1
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Modi A, Lopez G, Conkrite KL, Su C, Leung TC, Ramanan S, Manduchi E, Johnson ME, Cheung D, Gadd S, Zhang J, Smith MA, Guidry Auvil JM, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SF, Diskin SJ. Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors. Cancer Res 2023; 83:3462-3477. [PMID: 37584517 PMCID: PMC10787516 DOI: 10.1158/0008-5472.can-22-3186] [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: 10/11/2022] [Revised: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
Long noncoding RNAs (lncRNA) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extracranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multidimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell type-specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies. SIGNIFICANCE Comprehensive characterization of lncRNAs in pediatric cancer leads to the identification of highly expressed lncRNAs across childhood cancers, annotation of lncRNAs showing histotype-specific elevated expression, and prediction of lncRNA gene regulatory networks.
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Affiliation(s)
- Apexa Modi
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Genomics and Computational Biology Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tsz Ching Leung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sathvik Ramanan
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew E. Johnson
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daphne Cheung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland 20892, USA
| | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Elizabeth J. Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Stephen P. Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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2
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Flores-Toro JA, Jagu S, Armstrong GT, Arons DF, Aune GJ, Chanock SJ, Hawkins DS, Heath A, Helman LJ, Janeway KA, Levine JE, Miller E, Penberthy L, Roberts CWM, Shalley ER, Shern JF, Smith MA, Staudt LM, Volchenboum SL, Zhang J, Zenklusen JC, Lowy DR, Sharpless NE, Guidry Auvil JM, Kerlavage AR, Widemann BC, Reaman GH, Kibbe WA, Doroshow JH. The Childhood Cancer Data Initiative: Using the Power of Data to Learn From and Improve Outcomes for Every Child and Young Adult With Pediatric Cancer. J Clin Oncol 2023; 41:4045-4053. [PMID: 37267580 PMCID: PMC10461939 DOI: 10.1200/jco.22.02208] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 10/11/2022] [Revised: 01/31/2023] [Accepted: 03/28/2023] [Indexed: 06/04/2023] Open
Abstract
Data-driven basic, translational, and clinical research has resulted in improved outcomes for children, adolescents, and young adults (AYAs) with pediatric cancers. However, challenges in sharing data between institutions, particularly in research, prevent addressing substantial unmet needs in children and AYA patients diagnosed with certain pediatric cancers. Systematically collecting and sharing data from every child and AYA can enable greater understanding of pediatric cancers, improve survivorship, and accelerate development of new and more effective therapies. To accomplish this goal, the Childhood Cancer Data Initiative (CCDI) was launched in 2019 at the National Cancer Institute. CCDI is a collaborative community endeavor supported by a 10-year, $50-million (in US dollars) annual federal investment. CCDI aims to learn from every patient diagnosed with a pediatric cancer by designing and building a data ecosystem that facilitates data collection, sharing, and analysis for researchers, clinicians, and patients across the cancer community. For example, CCDI's Molecular Characterization Initiative provides comprehensive clinical molecular characterization for children and AYAs with newly diagnosed cancers. Through these efforts, the CCDI strives to provide clinical benefit to patients and improvements in diagnosis and care through data-focused research support and to build expandable, sustainable data resources and workflows to advance research well past the planned 10 years of the initiative. Importantly, if CCDI demonstrates the success of this model for pediatric cancers, similar approaches can be applied to adults, transforming both clinical research and treatment to improve outcomes for all patients with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | - Allison Heath
- Children's Hospital of Philadelphia, Philadelphia, PA
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3
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Sun JM, Chow WY, Xu G, Hicks MJ, Nakka M, Shen J, Ng PKS, Taylor AM, Yu A, Farrar JE, Barkauskas DA, Gorlick R, Guidry Auvil JM, Gerhard D, Meltzer P, Guerra R, Man TK, Lau CC. The Role of FAS Receptor Methylation in Osteosarcoma Metastasis. Int J Mol Sci 2023; 24:12155. [PMID: 37569529 PMCID: PMC10418590 DOI: 10.3390/ijms241512155] [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: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Osteosarcoma is the most frequent primary malignant bone tumor with an annual incidence of about 400 cases in the United States. Osteosarcoma primarily metastasizes to the lungs, where FAS ligand (FASL) is constitutively expressed. The interaction of FASL and its cell surface receptor, FAS, triggers apoptosis in normal cells; however, this function is altered in cancer cells. DNA methylation has previously been explored as a mechanism for altering FAS expression, but no variability was identified in the CpG island (CGI) overlapping the promoter. Analysis of an expanded region, including CGI shores and shelves, revealed high variability in the methylation of certain CpG sites that correlated significantly with FAS mRNA expression in a negative manner. Bisulfite sequencing revealed additional CpG sites, which were highly methylated in the metastatic LM7 cell line but unmethylated in its parental non-metastatic SaOS-2 cell line. Treatment with the demethylating agent, 5-azacytidine, resulted in a loss of methylation in CpG sites located within the FAS promoter and restored FAS protein expression in LM7 cells, resulting in reduced migration. Orthotopic implantation of 5-azacytidine treated LM7 cells into severe combined immunodeficient mice led to decreased lung metastases. These results suggest that DNA methylation of CGI shore sites may regulate FAS expression and constitute a potential target for osteosarcoma therapy, utilizing demethylating agents currently approved for the treatment of other cancers.
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Affiliation(s)
- Jiayi M. Sun
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
| | - Wing-Yuk Chow
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Gufeng Xu
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - M. John Hicks
- Department of Pathology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Manjula Nakka
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Jianhe Shen
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | | | - Aaron M. Taylor
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
| | - Alexander Yu
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Jason E. Farrar
- Arkansas Children’s Research Institute and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Donald A. Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Richard Gorlick
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Jaime M. Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA; (J.M.G.A.)
| | - Daniela Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA; (J.M.G.A.)
| | - Paul Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Rudy Guerra
- Department of Statistics, Rice University, Houston, TX 77005, USA;
| | - Tsz-Kwong Man
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Ching C. Lau
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
- Center for Cancer and Blood Disorders, Connecticut Children’s Medical Center, Hartford, CT 06106, USA
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4
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Forrest SJ, Gupta H, Ward A, Li Y, Doan D, Al-Ibraheemi A, Alexandrescu S, Bandopadhayay P, Shusterman S, Mullen EA, Collins N, Chi SN, Wright KD, Kumari P, Mazor T, Ligon KL, Shivdasani P, Davineni P, Manam M, Schilsky RL, Bruinooge SS, Auvil JMG, Cerami E, Rollins BJ, Meyerson ML, Lindeman NI, MacConaill L, Johnson BE, Cherniack AD, Church AJ, Janeway KA. Abstract 3890: Sequencing of 888 pediatric solid tumors informs precision oncology trial design and data sharing initiatives in pediatric cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3890] [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
Pediatric pan-cancer genome analyses do not capture the full range of diagnoses encountered in clinical practice. To inform basket trial design and real-world precision oncology practice, we classified diagnoses and assessed the landscape of mutations, including trial-matching, in an unselected cohort of pediatric solid tumors.
Since 2013 all Dana-Farber/Boston Children’s patients have been offered participation in the Profile study. Participant tumor samples were sequenced with DFCI-OncoPanel, a targeted panel test sequencing exons of up to 447 cancer genes for single nucleotide variants, insertions and deletions and copy number alterations, and introns and exons of up to 60 genes for rearrangements. Patient diagnosis was classified according to ICD-O, version 3.2. Genomic alterations were analyzed for matching to the actionable mutation lists of precision oncology basket trials (NCI-COG Pediatric MATCH, NCI-MATCH, and the ASCO TAPUR Study v.3). Data will be shared with the Childhood Cancer Data Initiative.
There were 888 pediatric patients with sequencing enrolled in Profile between January 2013 and March 2019; 512 (58%) with solid tumors and 376 (42%) with CNS tumors. Fifty-five percent (491/888) of patients had one of ten common pediatric cancer diagnoses: neuroblastoma (n=80), low-grade glioma (n=72), Wilms tumor (n=57), medulloblastoma (n=55), pilocytic astrocytoma (n=47), rhabdomyosarcoma (n=44), osteosarcoma (n=42), ependymoma (n=39), Ewing sarcoma (n=28) and glioblastoma (n=27). The remaining 45% (397/888) had one of 85 distinct rare malignancies with less than 25 cases per diagnosis. Most (80/85) of these rare diagnoses are not represented in prior pediatric pan-cancer sequencing studies. Recurrent (>5%) pathogenic alterations were, in common and rare diagnoses, TP53 mutations(m) and deletions(del) and BRAFm and rearrangements(r), in common diagnoses, MYC/MYCN amplification (amp) and EWSR1r and, in rare diagnoses, CTNNB1m, CDKN2A/Bdel and NF1m/del. We found that 31% (n=271/888) of patients had at least 1 variant matching a basket trial treatment arm. Genes with matching alterations include BRAF (10%), NF1 (4%), PI3KCA (3%), NRAS (2%), BRCA2 (2%), ALK (1%), and FGFR1 (1%).
Sequencing of pediatric malignancies is increasing. This study highlights opportunities to use the resulting genomic data to inform genome-selected clinical trial design and uncover drivers in pediatric cancers. The proportion of cases in this cohort with genomic alterations meeting eligibility for basket trials is equivalent to that seen in the pediatric MATCH screening study. Due to the low prevalence of the diagnoses in the long tail of cancer types in this study, defining the genomic landscape of ultra-rare cancers will require data sharing. Classifying pediatric cancer diagnoses using the ICD-O standard ontology system is feasible and will facilitate data sharing.
