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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024; 56:281-293. [PMID: 38212634 PMCID: PMC10864188 DOI: 10.1038/s41588-023-01640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- 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
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie L Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Todd A Alonzo
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Fan Y, Wu G, Baker SD, Ma X, Wang L, Rubnitz JE, Pounds S, Klco JM. Proposal of a new genomic framework for categorization of pediatric acute myeloid leukemia associated with prognosis. Res Sq 2023:rs.3.rs-2925426. [PMID: 37398194 PMCID: PMC10312943 DOI: 10.21203/rs.3.rs-2925426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 895 pAML into 23 molecular categories that are mutually distinct from one another, including new entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3, or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a prognostic framework for pAML based on molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Tamara Westover
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Benjamin J. Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, US
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sharyn D. Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lu Wang
- 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
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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3
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Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:194-207. [PMID: 35176137 PMCID: PMC9780084 DOI: 10.1158/2643-3230.bcd-21-0160] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 08/27/2021] [Accepted: 01/24/2022] [Indexed: 01/21/2023] Open
Abstract
The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML. SIGNIFICANCE We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Benjamin J. Huang
- Department of Pediatrics, University of California, Benioff Children's Hospital, San Francisco, California
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juan M. Barajas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Melvin E. Thomas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott G. Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew B. Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Bengsheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny L. Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan Parganas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan Miller
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Todd A. Alonzo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James R. Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M. Madan Babu
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
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Newman S, Nakitandwe J, Kesserwan CA, Azzato EM, Wheeler DA, Rusch M, Shurtleff S, Hedges DJ, Hamilton KV, Foy SG, Edmonson MN, Thrasher A, Bahrami A, Orr BA, Klco JM, Gu J, Harrison LW, Wang L, Clay MR, Ouma A, Silkov A, Liu Y, Zhang Z, Liu Y, Brady SW, Zhou X, Chang TC, Pande M, Davis E, Becksfort J, Patel A, Wilkinson MR, Rahbarinia D, Kubal M, Maciaszek JL, Pastor V, Knight J, Gout AM, Wang J, Gu Z, Mullighan CG, McGee RB, Quinn EA, Nuccio R, Mostafavi R, Gerhardt EL, Taylor LM, Valdez JM, Hines-Dowell SJ, Pappo AS, Robinson G, Johnson LM, Pui CH, Ellison DW, Downing JR, Zhang J, Nichols KE. Genomes for Kids: The scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing. Cancer Discov 2021; 11:3008-3027. [PMID: 34301788 DOI: 10.1158/2159-8290.cd-20-1631] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022]
Abstract
Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole genome (WGS), exome, and RNA sequencing, to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically-relevant (25%), and/or cancer predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors) and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers.
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Affiliation(s)
- Scott Newman
- Computational Biology, St. Jude Children's Research Hospital
| | - Joy Nakitandwe
- Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | | | | | | | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | - Dale J Hedges
- Computational Biology, St. Jude Children's Research Hospital
| | - Kayla V Hamilton
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Scott G Foy
- Computational Biology, St. Jude Children's Research Hospital
| | | | - Andrew Thrasher
- Computational Biology, St. Jude Children's Research Hospital
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital
| | - Brent A Orr
- Pathology, St. Jude Children's Research Hospital
| | | | - Jiali Gu
- Department of Pathology, St. Jude Children's Research Hospital
| | - Lynn W Harrison
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Lu Wang
- Pathology, St. Jude Children's Research Hospital
| | | | - Annastasia Ouma
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Antonina Silkov
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | | | - Yu Liu
- Computational Biology, St. Jude Children's Research Hospital
| | - Samuel W Brady
- Computational Biology, St. Jude Children's Research Hospital
| | - Xin Zhou
- St. Jude Children's Research Hospital
| | - Ti-Cheng Chang
