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Abstract
The genetic basis for pediatric acute myeloid leukemia (AML) is highly heterogeneous, often involving the cooperative action of characteristic chromosomal rearrangements and somatic mutations in progrowth and antidifferentiation pathways that drive oncogenesis. Although some driver mutations are shared with adult AML, many genetic lesions are unique to pediatric patients, and their appropriate identification is essential for patient care. The increased understanding of these malignancies through broad genomic studies has begun to risk-stratify patients based on their combinations of genomic alterations, a trend that will enable precision medicine in this population.
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Affiliation(s)
- Bryan Krock
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ, USA
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52
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Asada K, Kaneko S, Takasawa K, Machino H, Takahashi S, Shinkai N, Shimoyama R, Komatsu M, Hamamoto R. Integrated Analysis of Whole Genome and Epigenome Data Using Machine Learning Technology: Toward the Establishment of Precision Oncology. Front Oncol 2021; 11:666937. [PMID: 34055633 PMCID: PMC8149908 DOI: 10.3389/fonc.2021.666937] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/26/2021] [Indexed: 12/17/2022] Open
Abstract
With the completion of the International Human Genome Project, we have entered what is known as the post-genome era, and efforts to apply genomic information to medicine have become more active. In particular, with the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in his State of the Union address at the beginning of 2015, "precision medicine," which aims to divide patients and potential patients into subgroups with respect to disease susceptibility, has become the focus of worldwide attention. The field of oncology is also actively adopting the precision oncology approach, which is based on molecular profiling, such as genomic information, to select the appropriate treatment. However, the current precision oncology is dominated by a method called targeted-gene panel (TGP), which uses next-generation sequencing (NGS) to analyze a limited number of specific cancer-related genes and suggest optimal treatments, but this method causes the problem that the number of patients who benefit from it is limited. In order to steadily develop precision oncology, it is necessary to integrate and analyze more detailed omics data, such as whole genome data and epigenome data. On the other hand, with the advancement of analysis technologies such as NGS, the amount of data obtained by omics analysis has become enormous, and artificial intelligence (AI) technologies, mainly machine learning (ML) technologies, are being actively used to make more efficient and accurate predictions. In this review, we will focus on whole genome sequencing (WGS) analysis and epigenome analysis, introduce the latest results of omics analysis using ML technologies for the development of precision oncology, and discuss the future prospects.
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Affiliation(s)
- Ken Asada
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Syuzo Kaneko
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ken Takasawa
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Hidenori Machino
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Takahashi
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Norio Shinkai
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryo Shimoyama
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Masaaki Komatsu
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ryuji Hamamoto
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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53
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Davis AR, Stone SL, Oran AR, Sussman RT, Bhattacharyya S, Morrissette JJD, Bagg A. Targeted massively parallel sequencing of mature lymphoid neoplasms: assessment of empirical application and diagnostic utility in routine clinical practice. Mod Pathol 2021; 34:904-921. [PMID: 33311649 DOI: 10.1038/s41379-020-00720-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Massively parallel sequencing (MPS) has become a viable diagnostic tool to interrogate genetic profiles of numerous tumors but has yet to be routinely adopted in the setting of lymphoma. Here, we report the empirical application of a targeted 40-gene panel developed for use in mature lymphoid neoplasms (MLNs) and report our experience on over 500 cases submitted for MPS during the first year of its clinical use. MPS was applied to both fresh and fixed specimens. The most frequent diagnoses were diffuse large B-cell lymphoma (116), chronic lymphocytic leukemia/small lymphocytic lymphoma (60), marginal zone lymphoma (52), and follicular lymphoma (43), followed by a spectrum of mature T-cell neoplasms (40). Of 534 cases submitted, 471 generated reportable results in MLNs, with disease-associated variants (DAVs) detected in 241 cases (51.2%). The most frequent DAVs affected TP53 (30%), CREBBP (14%), MYD88 (14%), TNFRSF14 (10%), TNFAIP3 (10%), B2M (7%), and NOTCH2 (7%). The bulk of our findings confirm what is reported in the scientific literature. While a substantial majority of mutations did not directly impact diagnosis, MPS results were utilized to either change, refine, or facilitate the final diagnosis in ~10.8% of cases with DAVs and 5.5% of cases overall. In addition, we identified preanalytic variables that significantly affect assay performance highlighting items for specimen triage. We demonstrate the technical viability and utility of the judicious use of a targeted MPS panel that may help to establish general guidelines for specimen selection and diagnostic application in MLNs in routine clinical practice.
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Affiliation(s)
- Adam R Davis
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sara L Stone
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda R Oran
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Robyn T Sussman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Siddharth Bhattacharyya
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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54
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Rosenthal SH, Gerasimova A, Ma C, Li HR, Grupe A, Chong H, Acab A, Smolgovsky A, Owen R, Elzinga C, Chen R, Sugganth D, Freitas T, Graham J, Champion K, Bhattacharya A, Racke F, Lacbawan F. Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms. PLoS One 2021; 16:e0243683. [PMID: 33909614 PMCID: PMC8081174 DOI: 10.1371/journal.pone.0243683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n = 2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n = 2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms even in technically challenging genes.
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Affiliation(s)
- Sun Hee Rosenthal
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Anna Gerasimova
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Charles Ma
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hai-Rong Li
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Andrew Grupe
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hansook Chong
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Allan Acab
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Alla Smolgovsky
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Renius Owen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Christopher Elzinga
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Rebecca Chen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Daniel Sugganth
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Tracey Freitas
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Jennifer Graham
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Kristen Champion
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Anindya Bhattacharya
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Frederick Racke
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Felicitas Lacbawan
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
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55
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Lalonde E, Rentas S, Wertheim G, Cao K, Surrey LF, Lin F, Zhao X, Obstfeld A, Aplenc R, Luo M, Li MM. Clinical impact of genomic characterization of 15 patients with acute megakaryoblastic leukemia-related malignancies. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005975. [PMID: 33832921 PMCID: PMC8040732 DOI: 10.1101/mcs.a005975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/30/2023] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia but is approximately 500 times more likely to develop in children with Down syndrome (DS) through transformation of transient abnormal myelopoiesis (TAM). This study investigates the clinical significance of genomic heterogeneity of AMKL in children with and without DS and in children with TAM. Genomic evaluation of nine patients with DS-related TAM or AMKL, and six patients with non-DS AMKL, included conventional cytogenetics and a comprehensive next-generation sequencing panel for single-nucleotide variants/indels and copy-number variants in 118 genes and fusions involving 110 genes. Recurrent gene fusions were found in all patients with non-DS, including two individuals with complex genomes and either a NUP98–KDM5A or a KMT2A–MLLT6 fusion, and the remaining harbored a CBFA2T3–GLIS2 fusion, which arose from both typical and atypical cytogenetic mechanisms. These fusions guided treatment protocols and resulted in a change in diagnosis in two patients. The nine patients with DS had constitutional trisomy 21 and somatic GATA1 mutations, and those with DS-AMKL had two to four additional clinically significant somatic mutations. Comprehensive genomic characterization provides critical information for diagnosis, risk stratification, and treatment decisions for patients with AMKL. Continued genetic and clinical characterization of these rare cancers will aid in improving patient management.