Citation Format: Suzanne J. Forrest, Hersh Gupta, Abigail Ward, Yvonne Li, Duong Doan, Alyaa Al-Ibraheemi, Sanda Alexandrescu, Pratiti Bandopadhayay, Suzanne Shusterman, Elizabeth A. Mullen, Natalie Collins, Susan N. Chi, Karen D. Wright, Priti Kumari, Tali Mazor, Keith L. Ligon, Priyanka Shivdasani, Phani Davineni, Monica Manam, Richard L. Schilsky, Suanna S. Bruinooge, Jaime M. Guidry Auvil, Ethan Cerami, Barrett J. Rollins, Matthew L. Meyerson, Neal I. Lindeman, Laura MacConaill, Bruce E. Johnson, Andrew D. Cherniack, Alanna J. Church, Katherine A. Janeway. Sequencing of 888 pediatric solid tumors informs precision oncology trial design and data sharing initiatives in pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3890.
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Affiliation(s)
- Suzanne J. Forrest
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
| | - Hersh Gupta
- 2Dana-Farber Cancer Institute and Broad Institute of Harvard and MIT, Boston, MA
| | - Abigail Ward
- 3Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | - Yvonne Li
- 2Dana-Farber Cancer Institute and Broad Institute of Harvard and MIT, Boston, MA
| | - Duong Doan
- 3Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
| | | | | | - Pratiti Bandopadhayay
- 5Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School and Broad Institute of Harvard and MIT, Boston, MA
| | - Suzanne Shusterman
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
| | - Elizabeth A. Mullen
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
| | - Natalie Collins
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
| | - Susan N. Chi
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
| | - Karen D. Wright
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
| | | | - Tali Mazor
- 6Dana-Farber Cancer Institute, Boston, MA
| | - Keith L. Ligon
- 7Dana-Farber Cancer Institute, Brigham & Women’s Hospital, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | | | - Barrett J. Rollins
- 11Dana-Farber Cancer Institute, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
| | - Matthew L. Meyerson
- 12Dana-Farber Cancer Institute, Brigham & Women’s Hospital, Harvard Medical School, and Broad Institute of Harvard and MIT, Boston, MA
| | - Neal I. Lindeman
- 13Dana-Farber Cancer Institute, Brigham & Women's Hospital and Harvard Medical School, Boston, MA
| | - Laura MacConaill
- 13Dana-Farber Cancer Institute, Brigham & Women's Hospital and Harvard Medical School, Boston, MA
| | - Bruce E. Johnson
- 11Dana-Farber Cancer Institute, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
| | - Andrew D. Cherniack
- 2Dana-Farber Cancer Institute and Broad Institute of Harvard and MIT, Boston, MA
| | - Alanna J. Church
- 4Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Katherine A. Janeway
- 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA
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5
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Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SO, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M. The Data Use Ontology to streamline responsible access to human biomedical datasets. Cell Genom 2021; 1:None. [PMID: 34820659 PMCID: PMC8591903 DOI: 10.1016/j.xgen.2021.100028] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/02/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022]
Abstract
Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.
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Affiliation(s)
- Jonathan Lawson
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Moran N. Cabili
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Giselle Kerry
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Tiffany Boughtwood
- Australian Genomics, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Adrian Thorogood
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, Canada,ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Pinar Alper
- ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | | | | | - Matthew Brush
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tony Burdett
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hayley Clissold
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stacey Donnelly
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephanie O.M. Dyke
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, Department of Neurology & Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Chihiro Hata
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Petr Holub
- BBMRI-ERIC, AT and Masaryk University, Brno, Czech Republic
| | | | - Aina Jene
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Minae Kawashima
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
| | - Shuichi Kawashima
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Japan
| | | | - Irene Kyomugisha
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Haoyuan Li
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Mikael Linden
- ELIXIR-Finland, CSC - IT Center for Science Ltd, Espoo, Finland
| | | | | | - Nicola Mulder
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d’Alsace, INSERM U1112, Université; de Strasbourg, Strasbourg, France,Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d’Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Satoshi Nagaie
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan
| | - Jamal Nasir
- Department of Life Sciences, University of Northampton, Northampton, UK
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan
| | - Vivian Ota Wang
- Office of Data Sharing, National Cancer Institute, NIH, Rockville, MD, USA
| | | | | | - Helen Parkinson
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Anthony A. Philippakis
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabian Prasser
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Jordi Rambla
- Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Kathy Reinold
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A. Rushton
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrea Saltzman
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - John D. Spalding
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Morris A. Swertz
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Esther J. van Enckevort
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Susheel Varma
- Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
| | | | | | | | - Lyndon Zass
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, UK,Corresponding author
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6
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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7
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Voisin C, Linden M, Dyke SO, Bowers SR, Alper P, Barkley MP, Bernick D, Chao J, Courtot M, Jeanson F, Konopko MA, Kuba M, Lawson J, Leinonen J, Li S, Ota Wang V, Philippakis AA, Reinold K, Rushton GA, Spalding JD, Törnroos J, Tulchinsky I, Guidry Auvil JM, Nyrönen TH. GA4GH Passport standard for digital identity and access permissions. Cell Genom 2021; 1:None. [PMID: 34820660 PMCID: PMC8591913 DOI: 10.1016/j.xgen.2021.100030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/08/2021] [Accepted: 09/02/2021] [Indexed: 12/21/2022]
Abstract
The Global Alliance for Genomics and Health (GA4GH) supports international standards that enable a federated data sharing model for the research community while respecting data security, ethical and regulatory frameworks, and data authorization and access processes for sensitive data. The GA4GH Passport standard (Passport) defines a machine-readable digital identity that conveys roles and data access permissions (called "visas") for individual users. Visas are issued by data stewards, including data access committees (DACs) working with public databases, the entities responsible for the quality, integrity, and access arrangements for the datasets in the management of human biomedical data. Passports streamline management of data access rights across data systems by using visas that present a data user's digital identity and permissions across organizations, tools, environments, and services. We describe real-world implementations of the GA4GH Passport standard in use cases from ELIXIR Europe, National Institutes of Health, and the Autism Sharing Initiative. These implementations demonstrate that the Passport standard has provided transparent mechanisms for establishing permissions and authorizing data access across platforms.
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Affiliation(s)
- Craig Voisin
- Google LLC, Kitchener, ON N2H 5G5, Canada,Corresponding author
| | - Mikael Linden
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland
| | - Stephanie O.M. Dyke
- McGill Centre for Integrative Neuroscience, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Pinar Alper
- ELIXIR Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367 Belvaux, Luxembourg
| | | | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| | | | - Melissa A. Konopko
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK,Global Alliance for Genomics and Health, Toronto, ON M5G 0A3, Canada
| | - Martin Kuba
- Masaryk University, Brno 602 00, Czech Republic
| | - Jonathan Lawson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Global Alliance for Genomics and Health, Toronto, ON M5G 0A3, Canada
| | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Kathy Reinold
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - J. Dylan Spalding
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland
| | | | | | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo 02101, Finland,ELIXIR Finland, Espoo 02101, Finland,Corresponding author
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8
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Kerlavage AR, Kirchhoff AC, Guidry Auvil JM, Sharpless NE, Davis KL, Reilly K, Reaman G, Penberthy L, Deapen D, Hwang A, Durbin EB, Gallotto SL, Aplenc R, Volchenboum SL, Heath AP, Aronow BJ, Zhang J, Vaske O, Alonzo TA, Nathan PC, Poynter JN, Armstrong G, Hahn EE, Wernli KJ, Greene C, DiGiovanna J, Resnick AC, Shalley ER, Nadaf S, Kibbe WA. Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. JCO Clin Cancer Inform 2021; 5:881-896. [PMID: 34428097 PMCID: PMC8763339 DOI: 10.1200/cci.21.00040] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022] Open
Abstract
Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. This consortium has regularly held topic-focused biannual face-to-face symposiums. These meetings are a place to review cancer informatics and data science priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues that we faced at our respective institutions and cancer centers. Here, we provide meeting highlights from the latest CI4CC Symposium, which was delayed from its original April 2020 schedule because of the COVID-19 pandemic and held virtually over three days (September 24, October 1, and October 8) in the fall of 2020. In addition to the content presented, we found that holding this event virtually once a week for 6 hours was a great way to keep the kind of deep engagement that a face-to-face meeting engenders. This is the second such publication of CI4CC Symposium highlights, the first covering the meeting that took place in Napa, California, from October 14-16, 2019. We conclude with some thoughts about using data science to learn from every child with cancer, focusing on emerging activities of the National Cancer Institute's Childhood Cancer Data Initiative.
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Affiliation(s)
- Anthony R Kerlavage
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Anne C Kirchhoff
- Huntsman Cancer Institute and University of Utah, School of Medicine, Salt Lake City, UT
| | - Jaime M Guidry Auvil
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | | | - Kara L Davis
- Maternal and Child Health Research Institute, Stanford School of Medicine, Stanford, CA
| | - Karlyne Reilly
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Gregory Reaman
- Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, MD
| | - Lynne Penberthy
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
| | - Dennis Deapen
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Amie Hwang
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Eric B Durbin
- University of Kentucky, Markey Cancer Center, Lexington, KY
| | | | | | | | | | | | | | - Olena Vaske
- University of California, Santa Cruz, Santa Cruz, CA
| | - Todd A Alonzo
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | | | - Jenny N Poynter
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN
| | | | - Erin E Hahn
- Kaiser Permanente Southern California, Los Angeles, CA
| | - Karen J Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA
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9
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Modi A, Lopez G, Conkrite KL, Leung TC, Ramanan S, Cheung D, Su C, Johnson ME, Manduchi E, Gadd S, Zhang J, Smith MA, Auvil JMG, Gerhard DS, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SF, Diskin SJ. Abstract 3028: Integrative genomics reveals lncRNAs associated with pediatric cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-3028] [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: Long non-coding RNAs (lncRNAs) have emerged as key components of transcriptional and post-transcriptional gene regulation. Dysregulation of lncRNA expression has been widely observed in cancer and several lncRNAs are known to influence tumor initiation and progression. Despite this, the lncRNA landscape and regulatory networks across pediatric cancers remain relatively uncharted.
