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Mooney B, Negri GL, Shyp T, Delaidelli A, Zhang HF, Spencer Miko SE, Weiner AK, Radaoui AB, Shraim R, Lizardo MM, Hughes CS, Li A, El-Naggar AM, Rouleau M, Li W, Dimitrov DS, Kurmasheva RT, Houghton PJ, Diskin SJ, Maris JM, Morin GB, Sorensen PH. Surface and Global Proteome Analyses Identify ENPP1 and Other Surface Proteins as Actionable Immunotherapeutic Targets in Ewing Sarcoma. Clin Cancer Res 2024; 30:1022-1037. [PMID: 37812652 PMCID: PMC10905525 DOI: 10.1158/1078-0432.ccr-23-2187] [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: 07/24/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE Ewing sarcoma is the second most common bone sarcoma in children, with 1 case per 1.5 million in the United States. Although the survival rate of patients diagnosed with localized disease is approximately 70%, this decreases to approximately 30% for patients with metastatic disease and only approximately 10% for treatment-refractory disease, which have not changed for decades. Therefore, new therapeutic strategies are urgently needed for metastatic and refractory Ewing sarcoma. EXPERIMENTAL DESIGN This study analyzed 19 unique Ewing sarcoma patient- or cell line-derived xenografts (from 14 primary and 5 metastatic specimens) using proteomics to identify surface proteins for potential immunotherapeutic targeting. Plasma membranes were enriched using density gradient ultracentrifugation and compared with a reference standard of 12 immortalized non-Ewing sarcoma cell lines prepared in a similar manner. In parallel, global proteome analysis was carried out on each model to complement the surfaceome data. All models were analyzed by Tandem Mass Tags-based mass spectrometry to quantify identified proteins. RESULTS The surfaceome and global proteome analyses identified 1,131 and 1,030 annotated surface proteins, respectively. Among surface proteins identified, both approaches identified known Ewing sarcoma-associated proteins, including IL1RAP, CD99, STEAP1, and ADGRG2, and many new cell surface targets, including ENPP1 and CDH11. Robust staining of ENPP1 was demonstrated in Ewing sarcoma tumors compared with other childhood sarcomas and normal tissues. CONCLUSIONS Our comprehensive proteomic characterization of the Ewing sarcoma surfaceome provides a rich resource of surface-expressed proteins in Ewing sarcoma. This dataset provides the preclinical justification for exploration of targets such as ENPP1 for potential immunotherapeutic application in Ewing sarcoma. See related commentary by Bailey, p. 934.
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Affiliation(s)
- Brian Mooney
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Taras Shyp
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hai-Feng Zhang
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra E. Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Amber K. Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alexander B. Radaoui
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael M. Lizardo
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Christopher S. Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Li
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Rouleau
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Dimiter S. Dimitrov
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Raushan T. Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Peter J. Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregg B. Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Korver W, Benet Z, Wong A, Negri GL, Chang K, Sanchez R, Leung J, De Freitas N, Luu T, Schanin J, Youngblood BA. Regulation of mast cells by overlapping but distinct protein interactions of Siglec-6 and Siglec-8. Allergy 2024; 79:629-642. [PMID: 38186079 DOI: 10.1111/all.16004] [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: 09/28/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Sialic acid-binding immunoglobulin-like lectin (Siglec)-6 and Siglec-8 are closely related mast cell (MC) receptors with broad inhibitory activity, but whose functional differences are incompletely understood. METHODS Proteomic profiling using quantitative mass spectrometry was performed on primary mouse MCs to identify proteins associated with Siglec-6 and Siglec-8. For functional characterization, each receptor was evaluated biochemically and in ex vivo and in vivo inhibition models of IgE and non-IgE-mediated MC activation in Siglec-6- or Siglec-8-expressing transgenic mice. RESULTS Siglec-6 and Siglec-8 were found in MCs within large complexes, interacting with 66 and 86 proteins, respectively. Strikingly, Siglec-6 and Siglec-8 interacted with a large cluster of proteins involved in IgE and non-IgE-mediated MC activation, including the high affinity IgE receptor, stem cell factor (SCF) receptor KIT/CD117, IL-4 and IL-33 receptors, and intracellular kinases LYN and JAK1. Protein interaction networks revealed Siglec-6 and Siglec-8 had overlapping yet distinct MC functions, with a potentially broader regulatory role for Siglec-6. Indeed, Siglec-6 preferentially interacted with the mature form of KIT at the cell surface, and treatment with an anti-Siglec-6 antibody significantly inhibited SCF-mediated MC activation more in comparison to targeting Siglec-8. CONCLUSION These data demonstrate a central role for Siglec-6 and Siglec-8 in controlling MC activation through interactions with multiple activating receptors and key signaling molecules. Our findings suggest that Siglec-6 has a role distinct from that of Siglec-8 in regulating MC function and represents a distinct potential therapeutic target in mast cell-driven diseases.
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Affiliation(s)
| | | | - Alan Wong
- Allakos Inc., San Carlos, California, USA
| | - Gian Luca Negri
- LM Biostat Consulting Inc., Victoria, British Columbia, Canada
| | | | | | - John Leung
- Allakos Inc., San Carlos, California, USA
| | | | - Thuy Luu
- Allakos Inc., San Carlos, California, USA
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Pozner A, Li L, Verma SP, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, John CM, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Mortenson KL, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97. Nat Commun 2024; 15:1165. [PMID: 38326311 PMCID: PMC10850509 DOI: 10.1038/s41467-024-45280-5] [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: 02/21/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
The t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributes with ASPSCR1::TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrate the oncogenic transcriptional signature of ASPSCR1::TFE3, by facilitating assembly of higher-order chromatin conformation structures demonstrated by HiChIP. Finally, ASPSCR1::TFE3 and VCP demonstrate co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.
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Affiliation(s)
- Amir Pozner
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Li Li
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shiv Prakash Verma
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shuxin Wang
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jared J Barrott
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Mary L Nelson
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Ju-Fen Zhu
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sydney L Lambert
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Lara S Carroll
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kyllie Smith-Fry
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael G Stewart
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarmishta Kannan
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Bodrie Jensen
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Cini M John
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Saif Sikdar
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Hongrui Liu
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer Bourdage
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jinxiu Li
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Katelyn L Mortenson
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - John S Groundland
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Rosanna Wustrack
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Donna L Senger
- Department of Oncology, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, McGill University and Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Franz J Zemp
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Douglas J Mahoney
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Xiaoyang Zhang
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Alexander J Lazar
- Departments of Anatomic Pathology, Translational Molecular Pathology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Peter S Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Kevin B Jones
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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Eskandari E, Negri GL, Tan S, MacAldaz ME, Ding S, Long J, Nielsen K, Spencer SE, Morin GB, Eaves CJ. Dependence of human cell survival and proliferation on the CASP3 prodomain. Cell Death Discov 2024; 10:63. [PMID: 38321033 PMCID: PMC10847432 DOI: 10.1038/s41420-024-01826-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
Mechanisms that regulate cell survival and proliferation are important for both the development and homeostasis of normal tissue, and as well as for the emergence and expansion of malignant cell populations. Caspase-3 (CASP3) has long been recognized for its proteolytic role in orchestrating cell death-initiated pathways and related processes; however, whether CASP3 has other functions in mammalian cells that do not depend on its known catalytic activity have remained unknown. To investigate this possibility, we examined the biological and molecular consequences of reducing CASP3 levels in normal and transformed human cells using lentiviral-mediated short hairpin-based knockdown experiments in combination with approaches designed to test the potential rescue capability of different components of the CASP3 protein. The results showed that a ≥50% reduction in CASP3 levels rapidly and consistently arrested cell cycle progression and survival in all cell types tested. Mass spectrometry-based proteomic analyses and more specific flow cytometric measurements strongly implicated CASP3 as playing an essential role in regulating intracellular protein aggregate clearance. Intriguingly, the rescue experiments utilizing different forms of the CASP3 protein showed its prosurvival function and effective removal of protein aggregates did not require its well-known catalytic capability, and pinpointed the N-terminal prodomain of CASP3 as the exclusive component needed in a diversity of human cell types. These findings identify a new mechanism that regulates human cell survival and proliferation and thus expands the complexity of how these processes can be controlled. The graphical abstract illustrates the critical role of CASP3 for sustained proliferation and survival of human cells through the clearance of protein aggregates.
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Affiliation(s)
- Ebrahim Eskandari
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Susanna Tan
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Margarita E MacAldaz
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Shengsen Ding
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Justin Long
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Karina Nielsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sandra E Spencer
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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Luu JK, Johnson FD, Jajarmi J, Sihota T, Shi R, Lu D, Farnsworth D, Spencer SE, Negri GL, Morin GB, Lockwood WW. Characterizing the secretome of EGFR mutant lung adenocarcinoma. Front Oncol 2024; 13:1286821. [PMID: 38260835 PMCID: PMC10801028 DOI: 10.3389/fonc.2023.1286821] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background Lung cancer is the leading cause of cancer related death worldwide, mainly due to the late stage of disease at the time of diagnosis. Non-invasive biomarkers are needed to supplement existing screening methods to enable earlier detection and increased patient survival. This is critical to EGFR-driven lung adenocarcinoma as it commonly occurs in individuals who have never smoked and do not qualify for current screening protocols. Methods In this study, we performed mass spectrometry analysis of the secretome of cultured lung cells representing different stages of mutant EGFR driven transformation, from normal to fully malignant. Identified secreted proteins specific to the malignant state were validated using orthogonal methods and their clinical activity assessed in lung adenocarcinoma patient cohorts. Results We quantified 1020 secreted proteins, which were compared for differential expression between stages of transformation. We validated differentially expressed proteins at the transcriptional level in clinical tumor specimens, association with patient survival, and absolute concentration to yield three biomarker candidates: MDK, GDF15, and SPINT2. These candidates were validated using ELISA and increased levels were associated with poor patient survival specifically in EGFR mutant lung adenocarcinoma patients. Conclusions Our study provides insight into changes in secreted proteins during EGFR driven lung adenocarcinoma transformation that may play a role in the processes that promote tumor progression. The specific candidates identified can harnessed for biomarker use to identify high risk individuals for early detection screening programs and disease management for this molecular subgroup of lung adenocarcinoma patients.
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Affiliation(s)
- Jennifer K. Luu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fraser D. Johnson
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Jana Jajarmi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Tianna Sihota
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Daniel Lu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dylan Farnsworth
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Sandra E. Spencer
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gian Luca Negri
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gregg B. Morin
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William W. Lockwood
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
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6
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Pozner A, Verma SP, Li L, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, Mortenson KL, John C, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97. bioRxiv 2023:2023.09.29.560242. [PMID: 37873234 PMCID: PMC10592841 DOI: 10.1101/2023.09.29.560242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The t(X,17) chromosomal translocation, generating the ASPSCR1-TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCC), frustrating efforts to identify therapeutic targets for these rare cancers. Proteomic analysis showed that VCP/p97, an AAA+ ATPase with known segregase function, was strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1-TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1-TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributed with ASPSCR1-TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrated the oncogenic transcriptional signature of ASPSCR1-TFE3, by facilitating assembly of higher-order chromatin conformation structures as demonstrated by HiChIP. Finally, ASPSCR1-TFE3 and VCP demonstrated co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.
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McKiel LA, Ballantyne LL, Negri GL, Woodhouse KA, Fitzpatrick LE. MyD88-dependent Toll-like receptor 2 signaling modulates macrophage activation on lysate-adsorbed Teflon™ AF surfaces in an in vitro biomaterial host response model. Front Immunol 2023; 14:1232586. [PMID: 37691934 PMCID: PMC10491479 DOI: 10.3389/fimmu.2023.1232586] [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: 05/31/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
The adsorbed protein layer on an implanted biomaterial surface is known to mediate downstream cell-material interactions that drive the host response. While the adsorption of plasma-derived proteins has been studied extensively, the adsorption of damage-associated molecular patterns (DAMPs) derived from damaged cells and matrix surrounding the implant remains poorly understood. Previously, our group developed a DAMP-adsorption model in which 3T3 fibroblast lysates were used as a complex source of cell-derived DAMPs and we demonstrated that biomaterials with adsorbed lysate potently activated RAW-Blue macrophages via Toll-like receptor 2 (TLR2). In the present study, we characterized the response of mouse bone marrow derived macrophages (BMDM) from wildtype (WT), TLR2-/- and MyD88-/- mice on Teflon™ AF surfaces pre-adsorbed with 10% plasma or lysate-spiked plasma (10% w/w total protein from 3T3 fibroblast lysate) for 24 hours. WT BMDM cultured on adsorbates derived from 10% lysate in plasma had significantly higher gene and protein expression of IL-1β, IL-6, TNF-α, IL-10, RANTES/CCL5 and CXCL1/KC, compared to 10% plasma-adsorbed surfaces. Furthermore, the upregulation of pro-inflammatory cytokine and chemokine expression in the 10% lysate in plasma condition was attenuated in TLR2-/- and MyD88-/- BMDM. Proteomic analysis of the adsorbed protein layers showed that even this relatively small addition of lysate-derived proteins within plasma (10% w/w) caused a significant change to the adsorbed protein profile. The 10% plasma condition had fibrinogen, albumin, apolipoproteins, complement, and fibronectin among the top 25 most abundant proteins. While proteins layers generated from 10% lysate in plasma retained fibrinogen and fibronectin among the top 25 proteins, there was a disproportionate increase in intracellular proteins, including histones, tubulins, actins, and vimentin. Furthermore, we identified 7 DAMPs or DAMP-related proteins enriched in the 10% plasma condition (fibrinogen, apolipoproteins), compared to 39 DAMPs enriched in the 10% lysate in plasma condition, including high mobility group box 1 and histones. Together, these findings indicate that DAMPs and other intracellular proteins readily adsorb to biomaterial surfaces in competition with plasma proteins, and that adsorbed DAMPs induce an inflammatory response in adherent macrophages that is mediated by the MyD88-dependent TLR2 signaling pathway.