- Computational Biology, St. Jude Children's Research Hospital
| | - Manjusha Pande
- Department of Computational Biology, St. Jude Children's Research Hospital
| | - Eric Davis
- Department of Computational Biology, St. Jude Children's Research Hospital
| | - Jared Becksfort
- Computational Biology, St. Jude Children's Research Hospital
| | - Aman Patel
- Computational Biology, St. Jude Children's Research Hospital
| | | | | | - Manish Kubal
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | | | - Jay Knight
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | | | | | - Emily A Quinn
- Pharmacy and Health Sciences, Keck Graduate Institute
| | - Regina Nuccio
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | - Elsie L Gerhardt
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Leslie M Taylor
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | | | | | | | - Liza-Marie Johnson
- Division of Quality of Life and Palliative Care, St. Jude Children's Research Hospital
| | | | | | | | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital
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5
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Wheeler DA, Newman S, Nakitandwe J, Kesserwan CA, Azzato EM, Rusch MC, Shurtleff S, Bahrami A, Orr B, Klco JM, Hedges DJ, Hamilton KV, Foy SG, Edmonson MN, Thrasher A, Gu J, Harrison LW, Wang L, Mostafavi R, Kubal M, Maciaszek J, Clay M, Ouma A, Silkov A, Liu Y, Zhang Z, Liu Y, Brady SW, Zhou X, Wilkinson M, Rahbarinia D, Knight J, Wang J, Mullighan CG, McGee RB, Quinn EA, Gerhardt EL, Taylor LM, Nuccio R, Valdez JM, Hines-Dowell SJ, Pappo A, Robinson G, Johnson LM, Pui CH, Ellison DW, Downing JR, Zhang J, Nichols KE. Abstract 642: Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-642] [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
Clinical genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. In the Genomes for Kids study (NCT02530658) we used a three-platform sequencing approach, including whole genome (WGS), whole exome (WES) and RNA sequencing, to examine tumor and paired germline genomes from prospectively identified children with cancer. The goal of the study was to assess the potential of comprehensive next generation sequencing to elucidate the molecular mechanisms underlying tumor formation and investigate the potential of this information to influence clinical decision-making.The cohort, with a median age of 6 yrs, range 0 - 26 yrs, included 301 patients with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type or stage. Patients with hematologic malignancies accounted for 41% of cases, 31% had CNS tumors, and 28% had other non-CNS solid tumors. This cohort also included 18 patients with very rare tumor types, defined here as occurring in less than 2 cases per million person per year.Two hundred fifty three patients (84%) had sufficient tumor for three-platform sequencing and all 301 had adequate paired germline samples. Following analysis, 86% of patients harbored diagnostic (53%), prognostic (57%), therapeutically relevant (25%), and/or cancer predisposing (18%) variants. The inclusion of WGS enabled detection of oncogenic gene fusions, as well as 22 cases in which oncogenes were activated through enhancer hijacking, a particularly frequent occurrence in hematologic malignancies. In addition, WGS effectively detected clinically relevant small intragenic deletions (15% of tumors) and a variety of mutational signatures, which were not detectable through analysis of whole exome data. Evaluation of 56 pathogenic germline variants in the context of paired tumor sequence data helped establish the disease relevance of several genes that are not typically associated with the cancer type in question, providing critical insights on a case-by-case basis. Examples include a pathogenic germline variant in MUTYH in a patient with retinoblastoma whose tumor exhibited a mutation signature associated with reactive oxygen species indicative of loss of MUTYH function; and conversely, a likely pathogenic variant in PMS2 in a rare brain cancer, which did not exhibit a mutation signature associated with microsatellite instability. This study successfully demonstrated the power of this three-platform approach to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers. As a result of these findings, we have incorporated this three-platform approach into our routine real-time clinical service at St. Jude Children's Hospital.
Citation Format: David A. Wheeler, Scott Newman, Joy Nakitandwe, Chimene A. Kesserwan, Elizabeth M. Azzato, Michael C. Rusch, Sheila Shurtleff, Armita Bahrami, Brent Orr, Jeffery M. Klco, Dale J. Hedges, Kayla V. Hamilton, Scott G. Foy, Michael N. Edmonson, Andrew Thrasher, Jiali Gu, Lynn W. Harrison, Lu Wang, Roya Mostafavi, Manish Kubal, Jamie Maciaszek, Michael Clay, Annastasia Ouma, Antonina Silkov, Yanling Liu, Zhaojie Zhang, Yu Liu, Samuel W. Brady, Xin Zhou, Mark Wilkinson, Delaram Rahbarinia, Jay Knight, Jian Wang, Charles G. Mullighan, Rose B. McGee, Emily A. Quinn, Elsie L. Gerhardt, Leslie M. Taylor, Regina Nuccio, Jessica M. Valdez, Stacy J. Hines-Dowell, Alberto Pappo, Giles Robinson, Liza-Marie Johnson, Ching-Hon Pui, David W. Ellison, James R. Downing, Jinghui Zhang, Kim E. Nichols. Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in 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 642.