Methods: To characterize the lncRNA landscape of pediatric cancers, we first curated RNA sequencing data for 1,044 pediatric leukemia and solid tumors from the Therapeutically Applicable Research To Generate Effective Treatments (TARGET) project to identify known and novel expressed lncRNAs. This data set included: 280 acute myeloid leukemia (AML), 190 acute B-cell leukemia (B-ALL), 244 acute T-cell leukemia (T-ALL), 121 Wilm's tumor (WT), 48 rhabdoid tumors (RT), and 161 neuroblastoma (NBL). Histotype-specific expression was assessed using the tau score. Whole genome sequencing (WGS) from 826 matched normal-tumor pairs was integrated to identify somatic copy number alterations (SCNAs) disrupting lncRNA expression. To further implicate cancer-relevant drivers of lncRNA expression, we used a unique combination of epigenetic data in pediatric cell lines, including ChIP-sequencing for cancer-specific transcription factors and genome-scale chromatin capture data. A global analysis of lncRNA function was performed using the lncMod method, in which expression data is modelled to identify lncRNA modulators that perturb transcription factor regulation of target genes. Functional prioritization of lncRNAs was obtained through integration of analyses per cancer. Biochemical assays in human-derived cell line models were utilized to validate the function of the top prioritized lncRNA in NBL.
Results: We report a total of 2,657 robustly expressed lncRNAs across six pediatric cancers, including 1,142 lncRNAs exhibiting histotype-specific expression. SCNAs contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. There were 207 (28%) lncRNAs in regions with SCNA that had significant expression dysregulation. LncMod analysis across the cancers revealed context-specific transcriptional gene networks per dysregulated lncRNA and enrichment for proliferation, metabolic, and DNA damage hallmarks. We further identified 547 cancer-associated lncRNAs in NBL based on upstream regulation via oncogenic transcription factors. The top-prioritized lncRNA, TBX2-AS1, was predicted to impact proliferation in NBL. Silencing of TBX2-AS1 using siRNAs achieved >90% knockdown in NBL cells and resulted in 46.6% decreased cell growth (p = 8.1 x 10-4).
Conclusion: This study defines the lncRNA landscape across six pediatric cancers and provides a detailed catalog of how lncRNAs impact regulatory gene networks. These data serve as a robust resource for future hypothesis-driven mechanistic studies.
Citation Format: Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Tsz Ching Leung, Sathvik Ramanan, Daphne Cheung, Chun Su, Matthew E. Johnson, Elisabetta Manduchi, Samantha Gadd, Jinghui Zhang, Malcolm A. Smith, Jaime M. Guidry Auvil, Daniela S. Gerhard, Soheil Meshinchi, Elizabeth J. Perlman, Stephen P. Hunger, John M. Maris, Andrew D. Wells, Struan F. Grant, Sharon J. Diskin. Integrative genomics reveals lncRNAs associated with pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3028.
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Affiliation(s)
- Apexa Modi
- 1University of Pennsylvania, Philadelphia, PA
| | - Gonzalo Lopez
- 2Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | | | - Chun Su
- 2Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Samantha Gadd
- 3Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | | | | | | | | | | | | | | | - John M. Maris
- 7Children's Hospital of Philadelphia, Philadelphia, PA
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10
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Meltzer PS, Davis S, Zhu J, Wang Y, Bilke S, Waterfall J, Walker R, Pineda M, Jiang Y, Savage S, Mirabello L, Man TK, Taylor A, Sun MJ, Wunder J, Andrulis I, Gokgoz N, Iwata S, Ohira M, Krailo M, Barkauskas D, Teot L, Triche T, de Toledo S, Petrilli AS, Auvil JMG, Gorlick R, Smith MA, Gerhard D, Lau CC. Abstract LB-307: Translational and mechanistic implications of osteosarcoma genomics: A TARGET report. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-307] [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
Osteosarcoma (OS) is the most common malignant bone tumor of children and young adults. Although the optimization of combination chemotherapy has led to significantly improved prognosis, survival remains poor for patients with recurrent tumor or metastatic disease at diagnosis. The international TARGET (Therapeutically Applicable Research to Generate Effective Therapy) OS project team collected 285 clinically annotated samples (age <40 years) for integrative genomics analyses. Eighty-nine cases, the discovery set, were characterized with paired tumor and normal DNA sequencing as well as profiling of transcriptomes, DNA methylation, and miRNA. An additional 196 validation cases were used for copy number analysis and targeted DNA sequencing guided by results from the discovery set. The most frequent recurrent somatic mutations cause loss of function in the tumor suppressors TP53, RB1, CDKN2A, PTEN, and NF1 as well as the chromatin remodeler ATRX. Structural rearrangements are an important mechanism of inactivation for all of these genes. In the discovery set, every case carried at least one mutation of a cell cycle regulator, with TP53 somatically altered in 87/89 cases. Analysis of TP53 mutations suggests that these are often truncal. OS genomes are strikingly complex and contain copy number aberrations (CNA) arising from aneuploidy and extensive structural rearrangements. Transcriptome analysis revealed profound remodeling of gene expression with statistically significant correlation of CNA and gene expression of 3340 genes (FDR<0.001). Regions of high copy number amplification include known therapeutically relevant cancer drivers (e.g. PDGFRA, MYC, CDK4, MDM2, IGF1R, and CCNE1). In contrast, activating mutations of signal transduction genes were rare. With few exceptions (e.g. MYC amplification), mutations or CNA of individual genes were not predictive of outcome. The pattern of significant co-occurrence or mutual exclusion of frequent mutations and amplifications allowed partitioning of 240 cases into four distinct genomic groups. One of these, characterized by relatively simple genomes lacking high copy number amplification, had a more favorable outcome. Unsupervised transcriptome analysis by NMF separated the discovery set into two groups with significantly different outcomes. A pathway-based approach identified a high-risk bone differentiation signature comprised of genes highly correlated with the expression of the osteogenic transcription factors. NMF analysis of DNA methylation and miRNA data also partitioned the discovery set into two groups with the methylation groups significantly correlated with clinical outcome. Our results provide a detailed picture of the genomic complexity and heterogeneity of these tumors that suggests a model wherein most OS are initiated by TP53 loss in a proliferative cell of the osteoblast lineage. TP53 deficiency leads directly to impairment of cell cycle control, DNA repair, and terminal differentiation, a state permissive for the development of secondary CNA and epigenetic changes. The TARGET OS data are publicly available (phs000218) and of immediate relevance to future investigations of the molecular mechanisms driving osteosarcoma. Findings suggest a path forward to improved assessment of risk for individual patients and support a precision medicine approach to future clinical trial development.
Citation Format: Paul S. Meltzer, Sean Davis, Jack Zhu, Yonghong Wang, Sven Bilke, Joshua Waterfall, Robert Walker, Marbin Pineda, Yuan Jiang, Sharon Savage, Lisa Mirabello, Tsz-Kwong Man, Aaron Taylor, Monika J. Sun, Jay Wunder, Irene Andrulis, Nalan Gokgoz, Shintaro Iwata, Miki Ohira, Mark Krailo, Don Barkauskas, Lisa Teot, Timothy Triche, Silvia de Toledo, Antonio S. Petrilli, Jaime M. Guidry Auvil, Richard Gorlick, Malcolm A. Smith, Daniela Gerhard, Ching C. Lau. Translational and mechanistic implications of osteosarcoma genomics: A TARGET report [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 LB-307.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Aaron Taylor
- 4Jackson Laboratory of Genomic Medicine, Farmington, CT
| | | | - Jay Wunder
- 5Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Irene Andrulis
- 6Lunenfeld Institute Mt. Sinai Hospital, Toronto, Ontario, Canada
| | - Nalan Gokgoz
- 6Lunenfeld Institute Mt. Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Mark Krailo
- 9Children's Oncology Group (COG), Monrovia, CA
| | | | - Lisa Teot
- 10Dana Farber Cancer Insitute, Boston, MA
| | | | | | | | | | | | | | | | - Ching C. Lau
- 4Jackson Laboratory of Genomic Medicine, Farmington, CT
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Pruitt FL, Gayle SS, Ghanem N, Mencarelli AV, Kerlavage AR, Wang VO, Auvil JMG. Abstract 3369: NCI’s Office of Data Sharing: Promoting broad & equitable policies and processes to improve cancer care. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3369] [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
Data sharing increases our understanding of factors that influence health and diseases by enabling additional research questions from secondary data users, improving statistical power through combining multiple data sources, facilitating reproducibility and validation of research results, and supporting innovation with the development of research tools and methodologies.
The NCI recently established an Office of Data Sharing (ODS), whose goal is to promote broad and equitable data sharing policies and processes to improve cancer knowledge and care. ODS advocates for open-access and broad data sharing policies to enable reproducibility, secondary use, knowledge sharing and innovation. ODS key priorities include: 1) coordinating the interpretation and implementation of the NCI and NIH Data-Sharing policies across the NCI, 2) streamlining data-access and -submission processes for NCI- and/or NIH-supported data repositories, 3) advocating for the proper balance of open-access, open-source, open-data-sharing policies while respecting the needs of research and participant communities.
The NIH and NCI Data Sharing policies facilitate scientific progress by encouraging data access and sharing of genomic, phenotype, environmental, and behavioral data. Data access and sharing management, stewardship, and operating procedures are coordinated through a NIH governance structure of senior leadership and staff across NIH Institutes/Centers (ICs). NIH Data Access Committees (DACs) ensure data access based on shared principles and procedural standards of data management, security, privacy, and research participant protections.
In efforts to improve data access efficiency, the ODS consolidated The Cancer Genome Atlas, intramural and extramural NCI DACs into a centralized operation, the NCI DAC. In comparison to other ICs, the NCI DAC receives the largest volume of data access requests (DARs) for access to controlled-tier level data. Specifically, the NCI DAC received 9214 DARs in 2017, representing 30% of all DARs received by NIH with a mean review time of 53 days, in comparison to the combined average of 35 days for all other NIH DACs. The NCI DAC oversees 216 studies registered in dbGaP, with 93 general research use (GRU) and 22 health, medical, biomedical (HMB) consent groups that allow data to be used for broader research uses. The centralized NCI DAC implemented data access review procedures for all DARs and expedited processes for projects requesting access to datasets with GRU and HMB data use limitations. These expedited procedures have produced a 26.5-fold decrease in time-to-decision from 53 to 2 days for researchers requesting access to NCI datasets.