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Affiliation(s)
- Laura A. McKiel
- Department of Chemical Engineering, Faculty of Engineering and Applied Sciences, Queen’s University, Kingston, ON, Canada
| | - Laurel L. Ballantyne
- Department of Chemical Engineering, Faculty of Engineering and Applied Sciences, Queen’s University, Kingston, ON, Canada
- Centre for Health Innovation, Queen’s University and Kingston Health Sciences, Kingston, ON, Canada
| | | | - Kimberly A. Woodhouse
- Department of Chemical Engineering, Faculty of Engineering and Applied Sciences, Queen’s University, Kingston, ON, Canada
| | - Lindsay E. Fitzpatrick
- Department of Chemical Engineering, Faculty of Engineering and Applied Sciences, Queen’s University, Kingston, ON, Canada
- Centre for Health Innovation, Queen’s University and Kingston Health Sciences, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Faculty of Health Sciences, Queen’s University, Kingston, ON, Canada
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8
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El-Naggar AM, Ding Y, Trigo-Gonzalez G, Li L, Chen S, Turgu B, Kalantari F, Vallejos R, Parmar K, Shen C, Negri GL, Yong P, Morin G, Huntsman DG. Abstract 2482: On the verge of metastasis: CTH defines a cell-state-dependent adaptive response to microenvironmental stresses. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Clear cell carcinoma of the ovary (CCC) is the 2nd most common ovarian cancer and is histologically and clinically distinct from other subtypes. Late stage CCC have a worse prognosis than other ovarian cancer histotypes as they are inherently resistant to the standard platinum/taxane chemotherapy. Deep endometriosis of the ovary, known as endometrioma or chocolate cyst, is the most common precursor for CCC. However, how transformation from endometriosis to CCC and, in particular, the important role of the hypoxic and ROS-rich microenvironment of endometriotic cysts are not well understood. As the molecular mechanisms pertinent to the genesis and progression of CCC are largely unknown, there are few, if any, therapeutic strategies for patients with advanced stage disease. Identifying factors that shape the development, progression and metastasis of CCC which can be targeted therapeutically could have tremendous potential to improve outcomes in this disease. Our recent findings identified cystathionine gamma-lyase (CTH), a key enzyme in the transsulfuration pathway, as a marker of Mullerian tract derived ciliated cells and CCC of both the ovary and uterus regardless of which mutations are present. Also, CTH is highly expressed both in CCC and the endometriosis adjacent to this cancer. Whether and how the transsulfuration pathway, notably CTH, enables CCC to adapt to the hostile microenvironment of an endometriotic cyst and ultimately to promote metastasis remain unanswered.
Methods: We generated CTH knockout (KO) cells using CRISPR/Cas9. We assessed effects of CTH loss in vitro -under ambient and stress conditions- and in vivo on cell viability, cell proliferation, ROS levels, migration, invasion, and metastasis. Further, we used an organoid model system to assess the impact of CTH loss in primary endometrial cells on organoid growth and response to stress conditions including exposure to endometriotic cyst contents.
Results: Our in-vitro, in-vivo data as well as data derived from the organoid modelling system show that CTH is critical for adaptive response to hypoxia. Further, it underpins the growth of CCC cells in-vitro and the growth of CTH in a mouse model of CCC. These data highly indicate that expression of the transsulfuration pathway enzyme CTH enables cells to survive in endometriotic cysts then upon transformation both marks CCC and potentiates tumor progression and metastasis.
Conclusion: Targeting CTH in CCC and potentially other cancers might represent a novel and impactful therapeutic approach.
Citation Format: Amal M. El-Naggar, Yuchen Ding, Genny Trigo-Gonzalez, Lucy Li, Shary Chen, Busra Turgu, Forouh Kalantari, Rodrigo Vallejos, Kiran Parmar, Cindy Shen, Gian Luca Negri, Paul Yong, Gregg Morin, David G. Huntsman. On the verge of metastasis: CTH defines a cell-state-dependent adaptive response to microenvironmental stresses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2482.
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Affiliation(s)
| | - Yuchen Ding
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | - Lucy Li
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Shary Chen
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Busra Turgu
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | | | - Kiran Parmar
- 2BC Centre for Pelvic Pain and Endometriosis, BC Women’s Hospital, Vancouver, British Columbia, Canada
| | - Cindy Shen
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Paul Yong
- 2BC Centre for Pelvic Pain and Endometriosis, BC Women’s Hospital, Vancouver, British Columbia, Canada
| | - Gregg Morin
- 3Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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9
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Riley RM, Spencer Miko SE, Morin RD, Morin GB, Negri GL. PeptideRanger: An R Package to Optimize Synthetic Peptide Selection for Mass Spectrometry Applications. J Proteome Res 2023; 22:526-531. [PMID: 36701129 DOI: 10.1021/acs.jproteome.2c00538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins including proteins of clinical significance. Despite their potential, the development of targeted and semitargeted assays is time-consuming and often requires the purchase of costly libraries of synthetic peptides. To improve the efficiency of this rate-limiting step, we developed PeptideRanger, a tool to identify peptides from protein of interest with physiochemical properties that make them more likely to be suitable for mass spectrometry analysis. PeptideRanger is a flexible, extensively annotated, and intuitive R package that uses a random forest model trained on a diverse data set of thousands of MS experiments spanning a variety of sample types profiled with different chromatography setups and instruments. To support a variety of applications and to leverage rapidly growing public MS databases, PeptideRanger can readily be retrained with experiment-specific data sets and customized to prioritize and filter peptides based on selected properties.
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Affiliation(s)
- Ryan M Riley
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada
| | | | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada
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10
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Ji JX, Cochrane DR, Negri GL, Colborne S, Spencer Miko SE, Hoang LN, Farnell D, Tessier-Cloutier B, Huvila J, Thompson E, Leung S, Chiu D, Chow C, Ta M, Köbel M, Feil L, Anglesio M, Goode EL, Bolton K, Morin GB, Huntsman DG. The proteome of clear cell ovarian carcinoma. J Pathol 2022; 258:325-338. [PMID: 36031730 PMCID: PMC9649886 DOI: 10.1002/path.6006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/29/2022] [Revised: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 01/19/2023]
Abstract
Clear cell ovarian carcinoma (CCOC) is the second most common subtype of epithelial ovarian carcinoma. Late-stage CCOC is not responsive to gold-standard chemotherapy and results in suboptimal outcomes for patients. In-depth molecular insight is urgently needed to stratify the disease and drive therapeutic development. We conducted global proteomics for 192 cases of CCOC and compared these with other epithelial ovarian carcinoma subtypes. Our results showed distinct proteomic differences in CCOC compared with other epithelial ovarian cancer subtypes including alterations in lipid and purine metabolism pathways. Furthermore, we report potential clinically significant proteomic subgroups within CCOC, suggesting the biologic plausibility of stratified treatment for this cancer. Taken together, our results provide a comprehensive understanding of the CCOC proteomic landscape to facilitate future understanding and research of this disease. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sandra E Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Lynn N Hoang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jutta Huvila
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedicine, University of Turku, Turku, Finland
| | - Emily Thompson
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Derek Chiu
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Monica Ta
- Genetic Pathology Evaluation Center, Vancouver, BC, Canada
| | - Martin Köbel
- Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Lucas Feil
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Michael Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Ellen L Goode
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Kelly Bolton
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
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11
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Delaidelli A, Yao B, Negri GL, Huang YZ, Huang A, Leprivier G, Sorensen P. TMET-33. ELONGATION CONTROL OF MRNA TRANSLATION SUPPORTS GROUP 3 MEDULLOBLASTOMA ADAPTATION TO NUTRIENT DEPRIVATION. Neuro Oncol 2022. [PMCID: PMC9661218 DOI: 10.1093/neuonc/noac209.1038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Group 3 affiliation and MYC genetic amplification are associated with poor life expectancy and substantial morbidity in children suffering from medulloblastoma (MB). However, the high metabolic demand induced by MYC-driven transformation sensitizes MYC-overexpressing MB to cell death under conditions of nutrient deprivation (ND). Additionally, MYC-driven transformation is known to promote mitochondrial oxidative phosphorylation (OXPHOS). We previously reported that eukaryotic Elongation Factor Kinase 2 (eEF2K), the master regulator of mRNA translation elongation, promotes survival of MYC-overexpressing tumors under ND. Interestingly, eEF2K is overexpressed in MYC-driven MB and our preliminary proteomics data highlight large-scale alterations in OXPHOS components affecting eEF2K deficient MB cells. We therefore hypothesized that eEF2K activity is required for the selective translation of mRNAs needed for efficient OXPHOS, and for the progression of MYC-driven MB. We performed Multiplexed enhanced Protein Dynamic Mass Spectrometry in eEF2K knockdown MYC-overexpressing D425 MB cells to identify mRNAs selectively translated upon eEF2K activation. Messenger RNAs encoding multiple (9 out of 10 detected) components of the mitochondrial OXPHOS pathway are selectively translated upon eEF2K activation. Inactivation of eEF2K by genetic KO leads to the disassembly of electron transport chain (ETC) complexes I-IV without affecting mRNA levels of their respective components. Consistently, eEF2K KO MB cells display decreased mitochondrial membrane potential and 20% increased proton leak thorough the mitochondrial membrane. In addition, eEF2K inactivation results in increased Group 3 MB cell death under ND and doubles survival of MB bearing mice fed with calorie restricted diets (p< 0.05). Control of mRNA translation elongation by eEF2K is critical for mitochondrial ETC complex assembly and efficient OXPHOS in MYC-overexpressing MB, likely representing an adaptive response by which MYC-driven MB cells cope with acute metabolic stress. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs as eEF2K activity appears critical under metabolic stress conditions.
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12
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Topham JT, Tsang ES, Karasinska JM, Metcalfe A, Ali H, Kalloger SE, Csizmok V, Williamson LM, Titmuss E, Nielsen K, Negri GL, Spencer Miko SE, Jang GH, Denroche RE, Wong HL, O'Kane GM, Moore RA, Mungall AJ, Loree JM, Notta F, Wilson JM, Bathe OF, Tang PA, Goodwin R, Morin GB, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma. Nat Commun 2022; 13:5941. [PMID: 36209277 PMCID: PMC9547977 DOI: 10.1038/s41467-022-33718-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/29/2022] [Indexed: 11/15/2022] Open
Abstract
Oncogenic KRAS mutations are absent in approximately 10% of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) and may represent a subgroup of mPDAC with therapeutic options beyond standard-of-care cytotoxic chemotherapy. While distinct gene fusions have been implicated in KRAS wildtype mPDAC, information regarding other types of mutations remain limited, and gene expression patterns associated with KRAS wildtype mPDAC have not been reported. Here, we leverage sequencing data from the PanGen trial to perform comprehensive characterization of the molecular landscape of KRAS wildtype mPDAC and reveal increased frequency of chr1q amplification encompassing transcription factors PROX1 and NR5A2. By leveraging data from colorectal adenocarcinoma and cholangiocarcinoma samples, we highlight similarities between cholangiocarcinoma and KRAS wildtype mPDAC involving both mutation and expression-based signatures and validate these findings using an independent dataset. These data further establish KRAS wildtype mPDAC as a unique molecular entity, with therapeutic opportunities extending beyond gene fusion events. KRAS wildtype metastatic pancreatic ductal adenocarcinoma (mPDAC) could represent a distinct molecular entity from other PDACs. Here, the authors analyse KRAS wildtype mPDAC tumours using genomics and transcriptomics and find molecular similarities with cholangiocarcinomas.