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Affiliation(s)
| | - Scott Newman
- St Jude Children's Research Hospital, Memphis, TN
| | | | | | | | | | | | | | - Brent Orr
- St Jude Children's Research Hospital, Memphis, TN
| | | | | | | | - Scott G. Foy
- St Jude Children's Research Hospital, Memphis, TN
| | | | | | - Jiali Gu
- St Jude Children's Research Hospital, Memphis, TN
| | | | - Lu Wang
- St Jude Children's Research Hospital, Memphis, TN
| | | | - Manish Kubal
- St Jude Children's Research Hospital, Memphis, TN
| | | | - Michael Clay
- St Jude Children's Research Hospital, Memphis, TN
| | | | | | - Yanling Liu
- St Jude Children's Research Hospital, Memphis, TN
| | | | - Yu Liu
- St Jude Children's Research Hospital, Memphis, TN
| | | | - Xin Zhou
- St Jude Children's Research Hospital, Memphis, TN
| | | | | | - Jay Knight
- St Jude Children's Research Hospital, Memphis, TN
| | - Jian Wang
- St Jude Children's Research Hospital, Memphis, TN
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6
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Thrasher A, Macias M, Gout AM, Rahbarinia D, Zhou X, Brady SW, McLeod C, Rusch MC, Chen X, Meshinchi S, Dyer MA, Baker SJ, Roussel MF, Zhang J. Abstract 2289: Empowering point-and-click genomic analysis with large pediatric genomic reference data on St. Jude Cloud. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2289] [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
Next-generation sequencing-based genomic profiling is now a mainstay of pediatric oncology research and clinical testing. Correlating genomic features of patient cancer genomes with curated data extracted from large reference cohorts is critical for identifying molecular subtypes and underlying mutagenesis processes. To facilitate such investigation, we developed two user-friendly workflows on St. Jude Cloud, a data sharing ecosystem hosting genomic data for >10,000 pediatric cancer patients and survivors. These workflows leverage St. Jude Cloud comprehensive pediatric cancer genomic data, including 1,616 RNA-seq of 135 cancer subtypes and 958 whole genome sequencing (WGS) of 35 subtypes, to enable user analysis of their data in the context of St. Jude Cloud cohorts without a need to download large datasets.
The RNA-Seq Expression Classification workflow enables a user to compare their patient RNA-Seq gene expression data with blood (832), brain (456), and solid tumor (319) pediatric cancer reference cohorts and PDX models (45), enabling subtype classification using t-Distributed Stochastic Neighbor Embedding (t-SNE). Reference cohorts include curated subtype-defining somatic alterations integrating genomic variant data with expression profile. Resulting interactive t-SNE plots can be explored and annotated - with options to highlight cancer subtypes or samples and display sample information (age of onset, clinical diagnosis, molecular driver). To demonstrate, we analyze PAWNXH, a Children's Oncology Group AML sample with a novel ZBTB7A-NUTM1 fusion and find it clusters with AML samples harboring KMT2A re-arrangements suggesting a potential mechanism of pathogenesis. Integrating PDX samples enables model selection for functional experiments by connecting patient subtypes with mouse models.
The Mutational Signatures workflow identifies and quantifies COSMIC mutational signatures in user-uploaded somatic VCF files for comparison to reference pediatric cancer cohorts. The interactive interface enables rapid identification of signatures within the query cohort and facilitates comparison to the reference using a cohort-level summary view. Identified signatures may also be explored at the sample-level for both query and reference cohorts, enabling the user to identify samples with signatures of interest for further analysis. We show an example comparison of mutational signatures identified in pediatric and adult AML samples.