Additionally, ODS is committed to addressing health disparities ethics and is developing an Ethical, Economic, Legal, and Social Implications program that will address policies, practices, and ethical issues that arise from data sharing.
Citation Format: Freddie L. Pruitt, Sylvia Shabaya Gayle, Nina Ghanem, Anna V. Mencarelli, Anthony R. Kerlavage, Vivian Ota Wang, Jaime M. Guidry Auvil. NCI’s Office of Data Sharing: Promoting broad & equitable policies and processes to improve cancer care [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 3369.
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12
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Wei JS, Kuznetsov IB, Zhang S, Song YK, Asgharzadeh S, Sindiri S, Wen X, Patidar R, Najaraj S, Walton A, Auvil JMG, Gerhard DS, Yuksel A, Catchpoole D, Hewitt SM, Sondel PM, Seeger R, Maris JM, Khan J. Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma. Clin Cancer Res 2018; 24:5673-5684. [PMID: 29784674 PMCID: PMC6504934 DOI: 10.1158/1078-0432.ccr-18-0599] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [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: 02/21/2018] [Revised: 04/12/2018] [Accepted: 05/14/2018] [Indexed: 11/16/2022]
Abstract
Purpose: High-risk neuroblastoma is an aggressive disease. DNA sequencing studies have revealed a paucity of actionable genomic alterations and a low mutation burden, posing challenges to develop effective novel therapies. We used RNA sequencing (RNA-seq) to investigate the biology of this disease, including a focus on tumor-infiltrating lymphocytes (TIL).Experimental Design: We performed deep RNA-seq on pretreatment diagnostic tumors from 129 high-risk and 21 low- or intermediate-risk patients with neuroblastomas. We used single-sample gene set enrichment analysis to detect gene expression signatures of TILs in tumors and examined their association with clinical and molecular parameters, including patient outcome. The expression profiles of 190 additional pretreatment diagnostic neuroblastomas, a neuroblastoma tissue microarray, and T-cell receptor (TCR) sequencing were used to validate our findings.Results: We found that MYCN-not-amplified (MYCN-NA) tumors had significantly higher cytotoxic TIL signatures compared with MYCN-amplified (MYCN-A) tumors. A reported MYCN activation signature was significantly associated with poor outcome for high-risk patients with MYCN-NA tumors; however, a subgroup of these patients who had elevated activated natural killer (NK) cells, CD8+ T cells, and cytolytic signatures showed improved outcome and expansion of infiltrating TCR clones. Furthermore, we observed upregulation of immune exhaustion marker genes, indicating an immune-suppressive microenvironment in these neuroblastomas.Conclusions: This study provides evidence that RNA signatures of cytotoxic TIL are associated with the presence of activated NK/T cells and improved outcomes in high-risk neuroblastoma patients harboring MYCN-NA tumors. Our findings suggest that these high-risk patients with MYCN-NA neuroblastoma may benefit from additional immunotherapies incorporated into the current therapeutic strategies. Clin Cancer Res; 24(22); 5673-84. ©2018 AACR.
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Affiliation(s)
- Jun S Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Igor B Kuznetsov
- Cancer Research Center and Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, New York
| | - Shile Zhang
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Young K Song
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, the Children's Hospital Los Angeles, Los Angeles, California
| | - Sivasish Sindiri
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xinyu Wen
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rajesh Patidar
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sushma Najaraj
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ashley Walton
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland
| | - Aysen Yuksel
- The Tumour Bank, Children's Cancer Research Unit, Kids Research Institute, the Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Daniel Catchpoole
- The Tumour Bank, Children's Cancer Research Unit, Kids Research Institute, the Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul M Sondel
- Departments of Pediatrics, Human Oncology and Genetics, the University of Wisconsin, Madison, Wisconsin
| | - Robert Seeger
- Division of Hematology/Oncology, the Children's Hospital Los Angeles, Los Angeles, California
| | - John M Maris
- Department of Pediatrics, University of Pennsylvania and Center for Childhood Cancer Research, the Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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13
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Alexander TB, Gu Z, Iacobucci I, Dickerson K, Choi JK, Xu B, Payne-Turner D, Yoshihara H, Loh ML, Horan J, Buldini B, Basso G, Elitzur S, de Haas V, Zwaan CM, Yeoh A, Reinhardt D, Tomizawa D, Kiyokawa N, Lammens T, De Moerloose B, Catchpoole D, Hori H, Moorman A, Moore AS, Hrusak O, Meshinchi S, Orgel E, Devidas M, Borowitz M, Wood B, Heerema NA, Carrol A, Yang YL, Smith MA, Davidsen TM, Hermida LC, Gesuwan P, Marra MA, Ma Y, Mungall AJ, Moore RA, Jones SJM, Valentine M, Janke LJ, Rubnitz JE, Pui CH, Ding L, Liu Y, Zhang J, Nichols KE, Downing JR, Cao X, Shi L, Pounds S, Newman S, Pei D, Guidry Auvil JM, Gerhard DS, Hunger SP, Inaba H, Mullighan CG. The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature 2018; 562:373-379. [PMID: 30209392 PMCID: PMC6195459 DOI: 10.1038/s41586-018-0436-0] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [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: 09/01/2017] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
Abstract
Mixed phenotype acute leukaemia (MPAL) is a high-risk subtype of leukaemia with myeloid and lymphoid features, limited genetic characterization, and a lack of consensus regarding appropriate therapy. Here we show that the two principal subtypes of MPAL, T/myeloid (T/M) and B/myeloid (B/M), are genetically distinct. Rearrangement of ZNF384 is common in B/M MPAL, and biallelic WT1 alterations are common in T/M MPAL, which shares genomic features with early T-cell precursor acute lymphoblastic leukaemia. We show that the intratumoral immunophenotypic heterogeneity characteristic of MPAL is independent of somatic genetic variation, that founding lesions arise in primitive haematopoietic progenitors, and that individual phenotypic subpopulations can reconstitute the immunophenotypic diversity in vivo. These findings indicate that the cell of origin and founding lesions, rather than an accumulation of distinct genomic alterations, prime tumour cells for lineage promiscuity. Moreover, these findings position MPAL in the spectrum of immature leukaemias and provide a genetically informed framework for future clinical trials of potential treatments for MPAL.
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Affiliation(s)
- Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC, USA
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John K Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - John Horan
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Department of Pediatrics, Atlanta, GA, USA
| | - Barbara Buldini
- Department of Women and Child Health, Hemato-Oncology Division, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Department of Women and Child Health, Hemato-Oncology Division, University of Padova, Padova, Italy
| | - Sarah Elitzur
- Pediatric Hematology-Oncology, Schneider Children's Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | - C Michel Zwaan
- Prinses Maxima Centre, Utrecht, The Netherlands
- Department of Pediatric Oncology, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Allen Yeoh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Daniel Catchpoole
- The Tumour Bank CCRU, The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Hiroki Hori
- Department of Pediatrics, Mie University, Tsu, Japan
| | - Anthony Moorman
- Wolfson Childhood Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Andrew S Moore
- The University of Queensland Diamantina Institute & Children's Health, Brisbane, Queensland, Australia
| | - Ondrej Hrusak
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
- Children's Oncology Group, Arcadia, CA, USA
| | - Etan Orgel
- Children's Center for Cancer and Blood Disease, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | - Brent Wood
- University of Washington, Seattle, WA, USA
| | - Nyla A Heerema
- The Ohio State University School of Medicine, Columbus, OH, USA
| | - Andrew Carrol
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yung-Li Yang
- Department of Laboratory Medicine and Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Tanja M Davidsen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Birriel PC, Barrett CW, Davidsen TM, Ferguson ML, Gesuwan P, Griner NB, Auvil JMG, He Y, Jagu S, Pruitt FL, Gerhard DS. Abstract 399: NCI Office of Cancer Genomics: Supporting structural and functional genomics and development of bioinformatic approaches to advance precision oncology. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-399] [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 National Cancer Institute's Office of Cancer Genomics (OCG) aims to advance the molecular understanding of cancer, with the goal of improving clinical outcomes. OCG supports large-scale cancer genomics and translational research programs that share data and resources with the research community, thereby accelerating discoveries into the clinic and contributing to precision oncology. The OCG initiatives promote: i) generation and dissemination of molecular and clinical data via programmatic databases and the Genomic Data Commons, ii) advances in bio- and chemi-informatic methodologies, and iii) creation of valuable experimental reagents, resources, models, and standard operating procedures.
OCG currently supports four innovative and collaborative programs which conjointly generate, analyze, and translate genomic and other datasets into biologically and clinically-relevant information for the scientific and medical communities. The Cancer Genome Characterization Initiative (CGCI) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiatives use comprehensive genomic, transcriptomic, and epigenomic approaches to analyze tumor and patient matched normal tissue samples with the goal of identifying therapeutic targets and biomarkers. CGCI characterizes both adult and pediatric cancers, including those prevalent in HIV-positive individuals, while TARGET focuses predominantly on high-risk cancers affecting children and young adults. The Cancer Target Discovery and Development (CTD2) Network advances cancer research by bridging the knowledge gap between cancer genomics and precision oncology for the development of effective combinatorial cancer treatments to minimize treatment resistance. The Network develops bioinformatics and analysis tools, generates diverse datasets, and further validates subsets of these data. The Human Cancer Models Initiative (HCMI) is an international consortium which will develop next generation patient-derived cancer models that are representative of the biology and complexity of human tumors. Models will be molecularly characterized and clinically annotated, and models along with the data will be available as a community resource.
Data, analytical tools, and resources generated by OCG programs are made available through the OCG website (https://ocg.cancer.gov/) to the research community to accelerate the discovery of efficient treatment strategies for cancer. This poster will include an overview of the programs and emphasize the usability and functionality of the OCG databases and resources. Presenters will also provide data access information and examples of past data use highlighting the benefit of the OCG programs to the scientific community.