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Affiliation(s)
| | - Erica S Tsang
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | - Hassan Ali
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Karina Nielsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Patricia A Tang
- Departments of Surgery and Oncology, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rachel Goodwin
- The Ottawa Hospital Cancer Centre, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, ON, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,University Health Network, University of Toronto, Toronto, ON, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada. .,Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada. .,Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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13
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Shyp T, Mousavizadeh R, Negri GL, Zhang HF, Lizardo M, Sorensen P. Abstract B013: STEAP1 facilitates iron transport in ewing sarcoma to support mitochondrial activity. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-b013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ewing sarcoma (EwS) is a highly aggressive bone-associated tumor of children and young adults with strong propensity to progress and dismal outcome for patients with advanced stages of the disease. EwS is defined by a pathognomonic recurrent potent transcription factor, in 85-90% of cases EWSR1-FLI1. One of the previously described transcriptional targets of EWSR1-FLI1 is six-transmembrane epithelial antigen of the prostate 1 (STEAP1). STEAP1 is a member of the STEAP membrane-bound protein family involved in reduction of iron and copper which is a crucial step for metal transport and overexpressed in various malignancies. However, a precise functional role of STEAP1 in cancers including EwS remains elusive. EwS cell lines with knockout (KO) or knockdown (KD) of STEAP1 were created to perform functional studies for elucidating the functions of STEAP1 in EwS, including transient metal measurements. Additionally, the measurement of functional mitochondrial activity was performed by an extracellular flux analyzer. The activity of the mitochondrial electron transport chain complexes was measured by blue native PAGE. We showed that STEAP1 functions as a metalloreductase and STEAP1 KO cells have lower intracellular iron levels. Furthermore, we discovered that STEAP1 KO cells have significantly lower levels of the mitochondrial labile iron pool. Consequently, EwS cells with STEAP1 KO demonstrated impaired mitochondrial respiration and increased glycolysis rates. Additionally, the functional activity of iron-sulfur containing proteins and the the assembly of subunits of the mitochondrial electron transport chain complexes were decreased. This study is the first to demonstrate in vitro involvement of STEAP1 in transitional metal homeostasis and mitochondrial activity. These discoveries unveil alternative therapeutic strategies for EwS patients such as using compounds that promote an iron-dependent form of cell death, ferroptosis, or drugs that decrease metabolic adaptability.
Citation Format: Taras Shyp, Rouhollah Mousavizadeh, Gian Luca Negri, Hai-Feng Zhang, Michael Lizardo, Poul Sorensen. STEAP1 facilitates iron transport in ewing sarcoma to support mitochondrial activity [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B013.
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Affiliation(s)
- Taras Shyp
- 1BC Cancer Research Institute, Vancouver, BC, Canada,
| | | | - Gian Luca Negri
- 3Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Poul Sorensen
- 1BC Cancer Research Institute, Vancouver, BC, Canada,
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14
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Delaidelli A, Yao B, Wang QX, Huang YZ, Negri GL, Hughes C, Zhang H, Leprivier G, Sorensen P. MEDB-18. Elongation control of mRNA translation supports Group 3 medulloblastoma adaptation to nutrient deprivation. Neuro Oncol 2022. [PMCID: PMC9164713 DOI: 10.1093/neuonc/noac079.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Group 3 affiliation and MYC genetic amplification are associated with poor life expectancy and substantial morbidity in children suffering from medulloblastoma (MB). However, the high metabolic demand induced by MYC-driven transformation sensitizes MYC-overexpressing MB to cell death under conditions of nutrient deprivation (ND). Additionally, MYC-driven transformation is known to promote mitochondrial oxidative phosphorylation (OXPHOS). We previously reported that eukaryotic Elongation Factor Kinase 2 (eEF2K), the master regulator of mRNA translation elongation, promotes survival of MYC-overexpressing tumors under ND. Interestingly, eEF2K is overexpressed in MYC-driven MB and our preliminary proteomics data highlight large-scale alterations in OXPHOS components affecting eEF2K deficient MB cells. We therefore hypothesized that eEF2K activity is required for the selective translation of mRNAs needed for efficient OXPHOS, and for the progression of MYC-driven MB. We pefrormed Multiplexed enhanced Protein Dynamic Mass Spectrometry in eEF2K knockdown MYC-overexpressing D425 MB cells to identify mRNAs selectively translated upon eEF2K activation. Messenger RNAs encoding multiple (9 out of 10 detected) components of the mitochondrial OXPHOS pathway are selectively translated upon eEF2K activation. Inactivation of eEF2K by genetic KO leads to the disassembly of electron transport chain (ETC) complexes I-IV without affecting mRNA levels of their respective components. Consistently, eEF2K KO MB cells display decreased mitochondrial membrane potential and 20% increased proton leak thorough the mitochondrial membrane. In addition, eEF2K inactivation results in increased Group 3 MB cell death under ND and doubles survival of MB bearing mice fed with calorie restricted diets (p< 0.05).Control of mRNA translation elongation by eEF2K is critical for mitochondrial ETC complex assembly and efficient OXPHOS in MYC-overexpressing MB, likely representing an adaptive response by which MYC-driven MB cells cope with acute metabolic stress. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs as eEF2K activity appears critical under metabolic stress conditions.
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Affiliation(s)
- Alberto Delaidelli
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver , Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre , Vancouver , Canada
| | - Betty Yao
- Department of Molecular Oncology, British Columbia Cancer Research Centre , Vancouver , Canada
| | - Que Xi Wang
- Department of Molecular Oncology, British Columbia Cancer Research Centre , Vancouver , Canada
| | - Yue Zhou Huang
- Department of Molecular Oncology, British Columbia Cancer Research Centre , Vancouver , Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer , Vancouver , Canada
| | - Christopher Hughes
- Department of Molecular Oncology, British Columbia Cancer Research Centre , Vancouver , Canada
| | - Haifeng Zhang
- Department of Molecular Oncology, British Columbia Cancer Research Centre , Vancouver , Canada
| | - Gabriel Leprivier
- Institute of Neuropathology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Poul Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver , Canada
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15
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Korver W, Wong A, Gebremeskel S, Negri GL, Schanin J, Chang K, Leung J, Benet Z, Luu T, Brock EC, Luehrsen K, Xu A, Youngblood BA. The Inhibitory Receptor Siglec-8 Interacts With FcεRI and Globally Inhibits Intracellular Signaling in Primary Mast Cells Upon Activation. Front Immunol 2022; 13:833728. [PMID: 35154156 PMCID: PMC8837033 DOI: 10.3389/fimmu.2022.833728] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Immunomodulation of mast cell (MC) activity is warranted in allergic and inflammatory diseases where MCs have a central role in pathogenesis. Targeting Siglec-8, an inhibitory receptor on MCs and eosinophils, has shown promising activity in preclinical and clinical studies. While the intracellular pathways that regulate Siglec-8 activity in eosinophils have been well studied, the signaling mechanisms that lead to MC inhibition have not been fully elucidated. Here, we evaluate the intracellular signaling pathways of Siglec-8-mediated inhibition in primary MCs using an anti-Siglec-8 monoclonal antibody (mAb). Phospho-proteomic profiling of FcεRI-activated MCs revealed Siglec-8 mAb-treatment globally inhibited proximal and downstream kinases, leading to attenuated MC activation and degranulation. In fact, Siglec-8 was found to directly interact with FcεRI signaling molecules. Siglec-8 inhibition was dependent on both cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs) that interact with the SH2 containing protein phosphatase Shp-2 upon Siglec-8 phosphorylation. Taken together, these data support a model in which Siglec-8 regulates proximal FcεRI-induced phosphorylation events through phosphatase recruitment and interaction with FcεRIγ, resulting in global inhibition of MCs upon Siglec-8 mAb engagement.
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Affiliation(s)
| | - Alan Wong
- Allakos Inc., Redwood City, CA, United States
| | | | | | | | | | - John Leung
- Allakos Inc., Redwood City, CA, United States
| | | | - Thuy Luu
- Allakos Inc., Redwood City, CA, United States
| | | | | | - Alan Xu
- Allakos Inc., Redwood City, CA, United States
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16
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Delaidelli A, Dunham C, Santi M, Negri GL, von Deimling A, Pfister S, Kool M, Ramaswamy V, Korshunov A, Taylor M, Sorensen P. BIOM-35. CLINICALLY TRACTABLE OUTCOME PREDICTION OF GROUP 3/4 MEDULLOBLASTOMA BASED ON TPD52 IMMUNOHISTOCHEMISTRY: A MULTICOHORT STUDY. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
International consensus and the 2021 WHO classification recognize eight molecular subgroups among Group 3/4 medulloblastoma (representing ~60% of tumors). However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation patterns or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk-stratification.
PATIENTS AND METHODS
We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. Risk stratification and prediction capability were computed utilizing uni- and multivariate survival analysis. Newly developed risk classifiers including TPD52 IHC were compared to state-of-the-art risk stratification schemes in terms of prediction error, area under the time-dependent receiver operating characteristic (ROC) curves and C-statistic. Biomarker-driven prognostic stratification models identified were cross validated in different cohorts.
RESULTS
TPD52 IHC positivity represents a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67-26.7 [95% CIs between 1.00-706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing disease risk-stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity is a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53-45.40], p < 0.0001), suggesting important implication for therapeutic choices.
CONCLUSION
The current study redefines the approach to risk-stratification in Group 3/4 medulloblastoma. Integration of TPD52 IHC in classification algorithms significantly improves outcome prediction and can be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
| | | | | | | | | | | | - Marcel Kool
- University of Heidelberg, Heidelberg, Germany
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17
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Delaidelli A, Negri GL, Yao B, Wang QX, Huang YZ, Hughes C, Leprivier G, Sorensen P. CSIG-23. ELONGATION CONTROL OF mRNA TRANSLATION DRIVES GROUP 3 MEDULLOBLASTOMA ADAPTATION TO NUTRIENT DEPRIVATION. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Group 3 affiliation and MYC genetic amplification are associated with poor life expectancy and substantial morbidity in children suffering from medulloblastoma (MB). However, the high metabolic demand induced by MYC-driven transformation sensitizes MYC-overexpressing MB to cell death under conditions of nutrient deprivation (ND). Additionally, MYC-driven transformation is known to promote mitochondrial oxidative phosphorylation (OXPHOS). We previously reported that eukaryotic Elongation Factor Kinase 2 (eEF2K), the master regulator of mRNA translation elongation, promotes survival of MYC-overexpressing tumors under ND. Interestingly, eEF2K is overexpressed in MYC-driven MB and our preliminary proteomics data highlight large-scale alterations in OXPHOS components affecting eEF2K deficient MB cells. We therefore hypothesized that eEF2K activity is required for the selective translation of mRNAs needed for efficient OXPHOS, and for the progression of MYC-driven MB. We pefrormed Multiplexed enhanced Protein Dynamic Mass Spectrometry in eEF2K knockdown MYC-overexpressing D425 MB cells to identify mRNAs selectively translated upon eEF2K activation. Messenger RNAs encoding multiple (9 out of 10 detected) components of the mitochondrial OXPHOS pathway are selectively translated upon eEF2K activation. Inactivation of eEF2K by genetic KO leads to the disassembly of electron transport chain (ETC) complexes I-IV without affecting mRNA levels of their respective components. Consistently, eEF2K KO MB cells display decreased mitochondrial membrane potential and 20% increased proton leak thorough the mitochondrial membrane. In addition, eEF2K inactivation results in increased Group 3 MB cell death under ND and doubles survival of MB bearing mice fed with calorie restricted diets (p< 0.05). Control of mRNA translation elongation by eEF2K is critical for mitochondrial ETC complex assembly and efficient OXPHOS in MYC-overexpressing MB, likely representing an adaptive response by which MYC-driven MB cells cope with acute metabolic stress. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs as eEF2K activity appears critical under metabolic stress conditions.
