2014; 15:1053. [PMID: 25467400 PMCID: PMC4301818 DOI: 10.1186/1471-2164-15-1053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 08/19/2014] [Accepted: 11/19/2014] [Indexed: 12/04/2022] Open
Abstract
Background Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying physiological regulation by the AHR remain poorly characterized. Previous studies identified several core genes that respond to xenobiotic AHR ligands across a broad range of species and tissues. However, only limited inferences have been made regarding its role in regulating constitutive gene activity, i.e. in the absence of exogenous ligands. To address this, we profiled transcriptomic variations between AHR-active and AHR-less-active animals in the absence of an exogenous agonist across five tissues, three of which came from rats (hypothalamus, white adipose and liver) and two of which came from mice (kidney and liver). Because AHR status alone has been shown sufficient to alter transcriptomic responses, we reason that by contrasting profiles amongst AHR-variant animals, we may elucidate effects of the AHR on constitutive mRNA abundances. Results We found significantly more overlap in constitutive mRNA abundances amongst tissues within the same species than from tissues between species and identified 13 genes (Agt, Car3, Creg1, Ctsc, E2f6, Enpp1, Gatm, Gstm4, Kcnj8, Me1, Pdk1, Slc35a3, and Sqrdl) that are affected by AHR-status in four of five tissues. One gene, Creg1, was significantly up-regulated in all AHR-less-active animals. We also find greater overlap between tissues at the pathway level than at the gene level, suggesting coherency to the AHR signalling response within these processes. Analysis of regulatory motifs suggests that the AHR mostly mediates transcriptional regulation via direct binding to response elements. Conclusions These findings, though preliminary, present a platform for further evaluating the role of the AHR in regulation of constitutive mRNA levels and physiologic function. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1053) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Paul C Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Canada.
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14
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Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, Erho N, Dunning MJ, Halim S, Lamb AD, Moon NC, Zafarana G, Warren AY, Meng X, Thoms J, Grzadkowski MR, Berlin A, Have CL, Ramnarine VR, Yao CQ, Malloff CA, Lam LL, Xie H, Harding NJ, Mak DYF, Chu KC, Chong LC, Sendorek DH, P'ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncol 2014; 15:1521-1532. [PMID: 25456371 DOI: 10.1016/s1470-2045(14)71021-6] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Clinical prognostic groupings for localised prostate cancers are imprecise, with 30-50% of patients recurring after image-guided radiotherapy or radical prostatectomy. We aimed to test combined genomic and microenvironmental indices in prostate cancer to improve risk stratification and complement clinical prognostic factors. METHODS We used DNA-based indices alone or in combination with intra-prostatic hypoxia measurements to develop four prognostic indices in 126 low-risk to intermediate-risk patients (Toronto cohort) who will receive image-guided radiotherapy. We validated these indices in two independent cohorts of 154 (Memorial Sloan Kettering Cancer Center cohort [MSKCC] cohort) and 117 (Cambridge cohort) radical prostatectomy specimens from low-risk to high-risk patients. We applied unsupervised and supervised machine learning techniques to the copy-number profiles of 126 pre-image-guided radiotherapy diagnostic biopsies to develop prognostic signatures. Our primary endpoint was the development of a set of prognostic measures capable of stratifying patients for risk of biochemical relapse 5 years after primary treatment. FINDINGS Biochemical relapse was associated with indices of tumour hypoxia, genomic instability, and genomic subtypes based on multivariate analyses. We identified four genomic subtypes for prostate cancer, which had different 5-year biochemical relapse-free survival. Genomic instability is prognostic for relapse in both image-guided radiotherapy (multivariate analysis hazard ratio [HR] 4·5 [95% CI 2·1-9·8]; p=0·00013; area under the receiver operator curve [AUC] 0·70 [95% CI 0·65-0·76]) and radical prostatectomy (4·0 [1·6-9·7]; p=0·0024; AUC 0·57 [0·52-0·61]) patients with prostate cancer, and its effect is magnified by intratumoral hypoxia (3·8 [1·2-12]; p=0·019; AUC 0·67 [0·61-0·73]). A novel 100-loci DNA signature accurately classified treatment outcome in the MSKCC low-risk to intermediate-risk cohort (multivariate analysis HR 6·1 [95% CI 2·0-19]; p=0·0015; AUC 0·74 [95% CI 0·65-0·83]). In the independent MSKCC and Cambridge cohorts, this signature identified low-risk to high-risk patients who were most likely to fail treatment within 18 months (combined cohorts multivariate analysis HR 2·9 [95% CI 1·4-6·0]; p=0·0039; AUC 0·68 [95% CI 0·63-0·73]), and was better at predicting biochemical relapse than 23 previously published RNA signatures. INTERPRETATION This is the first study of cancer outcome to integrate DNA-based and microenvironment-based failure indices to predict patient outcome. Patients exhibiting these aggressive features after biopsy should be entered into treatment intensification trials. FUNDING Movember Foundation, Prostate Cancer Canada, Ontario Institute for Cancer Research, Canadian Institute for Health Research, NIHR Cambridge Biomedical Research Centre, The University of Cambridge, Cancer Research UK, Cambridge Cancer Charity, Prostate Cancer UK, Hutchison Whampoa Limited, Terry Fox Research Institute, Princess Margaret Cancer Centre Foundation, PMH-Radiation Medicine Program Academic Enrichment Fund, Motorcycle Ride for Dad (Durham), Canadian Cancer Society.