Citation Format: Pamela C. Birriel, Caitlyn W. Barrett, Tanja M. Davidsen, Martin L. Ferguson, Patee Gesuwan, Nicholas B. Griner, Jaime M. Guidry Auvil, Yiwen He, Subhashini Jagu, Freddie L. Pruitt, Daniela S. Gerhard. NCI Office of Cancer Genomics: Supporting structural and functional genomics and development of bioinformatic approaches to advance precision oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 399.
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Affiliation(s)
| | | | | | | | | | | | | | - Yiwen He
- 2National Cancer Institute, Rockville, MD
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Bolouri H, Farrar JE, Triche T, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med 2017; 24:103-112. [PMID: 29227476 DOI: 10.1038/nm.4439] [Citation(s) in RCA: 463] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults. Conversely, mutations in DNMT3A and TP53, which were common in adults, were conspicuously absent from virtually all pediatric cases. New mutations in GATA2, FLT3 and CBL and recurrent mutations in MYC-ITD, NRAS, KRAS and WT1 were frequent in pediatric AML. Deletions, mutations and promoter DNA hypermethylation convergently impacted Wnt signaling, Polycomb repression, innate immune cell interactions and a cluster of zinc finger-encoding genes associated with KMT2A rearrangements. These results highlight the need for and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.
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Affiliation(s)
- Hamid Bolouri
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jason E Farrar
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Timothy Triche
- Jane Anne Nohl Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Emilia L Lim
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Todd A Alonzo
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Children's Oncology Group, Monrovia, California, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jinghui Zhang
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xiaotu Ma
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yu Liu
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yanling Liu
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Tanja M Davidsen
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stephen Capone
- Jane Anne Nohl Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Giridharan Ramsingh
- Jane Anne Nohl Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Christian Michel Zwaan
- Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Sanne Noort
- Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, Utah, USA.,Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA
| | - E Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Alan S Gamis
- Division of Hematology, Oncology and Bone Marrow Transplantation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri, USA
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Gadd S, Huff V, Walz AL, Ooms AHAG, Armstrong AE, Gerhard DS, Smith MA, Auvil JMG, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ. A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat Genet 2017; 49:1487-1494. [PMID: 28825729 PMCID: PMC5712232 DOI: 10.1038/ng.3940] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
Genome-wide sequencing, mRNA and miRNA expression, DNA copy number and methylation analyses were performed on 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, FAM123B, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), mutations were identified in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A. DNA copy number changes resulted in recurrent 1q gain, MYCN amplification, LIN28B gain, and let-7a loss. Unexpected germline variants involved PALB2 and CHEK2. Integrated analyses support two major classes of genetic changes that preserve the progenitor state and/or interrupt normal development.
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Affiliation(s)
- Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy L Walz
- Division of Hematology-Oncology and Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ariadne H A G Ooms
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA.,Department of Pathology, Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Amy E Armstrong
- Division of Hematology-Oncology and Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Chih Hao Hsu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Tanja Davidsen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey S Dome
- Division of Pediatric Hematology/Oncology, Children's National Medical Center, Washington DC, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Nicole Ross
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Stefan T Arold
- Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA
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Ooms AHAG, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Huff V, Dome JS, Chi YY, Tian J, Geller JI, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Walz AL, van den Heuvel-Eibrink MM, de Krijger RR, Ross N, Gastier-Foster JM, Perlman EJ. Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group. Clin Cancer Res 2016; 22:5582-5591. [PMID: 27702824 DOI: 10.1158/1078-0432.ccr-16-0985] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/17/2016] [Accepted: 08/14/2016] [Indexed: 12/24/2022]
Abstract
PURPOSE To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumors (DAWTs). EXPERIMENTAL DESIGN All DAWTs registered on National Wilms Tumor Study-5 (n = 118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. RESULTS Following analysis of a single random sample, 57 DAWTs (48%) demonstrated TP53 mutations, 13 (11%) copy loss without mutation, and 48 (41%) lacked both [defined as TP53-wild-type (wt)]. Patients with stage III/IV TP53-wt DAWTs (but not those with stage I/II disease) had significantly lower relapse and death rates than those with TP53 abnormalities. In-depth analysis of a subset of 39 DAWTs showed seven (18%) to be TP53-wt: These demonstrated gene expression evidence of an active p53 pathway. Retrospective pathology review of TP53-wt DAWT revealed no or very low volume of anaplasia in six of seven tumors. When samples from TP53-wt tumors known to contain anaplasia histologically were available, abnormal p53 protein accumulation was observed by immunohistochemistry. CONCLUSIONS These data support the key role of TP53 loss in the development of anaplasia in WT, and support its significant clinical impact in patients with residual anaplastic tumor following surgery. These data also suggest that most DAWTs will show evidence of TP53 mutation when samples selected for the presence of anaplasia are analyzed. This suggests that modifications of the current criteria to also consider volume of anaplasia and documentation of TP53 aberrations may better reflect the risk of relapse and death and enable optimization of therapeutic stratification. Clin Cancer Res; 22(22); 5582-91. ©2016 AACR.
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Affiliation(s)
- Ariadne H A G Ooms
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois.,Princess Maxima Centre for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pathology, Pathan BV, Sint Franciscus Gasthuis, Rotterdam, the Netherlands
| | - Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland
| | | | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Chih Hao Hsu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey S Dome
- Division of Pediatric Hematology/Oncology, Children's National Medical Center, Washington, DC
| | - Yueh-Yun Chi
- Department of Biostatistics, University of Florida, Gainesville, Florida
| | - Jing Tian
- Department of Biostatistics, University of Florida, Gainesville, Florida
| | - James I Geller
- Division of Pediatric Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Amy L Walz
- Division of Hematology-Oncology and Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois.,Northwestern Medicine Developmental Therapeutics Institute, Northwestern Memorial Hospital, Chicago, Illinois
| | | | - Ronald R de Krijger
- Princess Maxima Centre for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pathology, Reinier de Graaf Hospital, Delft, the Netherlands
| | - Nicole Ross
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio.,Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, Ohio
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois.
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Gadd SL, Walz AL, Ooms AHAG, Huff V, Gerhard DS, Smith MA, Guidry Auvil JM, Hermida L, Davidsen T, Gesuwan P, Meerzaman D, Ma Y, Marra MA, Dome JS, Mullighan CG, Wheeler DA, Hampton OA, Gastier-Foster JM, Ross N, Perlman EJ. Abstract LB-180: The genetic landscape of Wilms tumor. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The National Cancer Institute's Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative seeks to characterize the genomes of high-risk pediatric tumors to identify therapeutic targets. The High-Risk Renal Tumor TARGET initiative includes the analysis of pre-therapy favorable histology Wilms Tumors (FHWT) that relapsed and tumors with diffuse anaplasia (unfavorable histology; DAWT). These two tumor subsets have survival rates of approximately 50% and 60%, respectively.
Experimental procedures: Genomic sequencing (whole genome [WGS] or exome [WXS]), global copy number analysis, and global gene expression analysis were performed on a discovery set of 117 (78 FHWT, 39 DAWT) pre-therapy high-risk WTs treated on National Wilms Tumor Study-5 (NWTS-5). To determine the frequency of recurrent variants, targeted sequencing (Illumina HiSeq2500) was performed on a validation set of pre-therapy tumor DNA from a case-cohort of all FHWT treated on NWTS-5 (531 FHWT) and all available 118 DAWT treated on NWTS-5 (these groups include tumors from the discovery set).
Results: WGS and WXS revealed an average of 21.74 ± 22.6 high-quality variants per DAWT (range, 3-131) and 13.8 ± 10.9 per FHWT (range 2-58). Genes previously reported to be recurrently mutated in WT were mutated at the following frequencies in the validation set: WTX (6%), CTNNB1 (15%), WT1 (7.5%), DROSHA (11%), DGCR8 (4.5%), XPO5 (2%), SIX1/2 (7%), and MLLT1 (3%). In addition, mutations were identified in three genes that impact the NMYC pathway, which is known to be involved in renal development. These include MYCN P44L/H (4%), MAX R60Q (2%), and novel mutations in NONO (2%); these mutations were mutually exclusive. Novel mutations in BCOR, a transcriptional corepressor that regulates both gene expression during development and chromatin modification, were found in 3% of validation set tumors. Analysis of global gene expression revealed significant up-regulation of genes associated with kidney development, extracellular matrix organization, and epithelial tube development in BCOR-mutant tumors compared with precursor lesions (5 hyperplastic perilobar nephrogenic rests). TP53 mutations were identified in 48% of DAWTs and 1% of FHWTs. The above data do not include copy number changes, which were recurrently detected in WT1, WTX, NMYC, and TP53.
Conclusions: Through the TARGET initiative, we have identified several novel, potential driver mutations that occur in WT and have not been reported in other pediatric tumors. The majority of these genes are known to function in processes critical to early development and/or specifically in renal development. Many of these mutations are accompanied by Wnt activating mutations or 11p15 biallelic expression. However, approximately 50% of WTs lack clear driver mutations. Future studies will need to focus on elucidating epigenetic alterations in these tumors as well as genetic changes outside of protein-coding regions.
Citation Format: Samantha L. Gadd, Amy L. Walz, Ariadne HAG Ooms, Vicki Huff, Daniela S. Gerhard, Malcolm A. Smith, Jaime M. Guidry Auvil, Leandro Hermida, Tanja Davidsen, Patee Gesuwan, Daoud Meerzaman, Yussanne Ma, Marco A. Marra, Jeffrey S. Dome, Charles G. Mullighan, David A. Wheeler, Oliver A. Hampton, Julie M. Gastier-Foster, Nicole Ross, Elizabeth J. Perlman. The genetic landscape of Wilms tumor. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-180.