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Affiliation(s)
| | | | - Betty Yao
- BC Cancer, Vancouver, British Columbia, Canada
| | - Que Xi Wang
- BC Cancer, Vancouver, British Columbia, Canada
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18
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Zhang HF, Hughes CS, Li W, He JZ, Surdez D, El-Naggar AM, Cheng H, Prudova A, Delaidelli A, Negri GL, Li X, Ørum-Madsen MS, Lizardo MM, Oo HZ, Colborne S, Shyp T, Scopim-Ribeiro R, Hammond CA, Dhez AC, Langman S, Lim JKM, Kung SHY, Li A, Steino A, Daugaard M, Parker SJ, Geltink RIK, Orentas RJ, Xu LY, Morin GB, Delattre O, Dimitrov DS, Sorensen PH. Proteomic Screens for Suppressors of Anoikis Identify IL1RAP as a Promising Surface Target in Ewing Sarcoma. Cancer Discov 2021; 11:2884-2903. [PMID: 34021002 PMCID: PMC8563374 DOI: 10.1158/2159-8290.cd-20-1690] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 11/21/2020] [Revised: 04/03/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023]
Abstract
Cancer cells must overcome anoikis (detachment-induced death) to successfully metastasize. Using proteomic screens, we found that distinct oncoproteins upregulate IL1 receptor accessory protein (IL1RAP) to suppress anoikis. IL1RAP is directly induced by oncogenic fusions of Ewing sarcoma, a highly metastatic childhood sarcoma. IL1RAP inactivation triggers anoikis and impedes metastatic dissemination of Ewing sarcoma cells. Mechanistically, IL1RAP binds the cell-surface system Xc - transporter to enhance exogenous cystine uptake, thereby replenishing cysteine and the glutathione antioxidant. Under cystine depletion, IL1RAP induces cystathionine gamma lyase (CTH) to activate the transsulfuration pathway for de novo cysteine synthesis. Therefore, IL1RAP maintains cyst(e)ine and glutathione pools, which are vital for redox homeostasis and anoikis resistance. IL1RAP is minimally expressed in pediatric and adult normal tissues, and human anti-IL1RAP antibodies induce potent antibody-dependent cellular cytotoxicity of Ewing sarcoma cells. Therefore, we define IL1RAP as a new cell-surface target in Ewing sarcoma, which is potentially exploitable for immunotherapy. SIGNIFICANCE: Here, we identify cell-surface protein IL1RAP as a key driver of metastasis in Ewing sarcoma, a highly aggressive childhood sarcoma. Minimal expression in pediatric and adult normal tissues nominates IL1RAP as a promising target for immunotherapy.See related commentary by Yoon and DeNicola, p. 2679.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Hai-Feng Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christopher S Hughes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Jian-Zhong He
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Didier Surdez
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Hongwei Cheng
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
- Modelling and translation Laboratory, Xinxiang Medical University, Xinxiang, Henan, China
| | - Anna Prudova
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Alberto Delaidelli
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Xiaojun Li
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Michael M Lizardo
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Htoo Zarni Oo
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Taras Shyp
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Renata Scopim-Ribeiro
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Colin A Hammond
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Anne-Chloe Dhez
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sofya Langman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jonathan K M Lim
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sonia H Y Kung
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Amy Li
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Anne Steino
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Mads Daugaard
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Seth J Parker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Ramon I Klein Geltink
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Rimas J Orentas
- Seattle Children's Research Institute, Seattle, Washington
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, 75005 Paris, France
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
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19
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Delaidelli A, Dunham C, Santi M, Negri GL, Triscott J, Zheludkova O, Golanov A, Ryzhova M, Okonechnikov K, Schrimpf D, Stichel D, Ellison DW, von Deimling A, Kool M, Pfister SM, Ramaswamy V, Korshunov A, Taylor MD, Sorensen PH. Clinically Tractable Outcome Prediction of non-WNT/non-SHH Medulloblastoma Based on TPD52 Immunohistochemistry in a Multicohort Study. Clin Cancer Res 2021; 28:116-128. [PMID: 34702771 DOI: 10.1158/1078-0432.ccr-21-2057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/12/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE International consensus and the 2021 WHO classification recognize eight molecular subgroups among non-WNT/non-SHH (Group 3/4) medulloblastoma, representing ~60% of tumors. However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation profiles or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk stratification. EXPERIMENTAL DESIGN We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. RESULTS TPD52 IHC positivity represented a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67-26.7 [95% CIs between 1.00-706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing state-of-the-art risk stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity was a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53-45.40], p < 0.0001), suggesting important implication for therapeutic choices. CONCLUSIONS The current study redefines the approach to risk stratification in Group 3/4 medulloblastoma in global practice. Since integration of TPD52 IHC in classification algorithms significantly improved outcome prediction, this test could be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
- Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, and University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariarita Santi
- Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Joanna Triscott
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Olga Zheludkova
- St Luka's Clinical Research Center for Children, Moscow, Russian Federation
| | - Andrey Golanov
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Marina Ryzhova
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
| | - Daniel Schrimpf
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andreas von Deimling
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrey Korshunov
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Gatev E, Inkster AM, Negri GL, Konwar C, Lussier AA, Skakkebaek A, Sokolowski MB, Gravholt CH, Dunn EC, Kobor MS, Aristizabal MJ. Autosomal sex-associated co-methylated regions predict biological sex from DNA methylation. Nucleic Acids Res 2021; 49:9097-9116. [PMID: 34403484 PMCID: PMC8450084 DOI: 10.1093/nar/gkab682] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/20/2020] [Revised: 07/07/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022] Open
Abstract
Sex is a modulator of health that has been historically overlooked in biomedical research. Recognizing this knowledge gap, funding agencies now mandate the inclusion of sex as a biological variable with the goal of stimulating efforts to illuminate the molecular underpinnings of sex biases in health and disease. DNA methylation (DNAm) is a strong molecular candidate for mediating such sex biases; however, a robust and well characterized annotation of sex differences in DNAm is yet to emerge. Beginning with a large (n = 3795) dataset of DNAm profiles from normative adult whole blood samples, we identified, validated and characterized autosomal sex-associated co-methylated genomic regions (sCMRs). Strikingly, sCMRs showed consistent sex differences in DNAm over the life course and a subset were also consistent across cell, tissue and cancer types. sCMRs included sites with known sex differences in DNAm and links to health conditions with sex biased effects. The robustness of sCMRs enabled the generation of an autosomal DNAm-based predictor of sex with 96% accuracy. Testing this tool on blood DNAm profiles from individuals with sex chromosome aneuploidies (Klinefelter [47,XXY], Turner [45,X] and 47,XXX syndrome) revealed an intimate relationship between sex chromosomes and sex-biased autosomal DNAm.
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Affiliation(s)
- Evan Gatev
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.,Graduate program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V5T 4S6, Canada.,Beedie School of Business, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,BC Children's Hospital Research Institute Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V6H 0B3, Canada
| | - Amy M Inkster
- BC Children's Hospital Research Institute Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Chaini Konwar
- BC Children's Hospital Research Institute Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V6H 0B3, Canada
| | - Alexandre A Lussier
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Psychiatry, Harvard Medical School, Boston, MA 02114, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne Skakkebaek
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus 8200, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.,Program in Child and Brain Development, CIFAR, MaRS Centre, West Tower, 661 University Ave, Suite 505, Toronto, ON M5G 1M1, Canada
| | - Claus H Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8200, Denmark.,Department of Endocrinology, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Erin C Dunn
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Psychiatry, Harvard Medical School, Boston, MA 02114, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Kobor
- BC Children's Hospital Research Institute Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V6H 0B3, Canada.,Program in Child and Brain Development, CIFAR, MaRS Centre, West Tower, 661 University Ave, Suite 505, Toronto, ON M5G 1M1, Canada
| | - Maria J Aristizabal
- BC Children's Hospital Research Institute Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V6H 0B3, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.,Program in Child and Brain Development, CIFAR, MaRS Centre, West Tower, 661 University Ave, Suite 505, Toronto, ON M5G 1M1, Canada.,Department of Biology, Queen's University, Kingston ON K7L 3N6, Canada
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21
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Delaidelli A, Negri GL, Wang QX, Huang A, Sidhu S, Zhang J, Huang YZ, Yao B, Langman S, Vislovukh A, Hovestadt V, Taylor M, Leprivier G, Sorensen P. EMBR-20. ELONGATION CONTROL OF MRNA TRANSLATION DRIVES GROUP 3 MEDULLOBLASTOMA. Neuro Oncol 2021. [PMCID: PMC8168111 DOI: 10.1093/neuonc/noab090.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Medulloblastoma (MB) is the most common pediatric intracranial tumor and leading cause of childhood related cancer deaths. Group 3 affiliation and genetic amplifications of the MYC oncogene are predictors of adverse outcome in MB, underscoring a dire need for novel and more effective therapeutic approaches. The let-7 family of small non-coding RNAs (miRNAs) is known to inhibit tumor progression and regulate metabolism by targeting and degrading several cellular mRNAs, including MYC. Indeed, let-7 miRNAs are frequently repressed in several cancer types, including in MYC-driven MB. We previously reported that the mRNA translation elongation regulator eukaryotic Elongation Factor-2 Kinase (eEF2K) is a pivotal mediator of cancer cell adaptation to nutrient deprivation. In the current work, we identified a potential binding site for let-7 miRNAs on the eEF2K 3’ untranslated region (UTR). In addition, eEF2K mRNA and let-7 miRNA expressions negatively correlate in MB, suggesting a potential regulation of the former by the latter. Let-7 miRNAs transfection decreases eEF2K mRNA and protein levels (by ~40–50%). Down-regulation of luciferase activity by let-7 miRNAs is impaired upon mutation of the let-7 binding site on the eEF2K 3’UTR. Inhibition of eEF2K significantly reduces survival of MYC-amplified MB cell lines under nutrient deprivation, altering their mRNA translation rates. Knockout of eEF2K increases survival of MYC-amplified MB xenografts when mice are kept under calorie restricted diets. We conclude that let-7 miRNAs degrade the eEF2K mRNA by binding to its 3’UTR, indicating that let-7 repression in MYC-driven MB is partially responsible for increased eEF2K levels. Moreover, the let-7-eEF2K axis constitutes a critical mechanism for MYC-driven MB adaptation to acute metabolic stress, representing a promising therapeutic target. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs, as eEF2K activity appears critical under metabolic stress conditions.
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Affiliation(s)
| | | | - Que Xi Wang
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Albert Huang
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Simran Sidhu
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Joyce Zhang
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - Betty Yao
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | | | | | - Michael Taylor
- Arthur and Sonia Labatt Brain Tumor Research Centre, Toronto, ON, Canada
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22
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Delaidelli A, Dunham C, Santi MR, Negri GL, Triscott J, Zheludkova O, Golanov A, Ryzhova M, Okonechnikov K, Schrimpf D, Stichel D, von Deimling A, Kool M, Pfister S, Ramaswamy V, Korshunov A, Taylor M, Sorensen P. EMBR-21. CLINICALLY TRACTABLE OUTCOME PREDICTION OF GROUP 3/4 MEDULLOBLASTOMA BASED ON TPD52 IMMUNOHISTOCHEMISTRY: A MULTICOHORT STUDY. Neuro Oncol 2021. [PMCID: PMC8168220 DOI: 10.1093/neuonc/noab090.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background International consensus and the 2021 WHO classification recognize eight molecular subtypes among Group 3/4 medulloblastoma (representing ~60% of tumors). However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation patterns or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk-stratification. Patients and Methods We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. Risk stratification and prediction capability were computed utilizing uni- and multivariate survival analysis. Newly developed risk classifiers including TPD52 IHC were compared to state-of-the-art risk stratification schemes in terms of prediction error, area under the time-dependent receiver operating characteristic (ROC) curves and C-statistic. Biomarker-driven prognostic stratification models identified were cross validated in different cohorts. Results TPD52 IHC positivity represents a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67–26.7 [95% CIs between 1.00–706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing disease risk-stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity is a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53–45.40], p < 0.0001), suggesting important implication for therapeutic choices. Conclusion The current study redefines the approach to risk-stratification in Group 3/4 medulloblastoma. Integration of TPD52 IHC in classification algorithms significantly improves outcome prediction and can be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
| | | | | | | | | | - Olga Zheludkova
- St Luka’s Clinical Research Center for Children, Moscow, Russian Federation
| | - Andrey Golanov
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Marina Ryzhova
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | | | | | - Damian Stichel
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Marcel Kool
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pfister
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
| | | | - Michael Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
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Asleh K, Negri GL, Miko SES, Colborne S, Hughes CS, Wang XQ, Gao D, Gilks CB, Chia SK, Nielsen TO, Morin GB. Abstract PS18-06: Proteomic analysis of breast cancer formalin-fixed paraffin-embedded clinical specimens identifies biologically-important subtypes with distinct clinical outcomes. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps18-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Genomic classification of breast cancer has advanced breast cancer diagnosis and outcomes. However, extensive heterogeneity still exists beyond their DNA or RNA profiles. Newer classifications based on protein profiling are being developed to investigate the molecular oncology of breast cancers at the level where most drugs act. Using a recently-developed technology, we performed global proteomic profiling of 300 breast cancer specimens linked to outcome data. Methods: Sections of 75 samples from each PAM50 intrinsic subtype (Luminal A, Luminal B, Her2-enriched, Basal-like; n = 300) were macrodissected and analyzed using the Single-Pot Solid-Phase enhanced Sample Preparation Clinical Tissue Proteomics, a highly sensitive 11-sample multiplex massspectrometry protocol applicable to formalin-fixed, paraffin embedded (FFPE) specimens. This methodology enables comprehensive quantification of protein expression for classifier and biomarker discovery. Patients were diagnosed during 2008-2013 (n = 178, dataset I) and 1986-1992 (n = 122, dataset II). Results: In-depth proteomic analysis measured 9088 proteins in total, including 4214 proteins quantified in every sample. Consensus clustering of 174 evaluable cases in dataset I identified four distinct groups based on expression values for 1054 highly variant proteins. Cluster 3 (n = 47, mostly basal-like with HER2-Enriched) displayed the most favorable recurrence free survival (RFS) when compared to other clusters (HR = 0.22, 95%CI [0.08-0.63], p = 0.005). This cluster was enriched for immune related pathways including antigen processing and presentation and type I & II interferon signaling, and displayed high tumor infiltrating lymphocyte counts, characterizing this cluster as “immune hot”. In contrast, cluster 2 (n = 50, mostly basal-like) exhibited the poorest RFS (HR = 2.88, 95%CI [1.45-5.70], p = 0.002) and was enriched for proteins related to stromal and extracellular matrix with few immune related peptides. Cluster 1 (n = 34, luminal B and HER2-Enriched) was associated with lipid metabolism, whereas cluster 4 (n = 43, mostly HER2-Enriched with luminal A and luminal B) had a profile enriched for extracellular matrix, blood coagulation and complement activation. Conclusions: Global proteomic analysis on FFPE specimens can characterize the heterogeneity of breast cancer in a reliable and clinically-applicable high throughput manner. Our methodology identifies protein candidates that potentially serve as therapeutic targets and could be adapted to archived clinical specimens from other tumors.
Citation Format: Karama Asleh, Gian Luca Negri, Sandra E. Spencer Miko, Shane Colborne, Christopher S. Hughes, Xiu Q. Wang, Dongxia Gao, C. Blake Gilks, Stephen K.L. Chia, Torsten O. Nielsen, Gregg B. Morin. Proteomic analysis of breast cancer formalin-fixed paraffin-embedded clinical specimens identifies biologically-important subtypes with distinct clinical outcomes [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-06.