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Affiliation(s)
- Emilie Lalonde
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Adrian S Ishkanian
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, USA
| | - Jenna Sykes
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Fraser
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen Ross-Adams
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Mark J Dunning
- Bioinformatics Core, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Silvia Halim
- Bioinformatics Core, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, UK
| | - Nathalie C Moon
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gaetano Zafarana
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - Xianyue Meng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John Thoms
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michal R Grzadkowski
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Alejandro Berlin
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Cherry L Have
- Department of Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Varune R Ramnarine
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Vancouver Prostate Centre and Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cindy Q Yao
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Chad A Malloff
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Lucia L Lam
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Honglei Xie
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Nicholas J Harding
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Denise Y F Mak
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Center for Addiction and Mental Health, Toronto, ON, Canada
| | - Kenneth C Chu
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lauren C Chong
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dorota H Sendorek
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Christine P'ng
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Colin C Collins
- Vancouver Prostate Centre and Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jeremy A Squire
- Department of Pathology and Forensic Medicine, University of São Paulo at Ribeirão Preto, Ribeirão Preto, Brazil
| | - Igor Jurisica
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Colin Cooper
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK; Department of Biological Sciences and School of Medicine, University of East Anglia, Norwich, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK; Royal Marsden National Health Service Foundation Trust, London, UK
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alan Dal Pra
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, Bern University Hospital, Bern, Switzerland
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Michael Milosevic
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, UK
| | - Theodorus van der Kwast
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Department of Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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15
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Chong LC, Albuquerque MA, Harding NJ, Caloian C, Chan-Seng-Yue M, de Borja R, Fraser M, Denroche RE, Beck TA, van der Kwast T, Bristow RG, McPherson JD, Boutros PC. SeqControl: process control for DNA sequencing. Nat Methods 2014; 11:1071-5. [PMID: 25173705 DOI: 10.1038/nmeth.3094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/27/2014] [Indexed: 12/15/2022]
Abstract
As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality. Using whole-genome sequences of 27 prostate cancers and 26 normal references, we derived multivariate models that predict sequencing quality and depth. SeqControl robustly predicted how much sequencing was required to reach a given coverage depth (area under the curve (AUC) = 0.993), accurately classified clinically relevant formalin-fixed, paraffin-embedded samples, and made predictions from as little as one-eighth of a sequencing lane (AUC = 0.967). These techniques can be immediately incorporated into existing sequencing pipelines to monitor data quality in real time. SeqControl is available at http://labs.oicr.on.ca/Boutros-lab/software/SeqControl/.
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Affiliation(s)
- Lauren C Chong
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marco A Albuquerque
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nicholas J Harding
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Cristian Caloian
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michelle Chan-Seng-Yue
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Richard de Borja
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael Fraser
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Robert E Denroche
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timothy A Beck
- Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Robert G Bristow
- 1] Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John D McPherson
- 1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [2] Genomics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul C Boutros
- 1] Informatics &Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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16
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Prokopec SD, Buchner NB, Fox NS, Chong LC, Mak DY, Watson JD, Petronis A, Pohjanvirta R, Boutros PC. Validating reference genes within a mouse model system of 2,3,7,8-tetrachlorodibenzo- p -dioxin (TCDD) toxicity. Chem Biol Interact 2013; 205:63-71. [DOI: 10.1016/j.cbi.2013.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/23/2013] [Accepted: 06/10/2013] [Indexed: 01/26/2023]
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17
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Lam Y, Yuen KKY, Chong LC. Acute torsion of a wandering spleen. Hong Kong Med J 2012; 18:160-162. [PMID: 22477742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
The 'wandering spleen' is a rare condition due to extreme laxity or absence of ligaments that fix the organ in its normal anatomical position within the left upper quadrant. Without early surgical intervention, wandering spleen can lead to torsion and subsequent splenic infarction or rupture. Clinical suspicion plus urgent investigation and intervention are important, so as to salvage the spleen and prevent complications. We present a case of torsion of a wandering spleen in a 21-year-old young woman, who presented with a painful pelvic mass. We also reviewed the literature on this entity.