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Affiliation(s)
- Samantha L. Gadd
- 1Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Amy L. Walz
- 1Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | | | - Vicki Huff
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | - Yussanne Ma
- 5British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- 5British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | | | | | - Nicole Ross
- 9Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH
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Wei JS, Zhang S, Song YK, Asgharzadeh S, Sindiri S, Wen X, Patidar R, Guidry Auvil JM, Gerhard DS, Seeger R, Maris JM, Khan J. Abstract 126: The transcriptome landscape of high-risk neuroblastoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-126] [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
Despite the success of multimodal therapies, the mortality and morbidity remains substantial for patients with high-risk neuroblastoma (NBL). Sequencing of paired tumor/normal DNA of NBL has revealed a low somatic mutation burden and few recurrent somatically-mutated genes. Here we hypothesize that the integrated analysis of DNA sequencing with whole transcriptome sequencing (WTS) in patients with high-risk NBL tumor will yield valuable insights into the biology of this disease. We performed WTS of 139 NBLs (118 high-risk stage 4 and 21 stage 4S tumors) which had whole genome sequencing or whole exome sequencing of case-matched tumor/normal pairs through the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. We identified expressed mutations, fusion genes, and correlations between gene expression and clinical parameters of patients such as survival to provide understandings of high-risk NBL biology.
Out of 1500 protein-coding changing somatic nucleotide variants detected by DNA sequencing, 614 variants (41%) were also detected in the transcriptome. Twenty-four genes known to be recurrently mutated in NBL showed the exact mutations in their transcriptome as seen in the DNA, including ALK (9.4%), ATRX (2.2%) and MYCN (1.4%). Fusion gene analysis identified in-frame fusions involving ALK (n = 2) and FOXR1 genes (n = 4). All tumors positive for ALK- and FOXR1-fusions expressed transcripts containing ALK or FOXR1 sequences at much higher levels (>10 folds) than those without fusion in these respective genes. Consensus clustering using tumor gene expression profiles revealed 4 subgroups with distinct survival probability. Among them, several molecular signatures including MYC activation and tumor microenvironment were observed. Intriguingly, 58% tumors without MYCN-amplification showed a MYC activation signature significantly associated with worse overall survival (p = 0.0017). Further examination of these tumors with the MYC activation signature revealed different somatic alterations including MYCN P44L mutations, high expression of other MYC family members (MYC and MYCL), mutations in the RAS pathway, and FOXR1 fusions. Interestingly, a gene expression signature representing tumor-associated macrophages (TAM) and regulatory T-cells significantly correlated with a worse outcome in NBLs with normal MYCN copy number, similar to that seen in tumors with the MYC activation signature. In contrast, NBL patients with tumors showing a signature of cytotoxic T-cells and B-cells have better outcomes. Furthermore, tumors of the latter subgroup express significantly more somatic SNVs comparing to the other two subgroups of worse outcome with MYC activation or TAM signatures, suggesting that expressed neo-antigens may elevate cytotoxic T-cell response in these tumors. Our study suggests that patients with high-risk neuroblastoma may benefit from immune-based therapies including check point inhibitors in the future trials.
Citation Format: Jun S. Wei, Shile Zhang, Young K. Song, Shahab Asgharzadeh, Sivasish Sindiri, Xinyu Wen, Rajesh Patidar, Jaime M. Guidry Auvil, Daniela S. Gerhard, Robert Seeger, John M. Maris, Javed Khan. The transcriptome landscape of high-risk neuroblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 126.
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Affiliation(s)
| | | | | | | | | | - Xinyu Wen
- 1National Cancer Inst., Bethesda, MD
| | | | | | | | - Robert Seeger
- 2The Children's Hospital Los Angeles, Los Angeles, CA
| | - John M. Maris
- 3The Children's Hospital of Philadelphia, Philadelphia, PA
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Jaber NL, Mazerik JN, Guidry Auvil JM, Jagu S, Griner N, Ferguson M, Gerhard DS. Abstract 5293: NCI Office of Cancer Genomics: Generating publicly available data and resources for the advancement of precision medicine. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-5293] [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 Office of Cancer Genomics (OCG), within the National Cancer Institute, supports cutting-edge genomics and translational research to advance the molecular understanding of cancer, with the ultimate goal of improving clinical outcomes through precision medicine. OCG-supported cancer research initiatives generate and analyze comprehensive genomics datasets, and translate these data into tools, resources, and clinically-relevant information. OCG currently supports three complimentary initiatives, each uniquely collaborative and innovative.
The Cancer Genome Characterization Initiative (CGCI) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) Initiative collect high quality, clinically annotated, tumor and normal matched tissue samples for both discovery and validation cohorts. These initiatives aim to identify therapeutic targets and biomarkers in some malignancies prevalent in HIV-positive individuals and high-risk pediatric cancers. Samples are analyzed by whole genome, whole exome, and transcriptome sequencing and datasets are available to the research community in ways that protect patient privacy.
The Cancer Target Discovery and Development (CTD⁁2) Network combines computational approaches, high-throughput functional assays, and high content small molecule and genetic screens to accelerate the translation of genomic data into discoveries that will inform patient-specific cancer treatments. The Network develops bioinformatics and analysis tools, generates diverse datasets, and further validates subsets of these data. All resources, datasets (https://ctd2.nci.nih.gov/dataPortal/), and validated results (http://ctd2-dashboard.nci.nih.gov/) are openly available to the research community.
Data, analytical tools, and resources generated by OCG initiatives are made publicly available and can be accessed through the OCG website (https://ocg.cancer.gov/). Investigators can use and analyze the data according to their research interests. In addition, datasets generated by OCG-supported programs can serve as valuable resources for those seeking to validate genomic findings. For this poster presentation we will present the most up-to-date information about what data and resources are available, and how to access them. The use of OCG datasets and resources by the research community will further the collaborative goal of enabling precision medicine in the clinic.
Citation Format: Nadia L. Jaber, Jessica N. Mazerik, Jaime M. Guidry Auvil, Subhashini Jagu, Nicholas Griner, Martin Ferguson, Daniela S. Gerhard. NCI Office of Cancer Genomics: Generating publicly available data and resources for the advancement of precision medicine. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5293.
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Gooskens SL, Gadd S, Guidry Auvil JM, Gerhard DS, Khan J, Patidar R, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Mullighan CG, Ma J, Jennings LJ, de Krijger RR, van den Heuvel-Eibrink MM, Smith MA, Ross N, Gastier-Foster JM, Perlman EJ. TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney. Oncotarget 2016; 6:15828-41. [PMID: 26158413 PMCID: PMC4599240 DOI: 10.18632/oncotarget.4682] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 04/10/2015] [Accepted: 06/07/2015] [Indexed: 01/31/2023] Open
Abstract
Clear Cell Sarcoma of the Kidney (CCSK) is a rare childhood tumor whose molecular pathogenesis remains poorly understood. We analyzed a discovery set of 13 CCSKs for changes in chromosome copy number, mutations, rearrangements, global gene expression and global DNA methylation. No recurrent segmental chromosomal copy number changes or somatic variants (single nucleotide or small insertion/deletion) were identified. One tumor with t(10;17)(q22;p13) involving fusion of YHWAE with NUTM2B was identified. Integrated analysis of expression and methylation data identified promoter hypermethylation and low expression of the tumor suppressor gene TCF21 (Pod-1/capsulin/epicardin) in all CCSKs except the case with t(10;17)(q22;p13). TARID, the long noncoding RNA responsible for demethylating TCF21, was virtually undetectable in most CCSKs. TCF21 hypermethylation and decreased TARID expression were validated in an independent set of CCSK tumor samples. The presence of significant hypermethylation of TCF21, a transcription factor known to be active early in renal development, supports the hypothesis that hypermethylation of TCF21 and/or decreased TARID expression lies within the pathogenic pathway of most CCSKs. Future studies are needed to functionally verify a tumorigenic role of TCF21 down-regulation and to tie this to the unique gene expression pattern of CCSK.
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Affiliation(s)
- Saskia L Gooskens
- Department of Pediatric Hematology and Oncology, Erasmus MC - Sophia Children's Hospital, Rotterdam, The Netherlands.,Department of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Samantha Gadd
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, Oncogenomics section, National Cancer Institute, Bethesda, MD, USA
| | - Rajesh Patidar
- Genetics Branch, Oncogenomics section, National Cancer Institute, Bethesda, MD, USA
| | - Daoud Meerzaman
- Computational Genomics Research Group, Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qing-Rong Chen
- Computational Genomics Research Group, Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chih Hao Hsu
- Computational Genomics Research Group, Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chunhua Yan
- Computational Genomics Research Group, Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cu Nguyen
- Computational Genomics Research Group, Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ying Hu
- Computational Genomics Research Group, Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lawrence J Jennings
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL, USA
| | - Ronald R de Krijger
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, Rotterdam, The Netherlands.,Department of Pathology, Reinier de Graaf Hospital, Delft, The Netherlands
| | | | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Nicole Ross
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Elizabeth J Perlman
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL, USA
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22
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Farrar JE, Schuback HL, Ries RE, Wai D, Hampton OA, Trevino LR, Alonzo TA, Guidry Auvil JM, Davidsen TM, Gesuwan P, Hermida L, Muzny DM, Dewal N, Rustagi N, Lewis LR, Gamis AS, Wheeler DA, Smith MA, Gerhard DS, Meshinchi S. Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse. Cancer Res 2016; 76:2197-205. [PMID: 26941285 DOI: 10.1158/0008-5472.can-15-1015] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 12/27/2015] [Indexed: 01/25/2023]
Abstract
The genomic and clinical information used to develop and implement therapeutic approaches for acute myelogenous leukemia (AML) originated primarily from adult patients and has been generalized to patients with pediatric AML. However, age-specific molecular alterations are becoming more evident and may signify the need to age-stratify treatment regimens. The NCI/COG TARGET-AML initiative used whole exome capture sequencing (WXS) to interrogate the genomic landscape of matched trios representing specimens collected upon diagnosis, remission, and relapse from 20 cases of de novo childhood AML. One hundred forty-five somatic variants at diagnosis (median 6 mutations/patient) and 149 variants at relapse (median 6.5 mutations) were identified and verified by orthogonal methodologies. Recurrent somatic variants [in (greater than or equal to) 2 patients] were identified for 10 genes (FLT3, NRAS, PTPN11, WT1, TET2, DHX15, DHX30, KIT, ETV6, KRAS), with variable persistence at relapse. The variant allele fraction (VAF), used to measure the prevalence of somatic mutations, varied widely at diagnosis. Mutations that persisted from diagnosis to relapse had a significantly higher diagnostic VAF compared with those that resolved at relapse (median VAF 0.43 vs. 0.24, P < 0.001). Further analysis revealed that 90% of the diagnostic variants with VAF >0.4 persisted to relapse compared with 28% with VAF <0.2 (P < 0.001). This study demonstrates significant variability in the mutational profile and clonal evolution of pediatric AML from diagnosis to relapse. Furthermore, mutations with high VAF at diagnosis, representing variants shared across a leukemic clonal structure, may constrain the genomic landscape at relapse and help to define key pathways for therapeutic targeting. Cancer Res; 76(8); 2197-205. ©2016 AACR.