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Affiliation(s)
- Karama Asleh
- 1Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - Gian Luca Negri
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Shane Colborne
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Xiu Q. Wang
- 1Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - Dongxia Gao
- 1Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - C. Blake Gilks
- 1Genetic Pathology Evaluation Centre, Vancouver, BC, Canada
| | - Stephen K.L. Chia
- 3Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Gregg B. Morin
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
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24
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Orlando KA, Douglas AK, Abudu A, Wang Y, Tessier-Cloutier B, Su W, Peters A, Sherman LS, Moore R, Nguyen V, Negri GL, Colborne S, Morin GB, Kommoss F, Lang JD, Hendricks WP, Raupach EA, Pirrotte P, Huntsman DG, Trent JM, Parker JS, Raab JR, Weissman BE. Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism. eLife 2020; 9:59073. [PMID: 33355532 PMCID: PMC7813545 DOI: 10.7554/elife.59073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 05/19/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 reexpression. BRG1 reexpression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription-factor-binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant-negative AP-1 cell line, we found that both AP-1 DNA-binding activity and BRG1 reexpression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 reexpression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.
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Affiliation(s)
- Krystal Ann Orlando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Amber K Douglas
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Aierken Abudu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Weiping Su
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Alec Peters
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States.,Department Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Rayvon Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Vinh Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Gian Luca Negri
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Shane Colborne
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | - Jessica D Lang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - William Pd Hendricks
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Elizabeth A Raupach
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Jeffrey M Trent
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Jesse R Raab
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
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25
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Gibbard E, Cochrane DR, Pors J, Negri GL, Colborne S, Cheng AS, Chow C, Farnell D, Tessier-Cloutier B, McAlpine JN, Morin GB, Schmidt D, Kommoss S, Kommoss F, Keul J, Gilks B, Huntsman DG, Hoang L. Whole-proteome analysis of mesonephric-derived cancers describes new potential biomarkers. Hum Pathol 2020; 108:1-11. [PMID: 33121982 DOI: 10.1016/j.humpath.2020.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/21/2020] [Indexed: 01/09/2023]
Abstract
Mesonephric carcinomas (MEs) and female adnexal tumors of probable Wolffian origin (FATWO) are derived from embryologic remnants of Wolffian/mesonephric ducts. Mesonephric-like carcinomas (MLCs) show identical morphology to ME of the cervix but occur in the uterus and ovary without convincing mesonephric remnants. ME, MLC, and FATWO are challenging to diagnose due to their morphologic similarities to Müllerian/paramesonephric tumors, contributing to a lack of evidence-based and tumor-specific treatments. We performed whole-proteomic analysis on 9 ME/MLC and 56 endometrial carcinomas (ECs) to identify potential diagnostic biomarkers. Although there were no convincing differences between ME and MLC, 543 proteins showed increased expression in ME/MLC relative to EC. From these proteins, euchromatic histone lysine methyltransferase 2 (EHMT2), glutathione S-transferase Mu 3 (GSTM3), eukaryotic translation elongation factor 1 alpha 2 (EEF1A2), and glycogen synthase kinase 3 beta were identified as putative biomarkers. Immunohistochemistry was performed on these candidates and GATA3 in 14 ME/MLC, 8 FATWO, 155 EC, and normal tissues. Of the candidates, only GATA3 and EHMT2 were highly expressed in mesonephric remnants and mesonephric-derived male tissues. GATA3 had the highest sensitivity and specificity for ME/MLC versus EC (93% and 99%) but was absent in FATWO. EHMT2 was 100% sensitive for ME/MLC & FATWO but was not specific (65%). Similarly, EEF1A2 was reasonably sensitive to ME/MLC (92%) and FATWO (88%) but was the least specific (38%). GSTM3 performed intermediately (sensitivity for ME/MLC and FATWO: 83% and 38%, respectively; specificity 67%). Although GATA3 remained the best diagnostic biomarker for ME/MLC, we have identified EHMT2, EEF1A2, and GSTM3 as proteins of interest in these cancers. FATWO's cell of origin is uncertain and remains an area for future research.
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Affiliation(s)
- Evan Gibbard
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, V6H 3N1, Canada; Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Dawn R Cochrane
- Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Jennifer Pors
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Angela S Cheng
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada
| | - David Farnell
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, The University of British Columbia, Vancouver, BC, V6Z 2K8, Canada
| | - Gregg B Morin
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, V6H 3N1, Canada; Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Dietmar Schmidt
- MVZ of Histology, Cytology and Molecular Diagnostics, Trier, 54296, Germany
| | - Stefan Kommoss
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, 72076, Germany
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, 88048, Germany
| | - Jacqueline Keul
- Department of Women's Health, Tübingen University Hospital, Tübingen, 72076, Germany
| | - Blake Gilks
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada; Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - David G Huntsman
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, V6H 3N1, Canada; Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, BC, V6H 3Z6, Canada; Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada.
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26
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Zhang HF, El-Naggar AM, Cheng H, Prudova A, Delaidelli A, He JZ, Negri GL, Lizardo M, Yang T, Morin G, Li W, Dimitrov DS, Sorensen PH. Abstract 6080: IL1RAP augments Cysteine metabolism and drives oxidative stress adaptation and lung metastasis in Ewing sarcoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The high oxidative stress cancer cells experience during the metastatic cascade is an important determinant of metastasis. How cancer cells adapt to those stressful conditions remains elusive. Here our global translatome and proteome analyses have uncovered novel signatures exploited by oncogene-transformed cells to adapt and survive oxidative stress. We revealed that various oncoproteins promote the expression of the IL1RAP to alleviate oxidative stress and facilitate stress adaptation. Mechanistically, IL1RAP controls Cysteine metabolism, a key substrate and determinant of antioxidant glutathione synthesis. CTH, a crucial enzyme for de novo Cysteine synthesis and redox regulation, was identified as a key functional mediator of IL1RAP. Moreover, global interactome analysis uncovered IL1RAP as a novel component and enhancer of the System Xc− transporter (SLC7A11), which is involved in Cystine uptake. Thus, IL1RAP enhances Cysteine supply via both uptake and biogenesis. IL1RAP depletion rendered Ewing sarcoma cells susceptible to oxidative stress and ferroptosis in vitro, and dramatically mitigated local invasion and lung metastasis in mice. In patients with Ewing sarcoma, high-expression of IL1RAP in the tumors correlated with poor event-free survival. Therefore, we have defined a novel pro-metastatic mechanism driven by IL1RAP-mediated Cysteine metabolism and redox regulation.
Citation Format: Hai-Feng Zhang, Amal M. El-Naggar, Hongwei Cheng, Anna Prudova, Alberto Delaidelli, Jian-Zhong He, Gian Luca Negri, Michael Lizardo, Tianqing Yang, Gregg Morin, Wei Li, Dimiter S. Dimitrov, Poul H. Sorensen. IL1RAP augments Cysteine metabolism and drives oxidative stress adaptation and lung metastasis in Ewing sarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6080.
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Affiliation(s)
- Hai-Feng Zhang
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Amal M. El-Naggar
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Anna Prudova
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | | | | | - Tianqing Yang
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregg Morin
- 2BC Cancer, Vancouver, British Columbia, Canada
| | - Wei Li
- 4University of Pittsburgh, Pittsburgh, PA
| | | | - Poul H. Sorensen
- 1University of British Columbia, Vancouver, British Columbia, Canada
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Zhang H, El-Naggar AM, Cheng H, Delaidelli A, Negri GL, Li W, Dimitrov DS, Sorensen PH. Abstract PR14: Ewing sarcoma cells exploit the IL1RAP-CTH axis to drive oxidative stress adaptation and lung metastasis. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-pr14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastasis is a highly inefficient process due to the high oxidative stress that cancer cells experience, such as in the circulation and at distant organs prior to colonization. How cancer cells adapt to those stressful conditions and develop anti-anoikis properties remains elusive. Here our global translatome and proteome analyses have uncovered novel signatures exploited by oncogene-transformed cells to adapt and survive anoikis-inducing stress. We reveal that EWS-ETS chimeric oncoproteins trigger the expression of the IL1RAP surface protein to alleviate oxidative stress and facilitate stress adaptation, thereby promoting lung metastasis in Ewing sarcoma. Proteomic profiling identifies CTH, a key enzyme for de novo cysteine synthesis and redox regulation, as an important functional downstream mediator of IL1RAP. Blockade of either IL1RAP or CTH, using genetic or pharmacologic approaches, renders EWS cells susceptible to oxidative stress in vitro, and dramatically mitigates primary tumor growth, local invasion and lung metastasis in mice. Importantly, high expression of this IL1RAP-CTH axis correlates with markedly decreased overall and event-free survival in EWS patients. Thus, our study has defined a novel mechanism exploited by EWS cells for metastasis, which can be a potential therapeutic target for high-risk metastatic EWS.
This abstract is also being presented as Poster B58.
Citation Format: Haifeng Zhang, Amal M. El-Naggar, Hongwei Cheng, Alberto Delaidelli, Gian Luca Negri, Wei Li, Dimiter S. Dimitrov, Poul H.B. Sorensen. Ewing sarcoma cells exploit the IL1RAP-CTH axis to drive oxidative stress adaptation and lung metastasis [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr PR14.
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Affiliation(s)
- Haifeng Zhang
- 1University of British Columbia, Vancouver, BC, Canada,
| | | | | | | | | | - Wei Li
- 3University of Pittsburgh, Pittsburgh, PA
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Delaidelli A, Negri GL, Wang XQ, Sidhu S, Cho B, Leprivier G, Hovestadt V, Pfister S, Taylor M, Kool M, Sorensen P. Abstract B27: A link between small noncoding RNAs and mRNA translation elongation: The let7-eEF2K axis in pediatric tumor adaptation to nutrient deprivation. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-b27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Medulloblastoma (MB) and neuroblastoma (NB) are the most common pediatric solid cancers and the leading cause of childhood cancer-related deaths. Genetic amplifications of the MYC and MYCN oncogenes are the strongest independent predictor of adverse outcomes in MB and NB, underscoring a dire need to improve therapeutic approaches. Tumors continually weather stress from acute microenvironmental changes, including limited nutrient availability. The let-7 family of small noncoding RNAs (miRNAs) inhibits tumor progression and regulates metabolism by selectively targeting and degrading mRNAs, including MYC and MYCN. Indeed, let-7 miRNAs are frequently repressed in several cancers, including in MYC-driven MB and NB. We previously reported that the mRNA translation elongation regulator eukaryotic eEF2K is a pivotal mediator of cancer cell adaptation to nutrient deprivation. Our preliminary data indicate that the eEF2K 3´ untranslated region (UTR) harbors a potential binding site for let-7 miRNAs. In addition, eEF2K mRNA and let-7 miRNA expressions negatively correlate in MB and NB. We therefore hypothesized that let-7 downregulation induces eEF2K expression, thereby supporting MYC-driven MB and NB adaptation to nutrient deprivation and tumor progression.
Methods: Effects of eEF2K pharmacologic and genetic inhibition on MB and NB cell death were evaluated in vitro by flow cytometry, while cellular mRNA translation rates were studied by polysome fractionation and Click chemistry. The ability of let-7 to degrade eEF2K mRNA was assessed by let-7 miRNAs transfection into MB cells, followed by RT-PCR and Western blotting for eEF2K. Binding of let-7 to the eEF2K 3´UTR was validated by luciferase reporter assay. Finally, NB xenograft mouse models confirmed in vitro observations.
Results: Inhibition of eEF2K significantly reduces survival of MYC/MYCN-amplified NB and MB cell lines under nutrient deprivation, altering their mRNA translation rates. Let-7 miRNAs transfection decreases eEF2K mRNA and protein levels by 40-50%. Downregulation of luciferase activity by let-7 miRNAs is impaired upon mutation of the let-7 binding site on the eEF2K 3´UTR. eEF2K knockdown decreases growth twofold in MYCN-amplified NB xenografts in mice under calorie-restriction diets.
Conclusions: Let-7 miRNAs degrade the eEF2K mRNA by binding to its 3´UTR, indicating that let-7 repression in MYC-driven NB and MB is partially responsible for increased eEF2K levels. Moreover, the let-7-eEF2K axis constitutes a critical mechanism for MYC-driven MB and NB adaptation to acute metabolic stress, representing a promising therapeutic target. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs, as eEF2K activity appears critical under metabolic stress conditions.
Citation Format: Alberto Delaidelli, Gian Luca Negri, Xue Qi Wang, Simran Sidhu, Brian Cho, Gabriel Leprivier, Volker Hovestadt, Stefan Pfister, Michael Taylor, Marcel Kool, Poul Sorensen. A link between small noncoding RNAs and mRNA translation elongation: The let7-eEF2K axis in pediatric tumor adaptation to nutrient deprivation [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B27.