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Affiliation(s)
- Y Lam
- Department of Surgery, United Christian Hospital, Kwun Tong, Hong Kong.
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18
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Yao CQ, Prokopec SD, Watson JD, Pang R, P'ng C, Chong LC, Harding NJ, Pohjanvirta R, Okey AB, Boutros PC. Inter-strain heterogeneity in rat hepatic transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Toxicol Appl Pharmacol 2012; 260:135-45. [PMID: 22342509 DOI: 10.1016/j.taap.2012.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/30/2012] [Accepted: 02/01/2012] [Indexed: 12/21/2022]
Abstract
The biochemical and toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) have been the subject of intense study for decades. It is now clear that essentially all TCDD-induced toxicities are mediated by DNA-protein interactions involving the Aryl Hydrocarbon Receptor (AHR). Nevertheless, it remains unknown which AHR target genes cause TCDD toxicities. Several groups, including our own, have developed rodent model systems to probe these questions. mRNA expression profiling of these model systems has revealed significant inter-species heterogeneity in rodent hepatic responses to TCDD. It has remained unclear if this variability also exists within a species, amongst rodent strains. To resolve this question, we profiled the hepatic transcriptomic response to TCDD of diverse rat strains (L-E, H/W, F344 and Wistar rats) and two lines derived from L-E×H/W crosses, at consistent age, sex, and dosing (100 μg/kg TCDD for 19 h). Using this uniquely consistent dataset, we show that the majority of TCDD-induced alterations in mRNA abundance are strain/line-specific: only 11 genes were affected by TCDD across all strains, including well-known dioxin-responsive genes such as Cyp1a1 and Nqo1. Our analysis identified two novel universally dioxin-responsive genes as well as 4 genes induced by TCDD in dioxin-sensitive rats only. These 6 genes are strong candidates to explain TCDD-related toxicities, so we validated them using 152 animals in time-course (0 to 384 h) and dose-response (0 to 3000 μg/kg) experiments. This study reveals that different rat strains exhibit dramatic transcriptional heterogeneity in their hepatic responses to TCDD and that inter-strain comparisons can help identify candidate toxicity-related genes.
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Affiliation(s)
- Cindy Q Yao
- Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Canada
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19
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Haslinda WH, Cheng LH, Chong LC, Noor Aziah AA. Chemical composition and physicochemical properties of green banana (Musa acuminata x balbisiana Colla cv. Awak) flour. Int J Food Sci Nutr 2010; 60 Suppl 4:232-9. [PMID: 19449278 DOI: 10.1080/09637480902915525] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Flour was prepared from peeled and unpeeled banana Awak ABB. Samples prepared were subjected to analysis for determination of chemical composition, mineral, dietary fibre, starch and total phenolics content, antioxidant activity and pasting properties. In general, flour prepared from unpeeled banana was found to show enhanced nutrition values with higher contents of mineral, dietary fibre and total phenolics. Hence, flour fortified with peel showed relatively higher antioxidant activity. On the other hand, better pasting properties were shown when banana flour was blended with peel. It was found that a relatively lower pasting temperature, peak viscosity, breakdown, final viscosity and setback were evident in a sample blended with peel.
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Affiliation(s)
- W H Haslinda
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
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20
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Cho CL, Yuen KKY, Yuen CH, Chong LC, Chu RWS. Splenic laceration after endoscopic retrograde cholangiopancreatography. Hong Kong Med J 2008; 14:145-147. [PMID: 18382023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Endoscopic retrograde cholangiopancreatography has been part of clinical practice for over 35 years. The procedure itself carries risks. Most complications associated with the procedure have been described in the literature. Splenic injury is an extremely rare complication after endoscopic retrograde cholangiopancreatography and only nine such cases have been reported to our knowledge since 1988. We report on a patient who presented with abdominal pain and was found to have abnormal liver function and a dilated pancreatic duct. An endoscopic retrograde cholangiopancreatography was performed and a splenic laceration was noted subsequently. As this operation is an increasingly important diagnostic and therapeutic modality for pancreatico-biliary disease, clinicians must be aware of this complication in order to make an early diagnosis and begin appropriate management.