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Affiliation(s)
- Emilie Lalonde
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Stefan Rentas
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Amrom Obstfeld
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Richard Aplenc
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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56
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Murray AK, McGee RB, Mostafavi RM, Wang X, Lu Z, Valdez JM, Terao MA, Nichols KE. Creating a cancer genomics curriculum for pediatric hematology-oncology fellows: A national needs assessment. Cancer Med 2021; 10:2026-2034. [PMID: 33624449 PMCID: PMC7957159 DOI: 10.1002/cam4.3787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/30/2021] [Accepted: 02/03/2021] [Indexed: 11/08/2022] Open
Abstract
Background With the advent of next generation sequencing, tumor and germline genomic testing are increasingly being used in the management of pediatric cancer patients. Despite this increase in testing, many pediatric hematology–oncology (PHO) providers are not confident interpreting or utilizing tumor or germline genomic results to care for their patients. Methods We developed and delivered a needs assessment survey to PHO program directors, attendings, and fellows in the United States to understand this deficiency, gather data on existing cancer genomics educational initiatives, and query preferences for creating a future curriculum. Results The survey includes 31 (41%) of 74 invited PHO program directors, 110 (11%) of 1032 invited attendings, and 79 fellows. The majority of attending physicians and fellows responding to the survey agree that understanding tumor (95% attending physicians; 95% fellows) and germline (86% attending physicians; 94% fellows) genomic information is essential for their practice. However, only 9 of 31 (29%) responding programs report that they have an existing cancer genomics curriculum. Most program directors indicated that the ideal genomics curriculum would occur during the first year of fellowship and incorporate direct patient care, online modules, and problem‐based learning. Attending physicians and fellows identified that addressing indications for ordering tumor and germline genomic testing, counseling about the risks and benefits of such testing, and interpreting and individualizing clinical management based on tumor and germline results should be included in a future curriculum. Conclusion The results of this study reveal a great need to develop a curriculum that can be offered across PHO fellowship programs to expand knowledge in the area of cancer genomics.
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Affiliation(s)
- Alise K Murray
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rose B McGee
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Roya M Mostafavi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaoqing Wang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaohua Lu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jessica M Valdez
- Department of Pediatrics, University of New Mexico, Albuquerque, NM, USA
| | - Michael A Terao
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Medstar Georgetown University Hospital, Washington, DC, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
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57
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Pikman Y, Tasian SK, Sulis ML, Stevenson K, Blonquist TM, Apsel Winger B, Cooper TM, Pauly M, Maloney KW, Burke MJ, Brown PA, Gossai N, McNeer JL, Shukla NN, Cole PD, Kahn JM, Chen J, Barth MJ, Magee JA, Gennarini L, Adhav AA, Clinton CM, Ocasio-Martinez N, Gotti G, Li Y, Lin S, Imamovic A, Tognon CE, Patel T, Faust HL, Contreras CF, Cremer A, Cortopassi WA, Garrido Ruiz D, Jacobson MP, Dharia NV, Su A, Robichaud AL, Saur Conway A, Tarlock K, Stieglitz E, Place AE, Puissant A, Hunger SP, Kim AS, Lindeman NI, Gore L, Janeway KA, Silverman LB, Tyner JW, Harris MH, Loh ML, Stegmaier K. Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium. Cancer Discov 2021; 11:1424-1439. [PMID: 33563661 DOI: 10.1158/2159-8290.cd-20-0564] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022]
Abstract
Despite a remarkable increase in the genomic profiling of cancer, integration of genomic discoveries into clinical care has lagged behind. We report the feasibility of rapid identification of targetable mutations in 153 pediatric patients with relapsed/refractory or high-risk leukemias enrolled on a prospective clinical trial conducted by the LEAP Consortium. Eighteen percent of patients had a high confidence Tier 1 or 2 recommendation. We describe clinical responses in the 14% of patients with relapsed/refractory leukemia who received the matched targeted therapy. Further, in order to inform future targeted therapy for patients, we validated variants of uncertain significance, performed ex vivo drug-sensitivity testing in patient leukemia samples, and identified new combinations of targeted therapies in cell lines and patient-derived xenograft models. These data and our collaborative approach should inform the design of future precision medicine trials. SIGNIFICANCE: Patients with relapsed/refractory leukemias face limited treatment options. Systematic integration of precision medicine efforts can inform therapy. We report the feasibility of identifying targetable mutations in children with leukemia and describe correlative biology studies validating therapeutic hypotheses and novel mutations.See related commentary by Bornhauser and Bourquin, p. 1322.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maria Luisa Sulis
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Traci M Blonquist
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth Apsel Winger
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Todd M Cooper
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, Washington
| | - Melinda Pauly
- Division of Hematology/Oncology, Emory University, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Kelly W Maloney
- Children's Hospital Colorado, University of Colorado Cancer Center, Aurora, Colorado
| | - Michael J Burke
- Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | | | - Nathan Gossai
- Center for Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota
| | | | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter D Cole
- Children's Hospital at Montefiore, Bronx, New York
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Justine M Kahn
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
| | - Jing Chen
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
- Children's Cancer Institute, Joseph M. Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey
| | | | - Jeffrey A Magee
- Division of Pediatric Hematology/Oncology, Washington University/St. Louis Children's Hospital, St. Louis, Missouri
| | | | - Asmani A Adhav
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine M Clinton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Giacomo Gotti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yuting Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alma Imamovic
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Cristina E Tognon
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Tasleema Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Haley L Faust
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cristina F Contreras
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Anjali Cremer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University Hospital Frankfurt, Department of Hematology/Oncology, Frankfurt/Main, Germany