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Affiliation(s)
| | | | - Xue Qi Wang
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Simran Sidhu
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Brian Cho
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | | | | | | | - Michael Taylor
- 4Arthur and Sonia Labatt Brain Tumor Research Centre, Toronto, ON, Canada
| | - Marcel Kool
- 3German Cancer Consortium (DKTK), Heidelberg, Germany,
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Kogler M, Tortola L, Negri GL, Leopoldi A, El-Naggar AM, Mereiter S, Gomez-Diaz C, Nitsch R, Tortora D, Kavirayani AM, Gapp BV, Rao S, Uribesalgo I, Hoffmann D, Cikes D, Novatchkova M, Williams DA, Trent JM, Ikeda F, Daugaard M, Hagelkruys A, Sorensen PH, Penninger JM. HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-Family GTPases. Cancer Res 2020; 80:3009-3022. [PMID: 32366477 PMCID: PMC7611202 DOI: 10.1158/0008-5472.can-19-2270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/24/2019] [Revised: 03/21/2020] [Accepted: 04/29/2020] [Indexed: 12/19/2022]
Abstract
HACE1 is an E3 ubiquitin ligase with important roles in tumor biology and tissue homeostasis. Loss or mutation of HACE1 has been associated with the occurrence of a variety of neoplasms, but the underlying mechanisms have not been defined yet. Here, we report that HACE1 is frequently mutated in human lung cancer. In mice, loss of Hace1 led to enhanced progression of KRasG12D -driven lung tumors. Additional ablation of the oncogenic GTPase Rac1 partially reduced progression of Hace1-/- lung tumors. RAC2, a novel ubiquitylation target of HACE1, could compensate for the absence of its homolog RAC1 in Hace1-deficient, but not in HACE1-sufficient tumors. Accordingly, ablation of both Rac1 and Rac2 fully averted the increased progression of KRasG12D -driven lung tumors in Hace1-/- mice. In patients with lung cancer, increased expression of HACE1 correlated with reduced levels of RAC1 and RAC2 and prolonged survival, whereas elevated expression of RAC1 and RAC2 was associated with poor prognosis. This work defines HACE1 as a crucial regulator of the oncogenic activity of RAC-family GTPases in lung cancer development. SIGNIFICANCE: These findings reveal that mutation of the tumor suppressor HACE1 disrupts its role as a regulator of the oncogenic activity of RAC-family GTPases in human and murine lung cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/14/3009/F1.large.jpg.
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Affiliation(s)
- Melanie Kogler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Luigi Tortola
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria.
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Switzerland
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Alexandra Leopoldi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - Stefan Mereiter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Carlos Gomez-Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Roberto Nitsch
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
- Advanced Medicines Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Davide Tortora
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Bianca V Gapp
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Shuan Rao
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Iris Uribesalgo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - David Hoffmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology, Vienna BioCentre, Vienna, Austria
| | - David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Jeffrey M Trent
- Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria.
- Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Orlando KA, Raab JR, Douglas AK, Abudu A, Wang Y, Negri GL, Colborne S, Morin GB, Lang JD, Hendricks WP, Raupach EA, Pirrotte P, Huntsman DG, Trent JM, Parker JS, Weissman BE. Abstract B25: SMARCA4/BRG1 and AP-1 co-regulate an epithelial-like signature in small-cell carcinoma of ovary, hypercalcemic type (SCCOHT). Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.ovca19-b25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex, occur in >95% of small cell carcinomas of the ovary, hypercalcemic type (SCCOHT), a rare and aggressive form of ovarian cancer. Because of its apparent role as a driver for SCCOHT, we performed integrative multi-omic analyses in a SCCOHT cell line +/- BRG1 re-expression to identify its role in SCCOHT tumorigenesis. After re-expression, BRG1 was recruited to both distal and promoter regions. We also observed increased chromatin accessibility at distal sites enriched for transcription factor binding motifs for AP-1 family members. Of interest, BRG1 re-expression induced an epithelial-like gene and protein expression concomitant with enrichment of AP-1 motifs at the TSS of highly upregulated epithelial genes. To determine the biologic relevance of these changes at AP-1 binding sites, we used a dominant negative AP-1 cell line to demonstrate that the necessity of AP-1 DNA binding activity and BRG1 re-expression for the protein expression of epithelial genes. Our study demonstrates that BRG1 loss may drive SCCOHT tumorigenesis by diminishing an epithelial-like gene and protein signature of its cell of origin driven by altered AP-1 binding.
Citation Format: Krystal A. Orlando, Jesse R. Raab, Amber K. Douglas, Aierken Abudu, Yemin Wang, Gian Luca Negri, Shane Colborne, Gregg B. Morin, Jessica D. Lang, William P.D. Hendricks, Elizabeth A. Raupach, Patrick Pirrotte, David G. Huntsman, Jeffrey M. Trent, Joel S. Parker, Bernard E. Weissman. SMARCA4/BRG1 and AP-1 co-regulate an epithelial-like signature in small-cell carcinoma of ovary, hypercalcemic type (SCCOHT) [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B25.
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Affiliation(s)
| | - Jesse R. Raab
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC,
| | | | | | - Yemin Wang
- 3University of British Columbia, Vancouver, BC, Canada,
| | | | | | | | - Jessica D. Lang
- 4Translational Genomics Research Institute (TGen), Phoenix, AZ
| | | | | | | | | | | | - Joel S. Parker
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC,
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31
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Ji JX, Cochrane DR, Tessier-Cloutier B, Chen SY, Ho G, Pathak KV, Alcazar IN, Farnell D, Leung S, Cheng A, Chow C, Colborne S, Negri GL, Kommoss F, Karnezis A, Morin GB, McAlpine JN, Gilks CB, Weissman BE, Trent JM, Hoang L, Pirrotte P, Wang Y, Huntsman DG. Arginine Depletion Therapy with ADI-PEG20 Limits Tumor Growth in Argininosuccinate Synthase-Deficient Ovarian Cancer, Including Small-Cell Carcinoma of the Ovary, Hypercalcemic Type. Clin Cancer Res 2020; 26:4402-4413. [PMID: 32409304 DOI: 10.1158/1078-0432.ccr-19-1905] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/02/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Many rare ovarian cancer subtypes, such as small-cell carcinoma of the ovary, hypercalcemic type (SCCOHT), have poor prognosis due to their aggressive nature and resistance to standard platinum- and taxane-based chemotherapy. The development of effective therapeutics has been hindered by the rarity of such tumors. We sought to identify targetable vulnerabilities in rare ovarian cancer subtypes. EXPERIMENTAL DESIGN We compared the global proteomic landscape of six cases each of endometrioid ovarian cancer (ENOC), clear cell ovarian cancer (CCOC), and SCCOHT to the most common subtype, high-grade serous ovarian cancer (HGSC), to identify potential therapeutic targets. IHC of tissue microarrays was used as validation of arginosuccinate synthase (ASS1) deficiency. The efficacy of arginine-depriving therapeutic ADI-PEG20 was assessed in vitro using cell lines and patient-derived xenograft mouse models representing SCCOHT. RESULTS Global proteomic analysis identified low ASS1 expression in ENOC, CCOC, and SCCOHT compared with HGSC. Low ASS1 levels were validated through IHC in large patient cohorts. The lowest levels of ASS1 were observed in SCCOHT, where ASS1 was absent in 12 of 31 cases, and expressed in less than 5% of the tumor cells in 9 of 31 cases. ASS1-deficient ovarian cancer cells were sensitive to ADI-PEG20 treatment regardless of subtype in vitro. Furthermore, in two cell line mouse xenograft models and one patient-derived mouse xenograft model of SCCOHT, once-a-week treatment with ADI-PEG20 (30 mg/kg and 15 mg/kg) inhibited tumor growth in vivo. CONCLUSIONS Preclinical in vitro and in vivo studies identified ADI-PEG20 as a potential therapy for patients with rare ovarian cancers, including SCCOHT.
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Affiliation(s)
- Jennifer X Ji
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Shary Yutin Chen
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Germain Ho
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - Khyatiben V Pathak
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Isabel N Alcazar
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona
| | - David Farnell
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Center, Vancouver, Canada
| | - Angela Cheng
- Genetic Pathology Evaluation Center, Vancouver, Canada
| | | | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Gian Luca Negri
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - Anthony Karnezis
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jessica N McAlpine
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, UNC-Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey M Trent
- Integrated Cancer Genomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Yemin Wang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada. .,Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada.,Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, Canada
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32
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El-Naggar AM, Somasekharan SP, Wang Y, Cheng H, Negri GL, Pan M, Wang XQ, Delaidelli A, Rafn B, Cran J, Zhang F, Zhang H, Colborne S, Gleave M, Mandinova A, Kedersha N, Hughes CS, Surdez D, Delattre O, Wang Y, Huntsman DG, Morin GB, Sorensen PH. Class I HDAC inhibitors enhance YB-1 acetylation and oxidative stress to block sarcoma metastasis. EMBO Rep 2019; 20:e48375. [PMID: 31668005 PMCID: PMC6893361 DOI: 10.15252/embr.201948375] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [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: 04/29/2019] [Revised: 09/29/2019] [Accepted: 10/06/2019] [Indexed: 12/13/2022] Open
Abstract
Outcomes for metastatic Ewing sarcoma and osteosarcoma are dismal and have not changed for decades. Oxidative stress attenuates melanoma metastasis, and melanoma cells must reduce oxidative stress to metastasize. We explored this in sarcomas by screening for oxidative stress sensitizers, which identified the class I HDAC inhibitor MS‐275 as enhancing vulnerability to reactive oxygen species (ROS) in sarcoma cells. Mechanistically, MS‐275 inhibits YB‐1 deacetylation, decreasing its binding to 5′‐UTRs of NFE2L2 encoding the antioxidant factor NRF2, thereby reducing NFE2L2 translation and synthesis of NRF2 to increase cellular ROS. By global acetylomics, MS‐275 promotes rapid acetylation of the YB‐1 RNA‐binding protein at lysine‐81, blocking binding and translational activation of NFE2L2, as well as known YB‐1 mRNA targets, HIF1A, and the stress granule nucleator, G3BP1. MS‐275 dramatically reduces sarcoma metastasis in vivo, but an MS‐275‐resistant YB‐1K81‐to‐alanine mutant restores metastatic capacity and NRF2, HIF1α, and G3BP1 synthesis in MS‐275‐treated mice. These studies describe a novel function for MS‐275 through enhanced YB‐1 acetylation, thus inhibiting YB‐1 translational control of key cytoprotective factors and its pro‐metastatic activity.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Shibin El Kom, Egypt
| | | | - Yemin Wang
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | | | | | - Melvin Pan
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Xue Qi Wang
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Alberto Delaidelli
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Bo Rafn
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Jordan Cran
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Fan Zhang
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Haifeng Zhang
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Shane Colborne
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Anna Mandinova
- Brigham and Women's Hospital, Harvard University, Boston, MA, USA
| | - Nancy Kedersha
- Massachusetts General Hospital, Harvard University, Boston, MA, USA
| | - Christopher S Hughes
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Didier Surdez
- Centre de recherche de l'Institut Curie, Paris, France
| | | | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Poul H Sorensen
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, Vancouver, BC, Canada
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Aristizabal MJ, Dever K, Negri GL, Shen M, Hawe N, Benschop JJ, Holstege FCP, Krogan NJ, Sadowski I, Kobor MS. Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast. J Biol Chem 2019; 294:16080-16094. [PMID: 31506296 DOI: 10.1074/jbc.ra119.008515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/23/2019] [Indexed: 11/06/2022] Open
Abstract
Fcp1 is a protein phosphatase that facilitates transcription elongation and termination by dephosphorylating the C-terminal domain of RNA polymerase II. High-throughput genetic screening and gene expression profiling of fcp1 mutants revealed a novel connection to Cdk8, the Mediator complex kinase subunit, and Skn7, a key transcription factor in the oxidative stress response pathway. Briefly, Skn7 was enriched as a regulator of genes whose mRNA levels were altered in fcp1 and cdk8Δ mutants and was required for the suppression of fcp1 mutant growth defects by loss of CDK8 under oxidative stress conditions. Targeted analysis revealed that mutating FCP1 decreased Skn7 mRNA and protein levels as well as its association with target gene promoters but paradoxically increased the mRNA levels of Skn7-dependent oxidative stress-induced genes (TRX2 and TSA1) under basal and induced conditions. The latter was in part recapitulated via chemical inhibition of transcription in WT cells, suggesting that a combination of transcriptional and posttranscriptional effects underscored the increased mRNA levels of TRX2 and TSA1 observed in the fcp1 mutant. Interestingly, loss of CDK8 robustly normalized the mRNA levels of Skn7-dependent genes in the fcp1 mutant background and also increased Skn7 protein levels by preventing its turnover. As such, our work suggested that loss of CDK8 could overcome transcriptional and/or posttranscriptional alterations in the fcp1 mutant through its regulatory effect on Skn7. Furthermore, our work also implicated FCP1 and CDK8 in the broader response to environmental stressors in yeast.