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Affiliation(s)
- Jason E Farrar
- Arkansas Children's Hospital Research Institute and the University of Arkansas for Medical Sciences, Little Rock, Arkansas. Children's Oncology Group, Monrovia, California
| | - Heather L Schuback
- Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine, Seattle, Washington
| | - Rhonda E Ries
- Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine, Seattle, Washington
| | - Daniel Wai
- Ron Matricaria Institute of Molecular Medicine, Phoenix Children's Hospital and the University of Arizona College of Medicine, Tucson, Arizona
| | - Oliver A Hampton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Lisa R Trevino
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas. Doctors Hospital at Renaissance, Edinburg, Texas
| | - Todd A Alonzo
- Children's Oncology Group, Monrovia, California. University of Southern California, Los Angeles, California
| | | | - Tanja M Davidsen
- Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, Maryland
| | - Patee Gesuwan
- Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, Maryland
| | - Leandro Hermida
- Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, Maryland
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Ninad Dewal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Lora R Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alan S Gamis
- Children's Mercy Hospitals and Clinics, Kansas City, Missouri
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Rockville, Maryland
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland
| | - Soheil Meshinchi
- Children's Oncology Group, Monrovia, California. Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine, Seattle, Washington.
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23
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Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature 2015; 528:418-21. [PMID: 26560027 DOI: 10.1038/nature15540] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022]
Abstract
Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation and transcription factor binding sites. We show that SNP rs2168101 G>T is the most highly associated variant (combined P = 7.47 × 10(-29), odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumour formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P = 0.028) in neuroblastoma primary tumours, and ablates GATA3 binding (P < 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P < 0.0001) and reporter assays (P = 0.002). These findings indicate that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumour cells.
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Affiliation(s)
- Derek A Oldridge
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew C Wood
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, Auckland Region 1142, New Zealand
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ian Crimmins
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Robyn Sussman
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cynthia Winter
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lee D McDaniel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Maura Diamond
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lori S Hart
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA
| | - Lars Anders
- Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Shile Zhang
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jun S Wei
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Javed Khan
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
| | | | | | - Mario Capasso
- University of Naples Federico II, 80131 Naples, Italy.,CEINGE Biotecnologie Avanzate, 80131 Naples, Italy
| | - Achille Iolascon
- University of Naples Federico II, 80131 Naples, Italy.,CEINGE Biotecnologie Avanzate, 80131 Naples, Italy
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jaime M Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA
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24
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Walz AL, Ooms A, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Bowlby R, Brooks D, Ma Y, Mungall AJ, Moore RA, Schein J, Marra MA, Huff V, Dome JS, Chi YY, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Jafari N, Ross N, Gastier-Foster JM, Perlman EJ. Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors. Cancer Cell 2015; 27:286-97. [PMID: 25670082 PMCID: PMC4800737 DOI: 10.1016/j.ccell.2015.01.003] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [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: 08/28/2014] [Revised: 11/28/2014] [Accepted: 01/12/2015] [Indexed: 12/21/2022]
Abstract
We report the most common single-nucleotide substitution/deletion mutations in favorable histology Wilms tumors (FHWTs) to occur within SIX1/2 (7% of 534 tumors) and microRNA processing genes (miRNAPGs) DGCR8 and DROSHA (15% of 534 tumors). Comprehensive analysis of 77 FHWTs indicates that tumors with SIX1/2 and/or miRNAPG mutations show a pre-induction metanephric mesenchyme gene expression pattern and are significantly associated with both perilobar nephrogenic rests and 11p15 imprinting aberrations. Significantly decreased expression of mature Let-7a and the miR-200 family (responsible for mesenchymal-to-epithelial transition) in miRNAPG mutant tumors is associated with an undifferentiated blastemal histology. The combination of SIX and miRNAPG mutations in the same tumor is associated with evidence of RAS activation and a higher rate of relapse and death.
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Affiliation(s)
- Amy L Walz
- Division of Hematology-Oncology and Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ariadne Ooms
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam CA 3000, the Netherlands
| | - Samantha Gadd
- Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chih Hao Hsu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Jacqueline Schein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey S Dome
- Division of Pediatric Hematology/Oncology, Children's National Medical Center, Washington, DC 20010, USA
| | - Yueh-Yun Chi
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nadereh Jafari
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nicole Ross
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA.
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25
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Assefnia S, Dakshanamurthy S, Guidry Auvil JM, Hampel C, Anastasiadis PZ, Kallakury B, Uren A, Foley DW, Brown ML, Shapiro L, Brenner M, Haigh D, Byers SW. Cadherin-11 in poor prognosis malignancies and rheumatoid arthritis: common target, common therapies. Oncotarget 2015; 5:1458-74. [PMID: 24681547 PMCID: PMC4039224 DOI: 10.18632/oncotarget.1538] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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] [Indexed: 12/21/2022] Open
Abstract
Cadherin-11 (CDH11), associated with epithelial to mesenchymal transformation in development, poor prognosis malignancies and cancer stem cells, is also a major therapeutic target in rheumatoid arthritis (RA). CDH11 expressing basal-like breast carcinomas and other CDH11 expressing malignancies exhibit poor prognosis. We show that CDH11 is increased early in breast cancer and ductal carcinoma in-situ. CDH11 knockdown and antibodies effective in RA slowed the growth of basal-like breast tumors and decreased proliferation and colony formation of breast, glioblastoma and prostate cancer cells. The repurposed arthritis drug celecoxib, which binds to CDH11, and other small molecules designed to bind CDH11 without inhibiting COX-2 preferentially affect the growth of CDH11 positive cancer cells in vitro and in animals. These data suggest that CDH11 is important for malignant progression, and is a therapeutic target in arthritis and cancer with the potential for rapid clinical translation
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Affiliation(s)
- Shahin Assefnia
- The Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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26
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Ma X, Loh ML, Rusch M, Edmonson M, Harvey RC, Wheeler DA, Hampton OA, Easton J, Yergeau D, Vadodaria B, Wu G, Carroll WL, Chen IM, Gerhard DS, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Auvil JMG, Downing JR, Willman CL, Mullighan CG, Hunger SP, Zhang J. Abstract 998: Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukemia (B-ALL): A report from the children's oncology group (COG) - Target - St. Jude Pediatric Cancer Genome Project. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-998] [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
Tumor clonal heterogeneity has been demonstrated in several cancers; however, the rise and fall of subclones under therapy have not been well characterized. To gain insight into the subclonal population architecture of pediatric B-ALL, we analyzed somatic lesions including sequence mutations, structural alterations and DNA copy number abnormalities derived from high coverage (200X) exome sequencing, whole-genome sequencing and SNP arrays of diagnosis (Dx)-remission-relapse DNA from 20 patients (median 7 yrs, range 2 to 19) treated on recent COG B-ALL trials. Cases were selected for analysis based upon occurrence of an early bone marrow relapse (median 19.2 months, range 3.8 to 35.7), which is associated with poor survival. We identified a high frequency of mutations in B-cell development (80%, e.g. PAX5, IKZF1, TCF3, BTG1, TOX, and EBF1 ), RAS signaling (65%, e.g. NRAS, KRAS, PTPN11 and FLT3), TP53 (60%, e.g. CDKN2A, TP53 and RB1), kinase signaling (25%, e.g. JAK2, CRLF2 and SH2B3) and chromatin remodeling (60%, e.g. WHSC1, MLL2, CREBBP, ARID2 and SETD2) pathways. Somatic lesions in these pathways were mostly retained (68%) between Dx and relapse. In contrast, mutations in the purine metabolism genes NT5C2 (45%) and NT5CB1 (15%) were relapse-specific. We constructed clonal lineage of somatic lesions for 15 cases based on subclonal population fractions estimated by a binomial mixture model that adjusts for sequence coverage of mutant alleles. The subclone number (median 3, range 1-5) at Dx was comparable to that at relapse (median=3, range 2-4). Notably, 6 Dx samples were observed with multiple subclones harboring distinct driver mutations in the same oncogene (e.g. NRAS, KRAS and JAK2). In almost all cases only one subclone from Dx arose to be the predominant clone present at relapse. Moreover, the mutation burden in an emergent subclone was comparable to those eradicated by therapy (P=0.43, Wilcoxon rank sum). In 80% of cases, the predominant clone at relapse originated from the smallest Dx subclone; in 45% of those cases, mutant allele present in relapse was detectable in remission DNA (∼0.1%) obtained at the end of the 1st month of therapy. Clonal lineage shows that the earliest acquired mutations at relapse are NT5C2 (n=5), NRAS (n=3), USH2A (n=3), WHSC1 (n=2), TP53 (n=2), IKZF1 (n=1) and CREBBP (n=1). Our study is the first that analyzes the genetic composition and population architecture of subclones that rise or fall after B-ALL therapy. The majority of the “rising” subclones are oligoclonal at Dx, which may explain acquisition of mutations such as those found in NT5C2 to confer growth advantage in relapse. Additional studies of patients who were cured of B-ALL are needed to determine if the presence of mutant clone at end induction might help to predict risk and tempo of relapse.