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Angela Su
- INSERM UMR 944, IRSL, St Louis Hospital, Paris, France
| | - Amanda L Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Katherine Tarlock
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, Washington
| | - Elliot Stieglitz
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | | | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lia Gore
- Children's Hospital Colorado, University of Colorado Cancer Center, Aurora, Colorado
| | - Katherine A Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Jeffrey W Tyner
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Mignon L Loh
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
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58
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Samoyedny A, Srinivasan A, States L, Mosse YP, Alai E, Pawel B, Pogoriler J, Shellikeri S, Vatsky S, Acord M, Escobar F, Edgar JC, Maris JM, Cahill AM. Image-Guided Biopsy for Relapsed Neuroblastoma: Focus on Safety, Adequacy for Genetic Sequencing, and Correlation of Tumor Cell Percent With Quantitative Lesion MIBG Uptake. JCO Precis Oncol 2021; 5:PO.20.00171. [PMID: 34250393 DOI: 10.1200/po.20.00171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Many novel therapies for relapsed and refractory neuroblastoma require tumor tissue for genomic sequencing. We analyze our experience with image-guided biopsy in these patients, focusing on safety, yield, adequacy for next-generation sequencing (NGS), and correlation of tumor cell percent (TC%) with quantitative uptake on 123I-meta-iodobenzylguanidine (MIBG) single-photon emission computed tomography with computed tomography (SPECT/CT). MATERIALS AND METHODS An 11-year retrospective review of image-guided biopsy on 66 patients (30 female), with a median age of 8.7 years (range, 0.9-49 years), who underwent 95 biopsies (55 bone and 40 soft tissue) of relapsed or refractory neuroblastoma lesions was performed. RESULTS There were seven minor complications (7%) and one major complication (1%). Neuroblastoma was detected in 88% of MIBG- or fluorodeoxyglucose-avid foci. The overall NGS adequacy was 69% (64% in bone and 74% in soft tissue, P = .37). NGS adequacy within neuroblastoma-positive biopsies was 88% (82% bone and 96% soft tissue, P = .11). NGS-adequate biopsies had a greater mean TC% than inadequates (51% v 18%, P = .03). NGS-adequate biopsies had a higher mean number of needle passes (7.5 v 3.4, P = .0002). The mean tissue volume from NGS-adequate soft-tissue lesions was 0.16 cm3 ± 0.12. Lesion:liver and lesion:psoas MIBG uptake ratios correlated with TC% (r = 0.74, r = 0.72, and n = 14). Mean TC% in NGS-adequate samples was 51%, corresponding to a lesion:liver ratio of 2.9 and a lesion:psoas ratio of 9.0. Thirty percent of biopsies showed an actionable ALK mutation or other therapeutically relevant variant. CONCLUSION Image-guided biopsy for relapsed or refractory neuroblastoma was safe and likely to provide NGS data to guide therapy decisions. A lesion:liver MIBG uptake ratio of ≥ 3 or a lesion:psoas ratio of > 9 was associated with a TC% sufficient to deliver NGS results.
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Affiliation(s)
- Andrew Samoyedny
- Children's Hospital of Philadelphia, Philadelphia, PA.,Drexel University College of Medicine, Philadelphia, PA
| | - Abhay Srinivasan
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Lisa States
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yael P Mosse
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Emma Alai
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bruce Pawel
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jennifer Pogoriler
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | - Seth Vatsky
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Michael Acord
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Fernando Escobar
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | - John M Maris
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Anne Marie Cahill
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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59
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Hiemenz MC, Oberley MJ, Doan A, Aye L, Ji J, Schmidt RJ, Biegel JA, Bhojwani D, Raca G. A multimodal genomics approach to diagnostic evaluation of pediatric hematologic malignancies. Cancer Genet 2021; 254-255:25-33. [PMID: 33571894 DOI: 10.1016/j.cancergen.2021.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/24/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Detection of somatic genetic drivers is important for risk stratification and treatment selection in pediatric leukemias; however, newly recognized genetic markers may not be detected by routine karyotyping and fluorescence in situ hybridization (FISH). To identify the combination of assays that provides the highest detection rate for clinically significant molecular abnormalities, we tested 160 B- lymphoblastic leukemia (B-ALL) by karyotyping, FISH, chromosomal microarray analysis (CMA) and the custom next-generation sequencing (NGS) panel, OncoKidsⓇ. In addition, we tested 40 myeloid malignancies with karyotyping, chromosomal microarray analysis (CMA), and OncoKidsⓇ; 36/40 myeloid malignancies were also tested with FISH. In B-ALL, individual testing methods had the following diagnostic yields for the key genetic drivers: karyotype 34%; basic FISH panel 45%; FISH panel with IGH and CRLF2 probes 65%; CMA 48%; OncoKidsⓇ 39%. CMA and OncoKidsⓇ testing allowed detection of key genetic drivers in 42% of the samples that remained unknown upon testing by conventional methods. In myeloid malignancies, OncoKidsⓇ had the highest yield for detection of both primary and secondary DNA mutations and RNA fusions. Our data highlights the complementarity between CMA and NGS and conventional cytogenetics/FISH in pediatric leukemia diagnostics. Due to rapid turn-around-time, FISH may be useful as an initial screening method in B-ALL. Our data also suggests NGS testing with a comprehensive panel, despite a longer turnaround time, is a good alternative to karyotyping and FISH in pediatric AML due to its superior detection rate.
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Affiliation(s)
- Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Matthew J Oberley
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Andrew Doan
- Division of Hematology-Oncology, Children's Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Le Aye
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Deepa Bhojwani
- Division of Hematology-Oncology, Children's Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
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60
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Zhao X, Kotch C, Fox E, Surrey LF, Wertheim GB, Baloch ZW, Lin F, Pillai V, Luo M, Kreiger PA, Pogoriler JE, Linn RL, Russo PA, Santi M, Resnick AC, Storm PB, Hunger SP, Bauer AJ, Li MM. NTRK Fusions Identified in Pediatric Tumors: The Frequency, Fusion Partners, and Clinical Outcome. JCO Precis Oncol 2021; 1:PO.20.00250. [PMID: 34036219 PMCID: PMC8140782 DOI: 10.1200/po.20.00250] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/26/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
Neurotrophic tyrosine receptor kinase (NTRK) fusions have been described as
oncogenic drivers in a variety of tumors. However, little is known about the
overall frequency of NTRK fusion in unselected pediatric tumors. Here, we
assessed the frequency, fusion partners, and clinical course in pediatric
patients with NTRK fusion–positive tumors.