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Affiliation(s)
- Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada
| | - Kristy Dever
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, British Columbia, Canada
| | - Mary Shen
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Nicole Hawe
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada
| | - Joris J Benschop
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
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Negri GL, Grande BM, Delaidelli A, El-Naggar A, Cochrane D, Lau CC, Triche TJ, Moore RA, Jones SJ, Montpetit A, Marra MA, Malkin D, Morin RD, Sorensen PH. Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. J Pathol 2019; 249:319-331. [PMID: 31236944 DOI: 10.1002/path.5319] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/23/2019] [Accepted: 06/20/2019] [Indexed: 01/14/2023]
Abstract
Despite being the most common childhood bone tumor, the genomic characterization of osteosarcoma remains incomplete. In particular, very few osteosarcoma metastases have been sequenced to date, critical to better understand mechanisms of progression and evolution in this tumor. We performed an integrated whole genome and exome sequencing analysis of paired primary and metastatic pediatric osteosarcoma specimens to identify recurrent genomic alterations. Sequencing of 13 osteosarcoma patients including 13 primary, 10 metastatic, and 3 locally recurring tumors revealed a highly heterogeneous mutational landscape, including cases of hypermutation and microsatellite instability positivity, but with virtually no recurrent alterations except for mutations involving the tumor suppressor genes RB1 and TP53. At the germline level, we detected alterations in multiple cancer related genes in the majority of the cohort, including those potentially disrupting DNA damage response pathways. Metastases retained only a minimal number of short variants from their corresponding primary tumors, while copy number alterations showed higher conservation. One recurrently amplified gene, KDR, was highly expressed in advanced cases and associated with poor prognosis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Amal El-Naggar
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Shebeen El-Kom, Egypt
| | - Dawn Cochrane
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Ching C Lau
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Childrens Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Alexandre Montpetit
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - David Malkin
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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Delaidelli A, Negri GL, Cho B, Sidhu S, Pfister S, Taylor M, Leprivier G, Kool M, Soresnsen P. Abstract 3660: A link between miRNAs and mRNA translation elongation: The let7-eEF2K axis in MYC-driven pediatric tumors adaptation to nutrient deprivation. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND/OBJECTIVES: MYC family proteins are implicated in many human cancers, but their therapeutic targeting has proven challenging. MYCN and MYC amplification in childhood neuroblastoma (NB) and medulloblastoma (MB) are associated with aggressive disease and high mortality, underscoring a dire need for novel therapies. Let-7 microRNAs (miRNAs) inhibit tumor progression and regulate metabolism by degrading several mRNAs, including MYC. Let-7 miRNAs are therefore frequently repressed in cancer, including MYC-driven NB and MB. We previously reported that the mRNA translation elongation regulator eukaryotic Elongation Factor-2 Kinase (eEF2K) is a pivotal mediator of cancer cells adaptation to nutrient deprivation (ND). Publicly available transcriptomic database analyses indicate that eEF2K expression significantly correlate with MYCN and MYC expression in multiple tumor cohorts. Our preliminary data also indicate that the eEF2K 3’ untranslated region (UTR) harbors a potential binding site for let-7 miRNAs. In addition, eEF2K mRNA and let-7 miRNA expression negatively correlates in NB and MB, suggesting a potential regulation of the former by the latter. We therefore hypothesized that let-7 down-regulation induces eEF2K expression, thereby supporting MYC-driven NB and MB adaptation to ND and tumor progression.
METHODS: Immunohistochemistry for eEF2K substrate (p-eEF2) was performed on NB and MB tissue microarrays to link results with MYC expression and outcome. Effects of eEF2K pharmacological and genetic inhibition on NB and MB cell survival were evaluated in vitro by MTT assay and PI staining. The ability of let-7 to degrade eEF2K mRNA was assessed by let-7 miRNAs transfection into MB cells, followed by RT-PCR and Western Blotting for eEF2K. Binding of let-7 to the eEF2K 3’UTR was validated by luciferase reporter assay. Finally, NB xenograft mouse models were used to confirm in vitro observations.
RESULTS: High eEF2K activity is linked to MYC over-expression and reduced survival in NB and MB (p<0.05). Pharmacological and genetic inhibition of eEF2K significantly reduces survival of MYC/MYCN-amplified NB and MB cell lines under ND. Let-7 miRNAs transfection decreases eEF2K mRNA and protein levels (by ~40-50%), and down-regulation of luciferase activity by let-7 miRNAs is impaired upon mutation of the let-7 binding site on the eEF2K 3’UTR. Knockdown of eEF2K determines a twofold growth decrease of MYCN-amplified NB xenografts when mice are kept under caloric restriction diet.
CONCLUSIONS: Let-7 miRNAs degrade eEF2K mRNA by binding to its 3'UTR, indicating that let-7 repression in MYC-driven NB and MB is partially responsible for eEF2K increased levels and activity. Moreover, the let-7-eEF2K axis represents a critical mechanism for MYC-driven NB and MB adaptation to ND, constituting a promising therapeutic target.
Citation Format: Alberto Delaidelli, Gian Luca Negri, Brian Cho, Simran Sidhu, Stefan Pfister, Michael Taylor, Gabriel Leprivier, Marcel Kool, Poul Soresnsen. A link between miRNAs and mRNA translation elongation: The let7-eEF2K axis in MYC-driven pediatric tumors adaptation to nutrient deprivation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3660.
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Affiliation(s)
| | - Gian Luca Negri
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Brian Cho
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Simran Sidhu
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | - Michael Taylor
- 3Arthur and Sonia Labatt Brain Tumor Research Centre, Toronto, Ontario, Canada
| | | | - Marcel Kool
- 2German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Poul Soresnsen
- 1BC Cancer Research Centre, Vancouver, British Columbia, Canada
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36
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El-Naggar AM, Clarkson PW, Negri GL, Turgu B, Zhang F, Anglesio MS, Sorensen PH. HACE1 is a potential tumor suppressor in osteosarcoma. Cell Death Dis 2019; 10:21. [PMID: 30622235 PMCID: PMC6325116 DOI: 10.1038/s41419-018-1276-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 08/25/2018] [Revised: 11/23/2018] [Accepted: 12/06/2018] [Indexed: 12/24/2022]
Abstract
Osteosarcoma is a malignant bone sarcoma characterized by extensive genomic disruption and a propensity for metastatic spread. Osteoid production suggests a close relationship with normal osteoblasts, and the latter are the presumptive cell of origin of this disease. The HACE1 gene, localized to human chromosome 6q21, encodes the HACE1 HECT E3 ligase, a tumor suppressor in diverse tumors that acts in part by targeting the activated form of RAC1 GTPase for proteasomal degradation. Disruption or loss of 6q21 is relatively common in osteosarcomas, and Hace1-/-/Tp53+/- mice frequently develop osteosarcomas, in contrast to Tp53+/- mice, which do not. This suggests an unexplored link between HACE1 loss and osteosarcoma. Here we compared HACE1 expression in normal osteoblasts and osteosarcoma cell lines in vitro by western blotting and quantitative RT-PCR, and in human osteosarcoma specimens by immunohistochemistry. Both HACE1 transcript and protein levels were reduced in osteosarcoma compared to osteoblasts in vitro. Reduced HACE1 expression in osteosarcoma tumors was observed in 76% of cases and associated with high-grade lesions. Further, clonally derived pairs of high and low metastatic osteosarcoma cell lines showed significant downregulation in the high compared to corresponding low metastatic cells. Ectopic expression of HACE1 markedly inhibited anchorage-independent growth and cell motility of HACE1 osteosarcoma cell lines, and was associated with reduced RAC1 activation and decreased reactive oxygen species (ROS). Finally, HACE1 overexpression blocked osteosarcoma xenograft growth and dramatically reduced pulmonary metastases. These findings point to a potential tumor suppressor function for HACE1 in osteosarcoma.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - Paul W Clarkson
- Department of Orthopedics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Busra Turgu
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Fan Zhang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Anglesio
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada. .,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
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37
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Delaidelli A, Luca Negri G, Cho B, Minaker S, El Naggar A, Hukin J, Yip S, Santi M, Maris J, Sorensen P. PDTM-02. STRESS GRANULES ARE INDUCED BY OXIDATIVE STRESS IN PEDIATRIC BRAIN TUMORS AND PREDICT POOR OUTCOME. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Brian Cho
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Sean Minaker
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Amal El Naggar
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Juliette Hukin
- Divisions of Neurology and Hematology and Oncology, Childrens and Womens Health Centre of BC, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mariarita Santi
- Department of Anatomic Pathology and Laboratory Medicine, Childrens Hospital of Philadelphia, Philadelphia, PA, USA
| | - John Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Poul Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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38
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Delaidelli A, Luca Negri G, Sidhu S, Remke M, Pfister S, Taylor M, Leprivier G, Kool M, Sorensen P. CBMT-05. ROLE OF THE let7-eEF2K AXIS IN MYC-DRIVEN MEDULLOBLASTOMA ADAPTATION TO NUTRIENT DEPRIVATION. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Simran Sidhu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Marc Remke
- Department of Neuropathology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Stefan Pfister
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Taylor
- Department of Developmental & Stem Cell Biology and Division of Neurosurgery, Hospital for Sick Children, Toronto, ON, Canada
| | - Gabriel Leprivier
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Poul Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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Jan A, Jansonius B, Delaidelli A, Bhanshali F, An YA, Ferreira N, Smits LM, Negri GL, Schwamborn JC, Jensen PH, Mackenzie IR, Taubert S, Sorensen PH. Activity of translation regulator eukaryotic elongation factor-2 kinase is increased in Parkinson disease brain and its inhibition reduces alpha synuclein toxicity. Acta Neuropathol Commun 2018; 6:54. [PMID: 29961428 PMCID: PMC6027557 DOI: 10.1186/s40478-018-0554-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 06/10/2018] [Indexed: 01/05/2023] Open
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disorder and the leading neurodegenerative cause of motor disability. Pathologic accumulation of aggregated alpha synuclein (AS) protein in brain, and imbalance in the nigrostriatal system due to the loss of dopaminergic neurons in the substantia nigra- pars compacta, are hallmark features in PD. AS aggregation and propagation are considered to trigger neurotoxic mechanisms in PD, including mitochondrial deficits and oxidative stress. The eukaryotic elongation factor-2 kinase (eEF2K) mediates critical regulation of dendritic mRNA translation and is a crucial molecule in diverse forms of synaptic plasticity. Here we show that eEF2K activity, assessed by immuonohistochemical detection of eEF2 phosphorylation on serine residue 56, is increased in postmortem PD midbrain and hippocampus. Induction of aggressive, AS-related motor phenotypes in a transgenic PD M83 mouse model also increased brain eEF2K expression and activity. In cultures of dopaminergic N2A cells, overexpression of wild-type human AS or the A53T mutant increased eEF2K activity. eEF2K inhibition prevented the cytotoxicity associated with AS overexpression in N2A cells by improving mitochondrial function and reduced oxidative stress. Furthermore, genetic deletion of the eEF2K ortholog efk-1 in C. elegans attenuated human A53T AS induced defects in behavioural assays reliant on dopaminergic neuron function. These data suggest a role for eEF2K activity in AS toxicity, and support eEF2K inhibition as a potential target in reducing AS-induced oxidative stress in PD.
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40
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Delaidelli A, Negri GL, Sidhu S, Cran J, Remke M, Pfister S, Kool M, Taylor M, Maris J, Leprivier G, Sorensen P. MBRS-57. TARGETING METABOLIC ADAPTATION IN MYC/MYCN AMPLIFIED PEDIATRIC MEDULLOBLASTOMA AND NEUROBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alberto Delaidelli
- BC Cancer Research Centre, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | | | - Simran Sidhu
- University of British Columbia, Vancouver, BC, Canada
| | - Jordan Cran
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Marc Remke
- University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK) and German Cancer Center (DKFZ), Heidelberg, Germany
| | - Stefan Pfister
- German Cancer Consortium (DKTK) and German Cancer Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- German Cancer Consortium (DKTK) and German Cancer Center (DKFZ), Heidelberg, Germany
| | | | - John Maris
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Poul Sorensen
- BC Cancer Research Centre, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
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41
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Kwon E, Todorova K, Wang J, Horos R, Lee KK, Neel VA, Negri GL, Sorensen PH, Lee SW, Hentze MW, Mandinova A. The RNA-binding protein YBX1 regulates epidermal progenitors at a posttranscriptional level. Nat Commun 2018; 9:1734. [PMID: 29712925 PMCID: PMC5928080 DOI: 10.1038/s41467-018-04092-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 10/24/2016] [Accepted: 03/29/2018] [Indexed: 01/10/2023] Open
Abstract
The integrity of stratified epithelia depends on the ability of progenitor cells to maintain a balance between proliferation and differentiation. While much is known about the transcriptional pathways underlying progenitor cells’ behavior in the epidermis, the role of posttranscriptional regulation by mRNA binding proteins—a rate-limiting step in sculpting the proteome—remains poorly understood. Here we report that the RNA binding protein YBX1 (Y-box binding protein-1) is a critical effector of progenitors’ function in the epidermis. YBX1 expression is restricted to the cycling keratinocyte progenitors in vivo and its genetic ablation leads to defects in the architecture of the skin. We further demonstrate that YBX1 negatively controls epidermal progenitor senescence by regulating the translation of a senescence-associated subset of cytokine mRNAs via their 3′ untranslated regions. Our study establishes YBX1 as a posttranscriptional effector required for maintenance of epidermal homeostasis. The integrity of the stratified epithelia relies on controlled cell turnover but it is unclear how mRNA binding proteins regulates this. Here, the authors show that the RNA binding protein Y-box binding protein-1 translationally represses cytokines, so preventing senescence and maintaining epidermal homeostasis.