These workflows enable users to leverage curated pediatric cancer data to make discoveries in their own samples. Enabling point-and-click analysis in St. Jude Cloud removes the barrier for non-computational researchers and eliminates the need to download large reference datasets for local analysis. Both workflows utilize post-processed rather than raw genomic data, reducing transfer costs for uploading user data to the cloud.
Citation Format: Andrew Thrasher, Michael Macias, Alexander M. Gout, Delaram Rahbarinia, Xin Zhou, Samuel W. Brady, Clay McLeod, Michael C. Rusch, Xiaolong Chen, Soheil Meshinchi, Michael A. Dyer, Suzanne J. Baker, Martine F. Roussel, Jinghui Zhang. Empowering point-and-click genomic analysis with large pediatric genomic reference data on St. Jude Cloud [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 2289.
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Affiliation(s)
| | | | | | | | - Xin Zhou
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | - Clay McLeod
- 1St. Jude Children's Research Hospital, Memphis, TN
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McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, Macias M, Birch K, Finkelstein D, Sunny J, Mudunuri R, Orr BA, Treadway M, Davidson B, Ard TK, Chiao A, Swistak A, Wiggins S, Foy S, Wang J, Sioson E, Wang S, Michael JR, Liu Y, Ma X, Patel A, Edmonson MN, Wilkinson MR, Frantz AM, Chang TC, Tian L, Lei S, Islam SMA, Meyer C, Thangaraj N, Tater P, Kandali V, Ma S, Nguyen T, Serang O, McGuire I, Robison N, Gentry D, Tang X, Palmer LE, Wu G, Suh E, Tanner L, McMurry J, Lear M, Pappo AS, Wang Z, Wilson CL, Cheng Y, Meshinchi S, Alexandrov LB, Weiss MJ, Armstrong GT, Robison LL, Yasui Y, Nichols KE, Ellison DW, Bangur C, Mullighan CG, Baker SJ, Dyer MA, Miller G, Newman S, Rusch M, Daly R, Perry K, Downing JR, Zhang J. St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem. Cancer Discov 2021; 11:1082-1099. [PMID: 33408242 DOI: 10.1158/2159-8290.cd-20-1230] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Effective data sharing is key to accelerating research to improve diagnostic precision, treatment efficacy, and long-term survival in pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a cloud-based data-sharing ecosystem for accessing, analyzing, and visualizing genomic data from >10,000 pediatric patients with cancer and long-term survivors, and >800 pediatric sickle cell patients. Harmonized genomic data totaling 1.25 petabytes are freely available, including 12,104 whole genomes, 7,697 whole exomes, and 2,202 transcriptomes. The resource is expanding rapidly, with regular data uploads from St. Jude's prospective clinical genomics programs. Three interconnected apps within the ecosystem-Genomics Platform, Pediatric Cancer Knowledgebase, and Visualization Community-enable simultaneously performing advanced data analysis in the cloud and enhancing the Pediatric Cancer knowledgebase. We demonstrate the value of the ecosystem through use cases that classify 135 pediatric cancer subtypes by gene expression profiling and map mutational signatures across 35 pediatric cancer subtypes. SIGNIFICANCE: To advance research and treatment of pediatric cancer, we developed St. Jude Cloud, a data-sharing ecosystem for accessing >1.2 petabytes of raw genomic data from >10,000 pediatric patients and survivors, innovative analysis workflows, integrative multiomics visualizations, and a knowledgebase of published data contributed by the global pediatric cancer community.This article is highlighted in the In This Issue feature, p. 995.
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Affiliation(s)
- Clay McLeod
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew Thrasher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Macias
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kirby Birch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jobin Sunny
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rahul Mudunuri
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Madison Treadway
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Arthur Chiao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew Swistak
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephanie Wiggins
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shuoguo Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - J Robert Michael
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Aman Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mark R Wilkinson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew M Frantz
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ti-Cheng Chang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shaohua Lei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | | | | | | | | | | | | | | | - Irina McGuire
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nedra Robison
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Darrell Gentry
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xing Tang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lance E Palmer
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ed Suh
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Leigh Tanner
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - James McMurry
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Matthew Lear
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alberto S Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center Professor of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Keith Perry
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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