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Affiliation(s)
- Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Chelsea Kotch
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth Fox
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Zubair W Baloch
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Portia A Kreiger
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jennifer E Pogoriler
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Pierre A Russo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Adam C Resnick
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Phillip B Storm
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephen P Hunger
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Andrew J Bauer
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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61
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Viaene AN, Pu C, Perry A, Li MM, Luo M, Santi M. Congenital tumors of the central nervous system: an institutional review of 64 cases with emphasis on tumors with unique histologic and molecular characteristics. Brain Pathol 2021; 31:45-60. [PMID: 32681571 PMCID: PMC8018134 DOI: 10.1111/bpa.12885] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Congenital brain tumors are rare accounting for 0.5%-1.9% of all pediatric brain tumors. While different criteria have been used to classify a tumor as congenital, those diagnosed prior to 6 months of age are considered to be "probably" congenital in origin. We performed an institutional review of all central nervous system (CNS) tumors (surgical and autopsy specimens from 1990 to 2019) in patients less than 6 months old. Sixty-four unique cases were identified, and these accounted for 2.0% of all CNS tumor specimens at our institution. The most common tumor types were high-grade gliomas, low-grade gliomas and medulloblastomas. Atypical teratoid rhabdoid tumors, choroid plexus tumors and germ cell tumors also accounted for a significant portion of the cohort. Seven tumors were diagnosed prenatally. The most common clinical presentation at diagnosis was increased head circumference. At the conclusion of the study, over half of the patients were alive including all patients with WHO grade I and II tumors. Ninety-two percent of cases were classifiable using the 2016 WHO system, and when available, molecular findings supported the histologic diagnoses. However, several gliomas had unusual histologic features and did not correspond to a well-defined entity. Molecular testing was essential for accurate classification of a subset of these tumors, and several high-grade gliomas exhibited fusions considered unique to infantile gliomas, including those involving the MET, ALK and NTRK genes. To our knowledge, this cohort represents the largest single-institution study of congenital CNS tumors and highlights many ways in which congenital CNS tumors are distinct from CNS tumors of older pediatric patients and adults.
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Affiliation(s)
- Angela N. Viaene
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Cunfeng Pu
- Department of Pathology and Laboratory MedicinePenn State College of MedicineHersheyPAUSA
| | - Arie Perry
- Department of PathologyUniversity of CaliforniaSan FranciscoCAUSA
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCAUSA
| | - Marilyn M. Li
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Minjie Luo
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Mariarita Santi
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
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62
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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63
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Zhong Y, Lin F, Xu F, Schubert J, Wu J, Wainwright L, Zhao X, Cao K, Fan Z, Chen J, Lang SS, Kennedy BC, Viaene AN, Santi M, Resnick AC, Storm PB, Li MM. Genomic characterization of a PPP1CB-ALK fusion with fusion gene amplification in a congenital glioblastoma. Cancer Genet 2020; 252-253:37-42. [PMID: 33341678 DOI: 10.1016/j.cancergen.2020.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/22/2020] [Accepted: 12/06/2020] [Indexed: 12/26/2022]
Abstract
ALK (Anaplastic lymphoma kinase) fusion proteins are oncogenic and have been seen in various tumors. PPP1CB-ALK fusions are rare but have been reported in a few patients with low- or high-grade gliomas. However, little is known regarding the mechanism of fusion formation and genomic break points of this fusion. We performed genomic characterization of a PPP1CB-ALK fusion with fusion gene amplification in a congenital glioblastoma. The PPP1CB-ALK consists of exons 1-5 of PPP1CB and exons 20-29 of ALK. The genomic translocation breakpoints were determined by real-time quantitative PCR (RT-qPCR) and Sanger sequencing of genomic DNA. Next generation sequencing, RT-qPCR and fluorescence in situ hybridization analyses demonstrated PPP1CB-ALK amplification. Copy number analyses of genes between PPP1CB and ALK using RT-qPCR suggest that the PPP1CB-ALK is likely the result of local chromothripsis followed by episomal amplification. Transcriptome sequencing demonstrated high-level SOX2 expression and predicted WNT/β-catenin pathway activation, suggesting possible therapeutic approaches.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Feng Xu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jeff Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Luanne Wainwright
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Shih-Shan Lang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Benjamin C Kennedy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Adam C Resnick
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Phillip B Storm
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
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64
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Demetri GD, Antonescu CR, Bjerkehagen B, Bovée JVMG, Boye K, Chacón M, Dei Tos AP, Desai J, Fletcher JA, Gelderblom H, George S, Gronchi A, Haas RL, Hindi N, Hohenberger P, Joensuu H, Jones RL, Judson I, Kang YK, Kawai A, Lazar AJ, Le Cesne A, Maestro R, Maki RG, Martín J, Patel S, Penault-Llorca F, Premanand Raut C, Rutkowski P, Safwat A, Sbaraglia M, Schaefer IM, Shen L, Serrano C, Schöffski P, Stacchiotti S, Sundby Hall K, Tap WD, Thomas DM, Trent J, Valverde C, van der Graaf WTA, von Mehren M, Wagner A, Wardelmann E, Naito Y, Zalcberg J, Blay JY. Diagnosis and management of tropomyosin receptor kinase (TRK) fusion sarcomas: expert recommendations from the World Sarcoma Network. Ann Oncol 2020; 31:1506-1517. [PMID: 32891793 PMCID: PMC7985805 DOI: 10.1016/j.annonc.2020.08.2232] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
Sarcomas are a heterogeneous group of malignancies with mesenchymal lineage differentiation. The discovery of neurotrophic tyrosine receptor kinase (NTRK) gene fusions as tissue-agnostic oncogenic drivers has led to new personalized therapies for a subset of patients with sarcoma in the form of tropomyosin receptor kinase (TRK) inhibitors. NTRK gene rearrangements and fusion transcripts can be detected with different molecular pathology techniques, while TRK protein expression can be demonstrated with immunohistochemistry. The rarity and diagnostic complexity of NTRK gene fusions raise a number of questions and challenges for clinicians. To address these challenges, the World Sarcoma Network convened two meetings of expert adult oncologists and pathologists and subsequently developed this article to provide practical guidance on the management of patients with sarcoma harboring NTRK gene fusions. We propose a diagnostic strategy that considers disease stage and histologic and molecular subtypes to facilitate routine testing for TRK expression and subsequent testing for NTRK gene fusions.