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Affiliation(s)
- C L Cho
- Department of Surgery, Tseung Kwan O Hospital, Tseung Kwan O, Hong Kong.
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21
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Kwok PC, Chung TK, Chong LC, Chan SC, Wong WK, Chan MK, Chu WS. Neurologic injury after endovascular stent-graft and bilateral internal iliac artery embolization for infrarenal abdominal aortic aneurysm. J Vasc Interv Radiol 2001; 12:761-3. [PMID: 11389230 DOI: 10.1016/s1051-0443(07)61450-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The authors report a rare neurologic complication after the implantation of a bifurcated stent-graft for abdominal aortic aneurysm. The stent-graft was extended to both external iliac arteries after embolization of both internal iliac arteries. The patient subsequently had weakness and numbness of both lower limbs with bowel and bladder incontinence. He probably had ischemic injury to the nerve roots or the lumbosacral plexus, which was related to extensive occlusion of their supplying arteries. The mechanism of spinal cord and neurologic ischemia after aortic stent-graft implantation is discussed.
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Affiliation(s)
- P C Kwok
- Department of Radiology and Imaging, Queen Elizabeth Hospital, 30 Gascoigne Road, Kowloon, Hong Kong.
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22
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Carter MC, Genevier ES, Chong LC, Sutherland IA, Woodhouse P, Murray HG, Kirk DL, Symonds EM, Steer PJ, Beard RW. Assessment of cardiotocographs. J Biomed Eng 1990; 12:267-70. [PMID: 2348718 DOI: 10.1016/0141-5425(90)90053-p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In recent years advances in medical electronic equipment for monitoring, diagnosis and treatment of patients have led to a large increase in the number and variety of instrumentation available to the medical profession. There is a considerable amount of duplication of equipment and in the absence of readily available information buyers are unlikely to make informed decisions about the ideal instrument for their particular circumstances. One method of increasing the users' awareness is a comparative, independent assessment of equipment, with the results disseminated to the interested parties. This paper describes the essential qualities of cardiotocographs: how they are assessed as part of the UK Department of Health's evaluation programme and the measures to inform users of the latest evaluation information.
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Affiliation(s)
- M C Carter
- Bio-Medical Technology Group, St. Mary's Hospital Medical School, London, UK
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23
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Ikeme MM, Iskander F, Chong LC. Seasonal changes in the prevalence of Haemonchus and Trichostrongylus hypobiotic larvae in tracer goats in Malaysia. Trop Anim Health Prod 1987; 19:184-90. [PMID: 3660455 DOI: 10.1007/bf02239718] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An investigation into the seasonal changes in the population structure of Haemonchus and Trichostrongylus in tracer goats was conducted over 12 months at Serdang, an area in southern West Malaysia with year-round tropical rainfall. Successive groups of parasite-free tracer goats were grazed for a month alongside naturally infected adult goats and necropsied for worm counts 14 days after their removal from pasture. No hypobiotic larvae of Trichostrongylus were recovered. Hypobiotic larvae of Haemonchus were evident during each month of the year but accounted for only a very small proportion of the total Haemonchus burden. Very low levels were encountered from December through to June. Comparatively higher levels of hypobiosis were observed thereafter with a peak of 7.4% in September. The factors responsible for hypobiosis were not clearly defined but the phenomenon was associated with increasing levels of soil moisture storage. Host resistance, adult worm population of tracers and population of ingested L3 were ruled out as possible inducing factors.
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Affiliation(s)
- M M Ikeme
- Universiti Pertanian Malaysia, Faculty of Veterinary Medicine and Animal Science, Serdang, Selangor
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24
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Chong LC. Population management in economic development: minimizing burden or maximizing resources. Scand J Dev Altern 1984; 3:27-37. [PMID: 12314066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
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25
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26
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Chong LC. Simple permanent mounting of small nematodes (up to 30mm in length). Southeast Asian J Trop Med Public Health 1982; 13:296. [PMID: 7147019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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