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Affiliation(s)
- Eunjeong Kwon
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Kristina Todorova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Jun Wang
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Rastislav Horos
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Kevin K Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Victor A Neel
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Sam W Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA.,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Anna Mandinova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA. .,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA. .,Harvard Stem Cell Institute, 7 Divinity Avenue Cambridge, Cambridge, MA, 02138, USA.
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Gabriele P, Magnano M, Albera R, Canale G, Redda MG, Krengli M, Negri GL. Carcinoma of the External Auditory Meatus and Middle Ear. Results of the Treatment of 28 Cases. Tumori 2018; 80:40-3. [PMID: 8191597 DOI: 10.1177/030089169408000108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 11/15/2022]
Abstract
Aims The authors report their experience on the treatment of 28 cases of middle ear (3) and external auditory meatus (EAM) cancers (25) with surgery and/or radiation therapy. According to histologic type, there were 23 squamous cell carcinomas, 4 basal cell carcinomas and 1 adenocystic carcinoma. Methods Surgery alone was performed in 2 cases, surgery combined with radiotherapy in 11 cases, and radiotherapy alone in 15 cases. Postoperative radiation therapy dose ranged between 4500 and 5500 cGy; the definitive dose was 6000-7000 cGy. The median follow-up was 61 months. Results Complete respons rate 6 weeks after the end of the treatment, evaluated by CT scan, was 85.7% (24/28). Definitive local control was obtained in 20/28 cases for the primary site and in 26/28 cases for the neck. Nine of the 10 recurrences were retreated with low-dose radiotherapy combined with surgery, chemotherapy or hyperthermia. A new local control was obtained in 2 cases. Four patients were lost during the follw-up at 13, 14, 17 and 23 months after the end of the treatment. The survival rate was 54% (13/24); disease-free survival was 50% (11/22). Conclusions Despite a not very aggressive treatment, our results are quite good.
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Affiliation(s)
- P Gabriele
- Department of Radiation Therapy, University of Turin, Italy
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43
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Abstract
From 1973 to 1988 47 patients with previously untreated T1 and T2 squamous cell carcinomas of the lower lip received a definitive course of interstitial brachytherapy by iridium 192 wires. The disease stage was T1 in 21 cases (44.7 %) and T2 in 26, and NO in all cases except 2 of N1. Radiation therapy dose ranged between 6000 and 8000 cGy. Local control was obtained in 44 patients (93.6 %). Treatment failure in the neck was observed in 3 patients (6.7 %) The 5- and 10-year actuarial disease-free survival rates were 92% and 85%, respectively. A surgical salvage was attempted in 3 patients, with postoperative definitive control of the disease in 2. The 10-year actuarial overall survival was 95 %. The incidence of complications was acceptable (10.6% of mucosal necrosis). An excellent or good cosmetic result was obtained in 91.7% of patients.
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Affiliation(s)
- R Orecchia
- Radiotherapy Department of the University of Turin, Italy
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Streubel G, Watson A, Jammula SG, Scelfo A, Fitzpatrick DJ, Oliviero G, McCole R, Conway E, Glancy E, Negri GL, Dillon E, Wynne K, Pasini D, Krogan NJ, Bracken AP, Cagney G. The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells. Mol Cell 2018; 70:371-379.e5. [PMID: 29606589 DOI: 10.1016/j.molcel.2018.02.027] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [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: 06/05/2017] [Revised: 12/22/2017] [Accepted: 02/23/2018] [Indexed: 12/12/2022]
Abstract
The Polycomb repressor complex 2 (PRC2) is composed of the core subunits Ezh1/2, Suz12, and Eed, and it mediates all di- and tri-methylation of histone H3 at lysine 27 in higher eukaryotes. However, little is known about how the catalytic activity of PRC2 is regulated to demarcate H3K27me2 and H3K27me3 domains across the genome. To address this, we mapped the endogenous interactomes of Ezh2 and Suz12 in embryonic stem cells (ESCs), and we combined this with a functional screen for H3K27 methylation marks. We found that Nsd1-mediated H3K36me2 co-locates with H3K27me2, and its loss leads to genome-wide expansion of H3K27me3. These increases in H3K27me3 occurred at PRC2/PRC1 target genes and as de novo accumulation within what were previously broad H3K27me2 domains. Our data support a model in which Nsd1 is a key modulator of PRC2 function required for regulating the demarcation of genome-wide H3K27me2 and H3K27me3 domains in ESCs.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sri Ganesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Rachel McCole
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gian Luca Negri
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Eugene Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland.
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45
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Delaidelli A, Negri GL, Jan A, Jansonius B, Lim JKM, Leprivier G, Kool M, Pfister SM, Remke M, Taylor M, Maris JM, Sorensen PH. PDTM-46. TARGETING METABOLIC ADAPTATION IN MYC DRIVEN PEDIATRIC NEURONAL TUMORS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a‐Hdac complex in embryonic stem cells required for self‐renewal. EMBO J 2017. [DOI: https://doi.org/10.15252/embj.201696307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology British Columbia Cancer Research Center Vancouver BC Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Diego Pasini
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
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47
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal. EMBO J 2017; 36:2216-2232. [PMID: 28554894 DOI: 10.15252/embj.201696307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022] Open
Abstract
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, which also contains Ogt and Tet1. Fam60a binds on H3K4me3-positive promoters in ES cells, together with Ogt, Tet1 and Sin3a, and is essential to maintain the complex on chromatin. Finally, we show that depletion of Fam60a phenocopies the loss of Sin3a, leading to reduced proliferation, an extended G1-phase and the deregulation of lineage genes. Taken together, Fam60a is an essential core subunit of a variant Sin3a complex in ES cells that is required to promote rapid proliferation and prevent unscheduled differentiation.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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Jan A, Jansonius B, Delaidelli A, Somasekharan SP, Bhanshali F, Vandal M, Negri GL, Moerman D, MacKenzie I, Calon F, Hayden MR, Taubert S, Sorensen PH. eEF2K inhibition blocks Aβ42 neurotoxicity by promoting an NRF2 antioxidant response. Acta Neuropathol 2017; 133:101-119. [PMID: 27752775 DOI: 10.1007/s00401-016-1634-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/11/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023]
Abstract
Soluble oligomers of amyloid-β (Aβ) impair synaptic plasticity, perturb neuronal energy homeostasis, and are implicated in Alzheimer's disease (AD) pathogenesis. Therefore, significant efforts in AD drug discovery research aim to prevent the formation of Aβ oligomers or block their neurotoxicity. The eukaryotic elongation factor-2 kinase (eEF2K) plays a critical role in synaptic plasticity, and couples neurotransmission to local dendritic mRNA translation. Recent evidence indicates that Aβ oligomers activate neuronal eEF2K, suggesting a potential link to Aβ induced synaptic dysfunction. However, a detailed understanding of the role of eEF2K in AD pathogenesis, and therapeutic potential of eEF2K inhibition in AD, remain to be determined. Here, we show that eEF2K activity is increased in postmortem AD patient cortex and hippocampus, and in the hippocampus of aged transgenic AD mice. Furthermore, eEF2K inhibition using pharmacological or genetic approaches prevented the toxic effects of Aβ42 oligomers on neuronal viability and dendrite formation in vitro. We also report that eEF2K inhibition promotes the nuclear factor erythroid 2-related factor (NRF2) antioxidant response in neuronal cells, which was crucial for the beneficial effects of eEF2K inhibition in neurons exposed to Aβ42 oligomers. Accordingly, NRF2 knockdown or overexpression of the NRF2 inhibitor, Kelch-Like ECH-Associated Protein-1 (Keap1), significantly attenuated the neuroprotection associated with eEF2K inhibition. Finally, genetic deletion of the eEF2K ortholog efk-1 reduced oxidative stress, and improved chemotaxis and serotonin sensitivity in C. elegans expressing human Aβ42 in neurons. Taken together, these findings highlight the potential utility of eEF2K inhibition to reduce Aβ-mediated oxidative stress in AD.
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Affiliation(s)
- Asad Jan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Brandon Jansonius
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Alberto Delaidelli
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | | | - Forum Bhanshali
- Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Centre for Molecular Medicine and Therapeutics, Vancouver, BC, V5Z 4H4, Canada
| | - Milène Vandal
- Faculté de Pharmacie, Université Laval, Pavillon Ferdinand-Vandry 1050, Avenue de la Médecine, Quebec, QC, G1V 0A6, Canada
| | - Gian Luca Negri
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Don Moerman
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ian MacKenzie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Frédéric Calon
- Faculté de Pharmacie, Université Laval, Pavillon Ferdinand-Vandry 1050, Avenue de la Médecine, Quebec, QC, G1V 0A6, Canada
| | - Michael R Hayden
- Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Centre for Molecular Medicine and Therapeutics, Vancouver, BC, V5Z 4H4, Canada
| | - Stefan Taubert
- Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Centre for Molecular Medicine and Therapeutics, Vancouver, BC, V5Z 4H4, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
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Aristizabal MJ, Negri GL, Kobor MS. The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition. PLoS Genet 2015; 11:e1005608. [PMID: 26496706 PMCID: PMC4619828 DOI: 10.1371/journal.pgen.1005608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 09/27/2015] [Indexed: 12/14/2022] Open
Abstract
RNA polymerase II (RNAPII) contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression. RNAPII is responsible for the transcription of most protein-coding genes, a subset of non-coding genes, and retrotransposons. Retrotransposon transcription is the first step in their multiplication cycle, given that the RNA intermediate is required for the synthesis of cDNA, the material that is ultimately incorporated into a new genomic location. Retrotransposition can have grave consequences to genome integrity, as integration events can change the gene expression landscape or lead to alteration or loss of genetic information. Given that RNAPII transcribes retrotransposons, we sought to investigate if the RNAPII-CTD played a role in the regulation of retrotransposon gene expression. Importantly, we found that the RNAPII-CTD functioned to maintaining genome integrity through inhibition of retrotransposon gene expression, as reducing CTD length significantly increased expression and transposition rates of Ty1 elements. Mechanistically, the increased Ty1 mRNA levels in the rpb1-CTD11 mutant were partly due to Cdk8-dependent alterations to the RNAPII-CTD phosphorylation status. In addition, Cdk8 alone contributed to Ty1 gene expression regulation by altering the occupancy of the gene-specific transcription factor Ste12. Loss of STE12 and TEC1 suppressed growth phenotypes of the RNAPII-CTD truncation mutant. Collectively, our results implicate Ste12 and Tec1 as general and important contributors to the Cdk8, RNAPII-CTD regulatory circuitry as it relates to the maintenance of genome integrity.
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Affiliation(s)
- Maria J. Aristizabal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Department of Molecular Oncology, BC Cancer Research Center, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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50
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El-Naggar AM, Veinotte CJ, Cheng H, Grunewald TGP, Negri GL, Somasekharan SP, Corkery DP, Tirode F, Mathers J, Khan D, Kyle AH, Baker JH, LePard NE, McKinney S, Hajee S, Bosiljcic M, Leprivier G, Tognon CE, Minchinton AI, Bennewith KL, Delattre O, Wang Y, Dellaire G, Berman JN, Sorensen PH. Translational Activation of HIF1α by YB-1 Promotes Sarcoma Metastasis. Cancer Cell 2015; 27:682-97. [PMID: 25965573 DOI: 10.1016/j.ccell.2015.04.003] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 02/28/2015] [Accepted: 04/10/2015] [Indexed: 12/27/2022]
Abstract
Metastatic dissemination is the leading cause of death in cancer patients, which is particularly evident for high-risk sarcomas such as Ewing sarcoma, osteosarcoma, and rhabdomyosarcoma. Previous research identified a crucial role for YB-1 in the epithelial-to-mesenchymal transition (EMT) and metastasis of epithelial malignancies. Based on clinical data and two distinct animal models, we now report that YB-1 is also a major metastatic driver in high-risk sarcomas. Our data establish YB-1 as a critical regulator of hypoxia-inducible factor 1α (HIF1α) expression in sarcoma cells. YB-1 enhances HIF1α protein expression by directly binding to and activating translation of HIF1A messages. This leads to HIF1α-mediated sarcoma cell invasion and enhanced metastatic capacity in vivo, highlighting a translationally regulated YB-1-HIF1α axis in sarcoma metastasis.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Chansey J Veinotte
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Hongwei Cheng
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Thomas G P Grunewald
- Laboratory for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Thalkirchner Strasse 36, 80337 Munich, Germany
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Syam Prakash Somasekharan
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Dale P Corkery
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Franck Tirode
- INSERM U830, Laboratoire de génétique et biologie des cancers, Institut Curie, 75248 Paris, France
| | - Joan Mathers
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Debjit Khan
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Alastair H Kyle
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Jennifer H Baker
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Nancy E LePard
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Shamil Hajee
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Momir Bosiljcic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Gabriel Leprivier
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Cristina E Tognon
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Andrew I Minchinton
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Kevin L Bennewith
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Olivier Delattre
- INSERM U830, Laboratoire de génétique et biologie des cancers, Institut Curie, 75248 Paris, France
| | - Yuzhuo Wang
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jason N Berman
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada; Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada.
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