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Affiliation(s)
- G D Demetri
- Dana-Farber Cancer Institute and Ludwig Center at Harvard Medical School, Boston, USA
| | - C R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - B Bjerkehagen
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - J V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - K Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - M Chacón
- Oncology Service Chair, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - A P Dei Tos
- Department of Pathology, University of Padua, Padova, Italy
| | - J Desai
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Australia
| | - J A Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - H Gelderblom
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands
| | - S George
- Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - A Gronchi
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - R L Haas
- Department of Radiotherapy, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - N Hindi
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain; Medical Oncology Department, University Hospital Virgen del Rocio, Sevilla, Spain
| | - P Hohenberger
- Division of Surgical Oncology and Thoracic Surgery, Mannheim University Medical Center, Mannheim, Germany
| | - H Joensuu
- Department of Oncology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - R L Jones
- Sarcoma Unit, Royal Marsden NHS Foundation Trust, London, UK; Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - I Judson
- Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Y-K Kang
- Department of Oncology, University of Ulsan College of Medicine, Seoul, Korea
| | - A Kawai
- Department of Musculoskeletal Oncology, National Cancer Center, Tokyo, Japan
| | - A J Lazar
- Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Le Cesne
- Medical Oncology, Insitut Gustave Roussy, Villejuif, Ile-de-France, France
| | - R Maestro
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO Aviano) IRCCS, National Cancer Institute, Aviano, Italy
| | - R G Maki
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - J Martín
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain; Medical Oncology Department, University Hospital Virgen del Rocio, Sevilla, Spain
| | - S Patel
- Department of Sarcoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | | | - C Premanand Raut
- Division of Surgical Oncology, Brigham and Women's Hospital, Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - P Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - A Safwat
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - M Sbaraglia
- Department of Pathology, University of Padua, Padova, Italy
| | - I-M Schaefer
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - L Shen
- Department of GI Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - C Serrano
- Sarcoma Translational Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain; Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain
| | - P Schöffski
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - S Stacchiotti
- Cancer Medicine Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - K Sundby Hall
- Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - W D Tap
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, USA
| | - D M Thomas
- The Kinghorn Cancer Centre and Cancer Theme, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - J Trent
- Sylvester Comprehensive Cancer Center at University of Miami Miller School of Medicine, Miami, USA
| | - C Valverde
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain
| | - W T A van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - M von Mehren
- Department of Hematology and Medical Oncology, Fox Chase Cancer Center, Philadelphia, USA
| | - A Wagner
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - E Wardelmann
- Gerhard Domagk Institute of Pathology, University of Münster, Münster, Germany
| | - Y Naito
- National Cancer Center Hospital East, Kashiwa, Japan
| | - J Zalcberg
- Department of Epidemiology and Preventative Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia; Department of Medical Oncology, Alfred Health, Melbourne, Australia
| | - J-Y Blay
- Centre Léon Bérard, Unicancer, LYRICAN and Université Claude Bernard Lyon 1, Lyon, France.
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65
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How I treat relapsed acute lymphoblastic leukemia in the pediatric population. Blood 2020; 136:1803-1812. [DOI: 10.1182/blood.2019004043] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/11/2020] [Indexed: 01/04/2023] Open
Abstract
Abstract
Relapsed acute lymphoblastic leukemia (ALL) has remained challenging to treat in children, with survival rates lagging well behind those observed at initial diagnosis. Although there have been some improvements in outcomes over the past few decades, only ∼50% of children with first relapse of ALL survive long term, and outcomes are much worse with second or later relapses. Recurrences that occur within 3 years of diagnosis and any T-ALL relapses are particularly difficult to salvage. Until recently, treatment options were limited to intensive cytotoxic chemotherapy with or without site-directed radiotherapy and allogeneic hematopoietic stem cell transplantation (HSCT). In the past decade, several promising immunotherapeutics have been developed, changing the treatment landscape for children with relapsed ALL. Current research in this field is focusing on how to best incorporate immunotherapeutics into salvage regimens and investigate long-term survival and side effects, and when these might replace HSCT. As more knowledge is gained about the biology of relapse through comprehensive genomic profiling, incorporation of molecularly targeted therapies is another area of active investigation. These advances in treatment offer real promise for less toxic and more effective therapy for children with relapsed ALL, and we present several cases highlighting contemporary treatment decision-making.
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66
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Wang M, Zhang R, Li J. CRISPR/cas systems redefine nucleic acid detection: Principles and methods. Biosens Bioelectron 2020; 165:112430. [PMID: 32729545 PMCID: PMC7341063 DOI: 10.1016/j.bios.2020.112430] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Methods that enable rapid, sensitive and specific analyses of nucleic acid sequences have positive effects on precise disease diagnostics and effective clinical treatments by providing direct insight into clinically relevant genetic information. Thus far, many CRISPR/Cas systems have been repurposed for diagnostic functions and are revolutionizing the accessibility of robust diagnostic tools due to their high flexibility, sensitivity and specificity. As RNA-guided targeted recognition effectors, Cas9 variants have been utilized for a variety of diagnostic applications, including biosensing assays, imaging assays and target enrichment for next-generation sequencing (NGS), thereby enabling the development of flexible and cost-effective tests. In addition, the ensuing discovery of Cas proteins (Cas12 and Cas13) with collateral cleavage activities has facilitated the development of numerous diagnostic tools for rapid and portable detection, and these tools have great potential for point-of-care settings. However, representative reviews proposed on this topic are mainly confined to classical biosensing applications; thus, a comprehensive and systematic description of this fast-developing field is required. In this review, based on the detection principle, we provide a detailed classification and comprehensive discussion of recent works that harness these CRISPR-based diagnostic tools from a new perspective. Furthermore, current challenges and future perspectives of CRISPR-based diagnostics are outlined.