Citation Format: Xiaotu Ma, Mignon L. Loh, Michael Rusch, Michael Edmonson, Richard C. Harvey, David A. Wheeler, Oliver A. Hampton, John Easton, Donald Yergeau, Bhavin Vadodaria, Gang Wu, William L. Carroll, I-Ming Chen, Daniela S. Gerhard, Julie M. Gastier-Foster, Mary V. Relling, Malcolm A. Smith, Meenakshi Devidas, Jaime M. Guidry Auvil, James R. Downing, Cheryl L. Willman, Charles G. Mullighan, Stephen P. Hunger, Jinghui Zhang. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukemia (B-ALL): A report from the children's oncology group (COG) - Target - St. Jude Pediatric Cancer Genome Project. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 998. doi:10.1158/1538-7445.AM2014-998
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Affiliation(s)
- Xiaotu Ma
- 1St. Jude Children's Research Hospital, Memphis, TN
| | - Mignon L. Loh
- 2University of California, San Francisco, San Francisco, CA
| | | | | | | | - David A. Wheeler
- 4Cancer Genomics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Oliver A. Hampton
- 4Cancer Genomics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - John Easton
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | | | - Gang Wu
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | | | | | | | | | | | | | | | | | - Stephen P. Hunger
- 9University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
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Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang YL, Pei D, McCastlain K, Ding L, Lu C, Song G, Ma J, Becksfort J, Rusch M, Chen SC, Easton J, Cheng J, Boggs K, Santiago-Morales N, Iacobucci I, Fulton RS, Wen J, Valentine M, Cheng C, Paugh SW, Devidas M, Chen IM, Reshmi S, Smith A, Hedlund E, Gupta P, Nagahawatte P, Wu G, Chen X, Yergeau D, Vadodaria B, Mulder H, Winick NJ, Larsen EC, Carroll WL, Heerema NA, Carroll AJ, Grayson G, Tasian SK, Moore AS, Keller F, Frei-Jones M, Whitlock JA, Raetz EA, White DL, Hughes TP, Guidry Auvil JM, Smith MA, Marcucci G, Bloomfield CD, Mrózek K, Kohlschmidt J, Stock W, Kornblau SM, Konopleva M, Paietta E, Pui CH, Jeha S, Relling MV, Evans WE, Gerhard DS, Gastier-Foster JM, Mardis E, Wilson RK, Loh ML, Downing JR, Hunger SP, Willman CL, Zhang J, Mullighan CG. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med 2014; 371:1005-15. [PMID: 25207766 PMCID: PMC4191900 DOI: 10.1056/nejmoa1403088] [Citation(s) in RCA: 965] [Impact Index Per Article: 96.5] [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] [Indexed: 01/05/2023]
Abstract
BACKGROUND Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is characterized by a gene-expression profile similar to that of BCR-ABL1-positive ALL, alterations of lymphoid transcription factor genes, and a poor outcome. The frequency and spectrum of genetic alterations in Ph-like ALL and its responsiveness to tyrosine kinase inhibition are undefined, especially in adolescents and adults. METHODS We performed genomic profiling of 1725 patients with precursor B-cell ALL and detailed genomic analysis of 154 patients with Ph-like ALL. We examined the functional effects of fusion proteins and the efficacy of tyrosine kinase inhibitors in mouse pre-B cells and xenografts of human Ph-like ALL. RESULTS Ph-like ALL increased in frequency from 10% among children with standard-risk ALL to 27% among young adults with ALL and was associated with a poor outcome. Kinase-activating alterations were identified in 91% of patients with Ph-like ALL; rearrangements involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, NTRK3, PDGFRB, PTK2B, TSLP, or TYK2 and sequence mutations involving FLT3, IL7R, or SH2B3 were most common. Expression of ABL1, ABL2, CSF1R, JAK2, and PDGFRB fusions resulted in cytokine-independent proliferation and activation of phosphorylated STAT5. Cell lines and human leukemic cells expressing ABL1, ABL2, CSF1R, and PDGFRB fusions were sensitive in vitro to dasatinib, EPOR and JAK2 rearrangements were sensitive to ruxolitinib, and the ETV6-NTRK3 fusion was sensitive to crizotinib. CONCLUSIONS Ph-like ALL was found to be characterized by a range of genomic alterations that activate a limited number of signaling pathways, all of which may be amenable to inhibition with approved tyrosine kinase inhibitors. Trials identifying Ph-like ALL are needed to assess whether adding tyrosine kinase inhibitors to current therapy will improve the survival of patients with this type of leukemia. (Funded by the American Lebanese Syrian Associated Charities and others.).
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Affiliation(s)
- Kathryn G Roberts
- From the Departments of Pathology (K.G.R., D.P.-T., Y.-L.Y., K. McCastlain, G.S., J.M., S.-C.C., J.C., N.S.-M., I.I., J.W., J.R.D., C.G.M.), Computational Biology and Bioinformatics (Y.L., J.B., M.R., E.H., P.G., P.N., G.W., X.C., J.Z.), Biostatistics (D.P., C.C.), Pharmaceutical Sciences (S.W.P., M.V.R., W.E.E.), and Oncology (C.-H.P., S.J.), the Pediatric Cancer Genome Project (Y.L., L.D., C.L., M.R., J.E., J.C., K.B., R.S.F., E.H., P.G., P.N., G.W., X.C., D.Y., B.V., H.M., M.V.R., W.E.E., E.M., R.K.W., J.R.D., J.Z., C.G.M.), and Cytogenetics Shared Resource (M.V.), St. Jude Children's Research Hospital, Memphis, TN; the University of New Mexico Cancer Center and School of Medicine, Albuquerque (R.C.H., I-M.C., C.L.W.); the Genome Institute at Washington University (L.D., C.L., R.S.F., E.M., R.K.W.), the Department of Genetics, Washington University School of Medicine (L.D., C.L., R.S.F., E.M., R.K.W.), and Siteman Cancer Center, Washington University (E.M., R.K.W.) - all in St. Louis; Epidemiology and Health Policy Research, College of Medicine, University of Florida, Gainesville (M.D.); the Research Institute at Nationwide Children's Hospital (S.R., A.S., J.M.G.-F.), the Department of Pathology, College of Medicine, Ohio State University (N.A.H.), and Ohio State University Comprehensive Cancer Center (G.M., C.D.B., K. Mrózek, J.K.) - all in Columbus, OH; the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas (N.J.W.), Scott and White Hospitals and Clinics and Texas A&M Health Science Center, Temple (G.G.), the University of Texas Health Science Center San Antonio, San Antonio (M.F.-J.), and the Departments of Leukemia and Stem Cell Transplantation, Division of Cancer Medicine, University of Texas M.D. Anderson Cancer Center, Houston (S.M.K., M.K.) - all in Texas; Maine Children's Cancer Program, Scarborough (E.C.L.); New York University Cancer Institute, New York (W.L.C.), and the Department of Medicine (Oncology), Albert Einstein
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Assefnia S, Dakshanamurthy S, Auvil JMG, Hampel C, Anastasiadis P, Kallakury B, Uren A, Foley DW, Brown M, Shapiro L, Brenner M, Haigh D, Byers SW. Abstract A045: Cadherin-11, a common therapeutic target in poor prognosis malignancies and rheumatoid arthritis. Mol Cancer Res 2013. [DOI: 10.1158/1557-3125.advbc-a045] [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
Rational: Poor prognosis epithelial-derived cancers often exhibit morphologic and molecular changes characteristic of an epithelial to mesenchymal transition (EMT). EMT markers are predominantly found in tumors with a basal-like phenotype. Increased expression of the mesenchymal cadherins N-cadherin and/or Cadherin-11 (CDH11) and decreased E-cadherin, have been associated with both EMT and tumor progression. Importantly, CDH11 is a therapeutic target in rheumatoid arthritis (RA), an inflammatory disease with properties often compared with cancer. As CDH11 antibody based therapeutics are in clinical trials for RA and we recently showed that the arthritis drug celecoxib has the structural potential to bind CDH11, there is a strong possibility that, if CDH11can be shown to drive malignant progression rather than simply be associated with it, therapeutic options may be rapidly developed.
Results: We show that CDH11 is increased early in breast cancer and ductal carcinoma in-situ. CDH11 knockdown and antibodies effective in RA slowed the growth of basal-like breast tumors. CDH11 attenuation decreased proliferation and colony formation of breast, glioblastoma and prostate cancer cells. The arthritis drug celecoxib, which has characteristics consistent with CDH11 binding, an analogue without COX-2 inhibitory activity and other molecules that target CDH11, preferentially affect CDH11 positive cancer cells.
Conclusion: Our work demonstrates that cadherin-11 is important for malignant progression, is a therapeutic target in several aggressive tumors and introduces an antibody, novel small molecules and an approved arthritis drug that inhibit its function with potential for rapid clinical translation.
Citation Format: Shahin Assefnia, Sivanesan Dakshanamurthy, Jaime M. Guidry Auvil, Constanze Hampel, Panos Anastasiadis, Bhaskar Kallakury, Aykut Uren, David W. Foley, Milton Brown, Lawrence Shapiro, Michael Brenner, David Haigh, Stephen W. Byers. Cadherin-11, a common therapeutic target in poor prognosis malignancies and rheumatoid arthritis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A045.
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Affiliation(s)
| | | | | | | | | | | | | | - David W. Foley
- 3Queen's University Belfast, Northern Ireland, United Kingdom,
| | | | | | | | - David Haigh
- 3Queen's University Belfast, Northern Ireland, United Kingdom,
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Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Guidry Auvil JM, Gerhard DS, Hogarty MD, Jones SJM, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. The genetic landscape of high-risk neuroblastoma. Nat Genet 2013; 45:279-84. [PMID: 23334666 PMCID: PMC3682833 DOI: 10.1038/ng.2529] [Citation(s) in RCA: 813] [Impact Index Per Article: 73.9] [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: 09/27/2012] [Accepted: 12/20/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%1. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers.
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Affiliation(s)
- Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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