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Affiliation(s)
- Meng Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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67
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Powers J, Pinto EM, Barnoud T, Leung JC, Martynyuk T, Kossenkov AV, Philips AH, Desai H, Hausler R, Kelly G, Le AN, Li MM, MacFarland SP, Pyle LC, Zelley K, Nathanson KL, Domchek SM, Slavin TP, Weitzel JN, Stopfer JE, Garber JE, Joseph V, Offit K, Dolinsky JS, Gutierrez S, McGoldrick K, Couch FJ, Levin B, Edelman MC, Levy CF, Spunt SL, Kriwacki RW, Zambetti GP, Ribeiro RC, Murphy ME, Maxwell KN. A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Cancers. Cancer Res 2020; 80:3732-3744. [PMID: 32675277 PMCID: PMC7484045 DOI: 10.1158/0008-5472.can-20-1390] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/28/2020] [Accepted: 06/29/2020] [Indexed: 01/14/2023]
Abstract
Germline mutations in TP53 cause a rare high penetrance cancer syndrome, Li-Fraumeni syndrome (LFS). Here, we identified a rare TP53 tetramerization domain missense mutation, c.1000G>C;p.G334R, in a family with multiple late-onset LFS-spectrum cancers. Twenty additional c.1000G>C probands and one c.1000G>A proband were identified, and available tumors showed biallelic somatic inactivation of TP53. The majority of families were of Ashkenazi Jewish descent, and the TP53 c.1000G>C allele was found on a commonly inherited chromosome 17p13.1 haplotype. Transient transfection of the p.G334R allele conferred a mild defect in colony suppression assays. Lymphoblastoid cell lines from the index family in comparison with TP53 normal lines showed that although classical p53 target gene activation was maintained, a subset of p53 target genes (including PCLO, PLTP, PLXNB3, and LCN15) showed defective transactivation when treated with Nutlin-3a. Structural analysis demonstrated thermal instability of the G334R-mutant tetramer, and the G334R-mutant protein showed increased preponderance of mutant conformation. Clinical case review in comparison with classic LFS cohorts demonstrated similar rates of pediatric adrenocortical tumors and other LFS component cancers, but the latter at significantly later ages of onset. Our data show that TP53 c.1000G>C;p.G334R is found predominantly in Ashkenazi Jewish individuals, causes a mild defect in p53 function, and leads to low penetrance LFS. SIGNIFICANCE: TP53 c.1000C>G;p.G334R is a pathogenic, Ashkenazi Jewish-predominant mutation associated with a familial multiple cancer syndrome in which carriers should undergo screening and preventive measures to reduce cancer risk.
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Affiliation(s)
- Jacquelyn Powers
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Emilia M Pinto
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Thibaut Barnoud
- Program in Molecular and Cellular Oncogenesis, Wistar Institute, Philadelphia, Pennsylvania
| | - Jessica C Leung
- Program in Molecular and Cellular Oncogenesis, Wistar Institute, Philadelphia, Pennsylvania
| | - Tetyana Martynyuk
- Program in Molecular and Cellular Oncogenesis, Wistar Institute, Philadelphia, Pennsylvania
| | - Andrew V Kossenkov
- Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania
| | - Aaron H Philips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Heena Desai
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ryan Hausler
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory Kelly
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anh N Le
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marilyn M Li
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Suzanne P MacFarland
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Louise C Pyle
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kristin Zelley
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katherine L Nathanson
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan M Domchek
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Thomas P Slavin
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, California
| | - Jeffrey N Weitzel
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, California
| | - Jill E Stopfer
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jill S Dolinsky
- Division of Clinical Affairs, Division of Bioinformatics, Ambry Genetics, Aliso Viejo, California
| | - Stephanie Gutierrez
- Division of Clinical Affairs, Division of Bioinformatics, Ambry Genetics, Aliso Viejo, California
| | - Kelly McGoldrick
- Division of Clinical Affairs, Division of Bioinformatics, Ambry Genetics, Aliso Viejo, California
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Brooke Levin
- MD Anderson Cancer Center at Cooper, Camden, New Jersey
| | - Morris C Edelman
- Cohen Children's Medical Center of New York, New Hyde Park, New York
| | - Carolyn Fein Levy
- Cohen Children's Medical Center of New York, New Hyde Park, New York
| | - Sheri L Spunt
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Raul C Ribeiro
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Maureen E Murphy
- Program in Molecular and Cellular Oncogenesis, Wistar Institute, Philadelphia, Pennsylvania
| | - Kara N Maxwell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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68
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Zhong Y, Schubert J, Wu J, Xu F, Lin F, Cao K, Zelley K, Luo M, Foster JB, Cole KA, MacFarland SP, Resnick AC, Storm PB, Li MM. A germline PALB2 pathogenic variant identified in a pediatric high-grade glioma. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005397. [PMID: 32554798 PMCID: PMC7476410 DOI: 10.1101/mcs.a005397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
PALB2 (partner and localizer of BRCA2) gene encodes a protein that colocalizes with BRCA2 in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. PALB2 plays a critical role in maintaining genome integrity through its role in the Fanconi anemia and homologous recombination DNA repair pathways. It has a known loss-of-function disease mechanism. Biallelic PALB2 pathogenic variants have been described in autosomal recessive Fanconi anemia. Heterozygous pathogenic variants in PALB2 are associated with increased risk for female and male breast cancer and pancreatic cancer (Science 324: 217; Cancer Res 71: 2222–2229; N Engl J Med 371: 497–506). Heterozygous germline PALB2 mutations have also been observed in patients with medulloblastoma (Lancet Oncol 19: 785–798). However, PALB2-related cancer predisposition to high-grade gliomas has not been reported. Here we report a germline PALB2 pathogenic variant (c.509_510delGA, p.Arg170Ilefs*14, NM_024675.3) found in a pediatric patient with high-grade glioma. This variant was first identified by tumor sequencing using the Children's Hospital of Philadelphia (CHOP) Comprehensive Solid Tumor Panel and then confirmed to be a germline change using the CHOP Comprehensive Hereditary Cancer Panel on DNA from a blood sample of this patient. Parental studies showed that this variant was paternally inherited. Further studies are needed to illustrate if pathogenic variants in PALB2 convey increased risk to developing brain tumor. This case also highlights the potential of identifying germline mutation through tumor sequencing.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Feng Xu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jessica B Foster
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kristina A Cole
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Suzanne P MacFarland
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Adam C Resnick
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Neurosurgery, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Phillip B Storm
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Neurosurgery, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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69
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Wu C, Zhao X, Welsh M, Costello K, Cao K, Abou Tayoun A, Li M, Sarmady M. Using Machine Learning to Identify True Somatic Variants from Next-Generation Sequencing. Clin Chem 2020; 66:239-246. [PMID: 31672855 DOI: 10.1373/clinchem.2019.308213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/19/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Molecular profiling has become essential for tumor risk stratification and treatment selection. However, cancer genome complexity and technical artifacts make identification of real variants a challenge. Currently, clinical laboratories rely on manual screening, which is costly, subjective, and not scalable. We present a machine learning-based method to distinguish artifacts from bona fide single-nucleotide variants (SNVs) detected by next-generation sequencing from nonformalin-fixed paraffin-embedded tumor specimens. METHODS A cohort of 11278 SNVs identified through clinical sequencing of tumor specimens was collected and divided into training, validation, and test sets. Each SNV was manually inspected and labeled as either real or artifact as part of clinical laboratory workflow. A 3-class (real, artifact, and uncertain) model was developed on the training set, fine-tuned with the validation set, and then evaluated on the test set. Prediction intervals reflecting the certainty of the classifications were derived during the process to label "uncertain" variants. RESULTS The optimized classifier demonstrated 100% specificity and 97% sensitivity over 5587 SNVs of the test set. Overall, 1252 of 1341 true-positive variants were identified as real, 4143 of 4246 false-positive calls were deemed artifacts, whereas only 192 (3.4%) SNVs were labeled as "uncertain," with zero misclassification between the true positives and artifacts in the test set. CONCLUSIONS We presented a computational classifier to identify variant artifacts detected from tumor sequencing. Overall, 96.6% of the SNVs received definitive labels and thus were exempt from manual review. This framework could improve quality and efficiency of the variant review process in clinical laboratories.
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Affiliation(s)
- Chao Wu
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Xiaonan Zhao
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mark Welsh
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Kajia Cao
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ahmad Abou Tayoun
- Department of Genetics, Al Jalila Children's Specialty Hospital, Dubai, UAE
| | - Marilyn Li
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA
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70
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Nasrallah MLP, Desai A, O’Rourke DM, Surrey LF, Stein JM. A dual-genotype oligoastrocytoma with histologic, molecular, radiological and time-course features. Acta Neuropathol Commun 2020; 8:115. [PMID: 32690110 PMCID: PMC7372861 DOI: 10.1186/s40478-020-00998-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
A case of a true dual-genotype IDH-mutant oligoastrocytoma with two different cell types within a single mass in a young woman is presented. Imaging findings of the left frontal infiltrating glioma predicted the two neoplastic components that were identified upon resection. Tissue examination demonstrated areas of tumor with contrasting histologic and molecular features, including specific IDH1, ATRX, TP53, TERT and CIC mutational profiles, consistent with oligodendroglioma and astrocytoma, respectively. The clinical and radiological course over 17 months from first diagnosis included three surgical resections with slow progression of the astrocytic component, and ultimately chemotherapy and radiation treatments were commenced. Reports of the clinical courses for these rare cases of dual-genotype oligoastrocytomas will inform therapy choices, to optimize benefit while minimizing side effects. The steadily increasing number of cases suggests that the neoplasm might be reconsidered as an official entity by the WHO.
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71
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Rentas S, Pillai V, Wertheim GB, Akgumus GT, Nichols KE, Deardorff MA, Conlin LK, Li MM, Olson TS, Luo M. Evolution of histomorphologic, cytogenetic, and genetic abnormalities in an untreated patient with MIRAGE syndrome. Cancer Genet 2020; 245:42-48. [PMID: 32619790 DOI: 10.1016/j.cancergen.2020.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 05/08/2020] [Accepted: 06/09/2020] [Indexed: 01/16/2023]
Abstract
Gain of function variants in SAMD9 cause MIRAGE syndrome, a rare Mendelian disorder that results in myeloid dysplastic syndrome (MDS), poor immune response, restricted growth, adrenal insufficiency, ambiguous genitalia, feeding difficulties and most often significantly reduced lifespan. In this study, we describe histomorphologic and genetic changes occurring in serial bone marrow measurements in a patient with MIRAGE syndrome and untreated MDS of 9 years. Histomorphological analysis during childhood showed progressive hypocellularity with erythroid and megakaryocytic dysplasia and cytogenetic testing demonstrated monosomy 7. Serial leukemia gene panel testing performed over a seven year period revealed multiple pre-leukemic clones arising at age 7 years followed by sequential mutational events in ETV6 and RUNX1 driving acute myeloid leukemia (AML) at age 9. Comprehensive genotype-phenotype analysis with 28 previously reported patients found the presence of MDS did not impact overall survival, but in silico variant pathogenicity prediction scores for SAMD9 distinguished patients with poor prognosis. Overall, our analysis shows progression of MDS to AML can be monitored by following mutation evolution in leukemia related genes in patients with MIRAGE syndrome, and specific SAMD9 mutations likely influence disease severity and overall survival.
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Affiliation(s)
- Stefan Rentas
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Gozde T Akgumus
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States
| | - Kim E Nichols
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Timothy S Olson
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States; Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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Hurtz C, Wertheim GB, Loftus JP, Blumenthal D, Lehman A, Li Y, Bagashev A, Manning B, Cummins KD, Burkhardt JK, Perl AE, Carroll M, Tasian SK. Oncogene-independent BCR-like signaling adaptation confers drug resistance in Ph-like ALL. J Clin Invest 2020; 130:3637-3653. [PMID: 32191635 PMCID: PMC7324172 DOI: 10.1172/jci134424] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/17/2020] [Indexed: 12/23/2022] Open
Abstract
Children and adults with Philadelphia chromosome-like B cell acute lymphoblastic leukemia (Ph-like B-ALL) experience high relapse rates despite best-available conventional chemotherapy. Ph-like ALL is driven by genetic alterations that activate constitutive cytokine receptor and kinase signaling, and early-phase trials are investigating the potential of the addition of tyrosine kinase inhibitors (TKIs) to chemotherapy to improve clinical outcomes. However, preclinical studies have shown that JAK or PI3K pathway inhibition is insufficient to eradicate the most common cytokine receptor-like factor 2-rearranged (CRLF2-rearranged) Ph-like ALL subset. We thus sought to define additional essential signaling pathways required in Ph-like leukemogenesis for improved therapeutic targeting. Herein, we describe an adaptive signaling plasticity of CRLF2-rearranged Ph-like ALL following selective TKI pressure, which occurs in the absence of genetic mutations. Interestingly, we observed that Ph-like ALL cells have activated SRC, ERK, and PI3K signaling consistent with activated B cell receptor (BCR) signaling, although they do not express cell surface μ-heavy chain (μHC). Combinatorial targeting of JAK/STAT, PI3K, and "BCR-like" signaling with multiple TKIs and/or dexamethasone prevented this signaling plasticity and induced complete cell death, demonstrating a more optimal and clinically pragmatic therapeutic strategy for CRLF2-rearranged Ph-like ALL.
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Affiliation(s)
- Christian Hurtz
- Division of Hematology and Oncology and
- Abramson Cancer Center, Department of Medicine, and
| | - Gerald B. Wertheim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Hematopathology
| | - Joseph P. Loftus
- Division of Oncology, and
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daniel Blumenthal
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Hematopathology
| | - Anne Lehman
- Division of Hematology and Oncology and
- Abramson Cancer Center, Department of Medicine, and
| | - Yong Li
- Division of Oncology, and
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Asen Bagashev
- Division of Oncology, and
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Bryan Manning
- Division of Hematology and Oncology and
- Abramson Cancer Center, Department of Medicine, and
| | - Katherine D. Cummins
- Division of Hematology and Oncology and
- Abramson Cancer Center, Department of Medicine, and
- Center for Cellular Immunotherapies
| | - Janis K. Burkhardt
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Hematopathology
| | - Alexander E. Perl
- Division of Hematology and Oncology and
- Abramson Cancer Center, Department of Medicine, and
| | - Martin Carroll
- Division of Hematology and Oncology and
- Abramson Cancer Center, Department of Medicine, and
| | - Sarah K. Tasian
- Division of Oncology, and
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, and
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Ryall S, Zapotocky M, Fukuoka K, Nobre L, Guerreiro Stucklin A, Bennett J, Siddaway R, Li C, Pajovic S, Arnoldo A, Kowalski PE, Johnson M, Sheth J, Lassaletta A, Tatevossian RG, Orisme W, Qaddoumi I, Surrey LF, Li MM, Waanders AJ, Gilheeney S, Rosenblum M, Bale T, Tsang DS, Laperriere N, Kulkarni A, Ibrahim GM, Drake J, Dirks P, Taylor MD, Rutka JT, Laughlin S, Shroff M, Shago M, Hazrati LN, D'Arcy C, Ramaswamy V, Bartels U, Huang A, Bouffet E, Karajannis MA, Santi M, Ellison DW, Tabori U, Hawkins C. Integrated Molecular and Clinical Analysis of 1,000 Pediatric Low-Grade Gliomas. Cancer Cell 2020; 37:569-583.e5. [PMID: 32289278 PMCID: PMC7169997 DOI: 10.1016/j.ccell.2020.03.011] [Citation(s) in RCA: 250] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/27/2020] [Accepted: 03/12/2020] [Indexed: 12/28/2022]
Abstract
Pediatric low-grade gliomas (pLGG) are frequently driven by genetic alterations in the RAS-mitogen-activated protein kinase (RAS/MAPK) pathway yet show unexplained variability in their clinical outcome. To address this, we characterized a cohort of >1,000 clinically annotated pLGG. Eighty-four percent of cases harbored a driver alteration, while those without an identified alteration also often exhibited upregulation of the RAS/MAPK pathway. pLGG could be broadly classified based on their alteration type. Rearrangement-driven tumors were diagnosed at a younger age, enriched for WHO grade I histology, infrequently progressed, and rarely resulted in death as compared with SNV-driven tumors. Further sub-classification of clinical-molecular correlates stratified pLGG into risk categories. These data highlight the biological and clinical differences between pLGG subtypes and opens avenues for future treatment refinement.
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Affiliation(s)
- Scott Ryall
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Michal Zapotocky
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Kohei Fukuoka
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Liana Nobre
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ana Guerreiro Stucklin
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Julie Bennett
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Christopher Li
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sanja Pajovic
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Anthony Arnoldo
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paul E Kowalski
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Monique Johnson
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Javal Sheth
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alvaro Lassaletta
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Pediatric Hematology and Oncology, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Ruth G Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wilda Orisme
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ibrahim Qaddoumi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angela J Waanders
- Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Hematology, Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA; Department of Pediatrics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Stephen Gilheeney
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Derek S Tsang
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Normand Laperriere
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Abhaya Kulkarni
- Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Neurosurgery, The Hospital for Sick Children, Toronto ON, Canada
| | - George M Ibrahim
- Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Neurosurgery, The Hospital for Sick Children, Toronto ON, Canada
| | - James Drake
- Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Neurosurgery, The Hospital for Sick Children, Toronto ON, Canada
| | - Peter Dirks
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Neurosurgery, The Hospital for Sick Children, Toronto ON, Canada
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Neurosurgery, The Hospital for Sick Children, Toronto ON, Canada
| | - James T Rutka
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Neurosurgery, The Hospital for Sick Children, Toronto ON, Canada
| | - Suzanne Laughlin
- Department of Radiology, The Hospital for Sick Children, Toronto ON, Canada; Department of Medical Imaging, University of Toronto, Toronto, ON, Canada
| | - Manohar Shroff
- Department of Radiology, The Hospital for Sick Children, Toronto ON, Canada; Department of Medical Imaging, University of Toronto, Toronto, ON, Canada
| | - Mary Shago
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lili-Naz Hazrati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pathology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Colleen D'Arcy
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pathology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Anatomical Pathology, The Alfred Hospital, Prahran, VIC, Australia
| | - Vijay Ramaswamy
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Ute Bartels
- Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Annie Huang
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eric Bouffet
- Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | | | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Uri Tabori
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pathology, The Hospital for Sick Children, Toronto, ON, Canada.
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74
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Lopez-Nunez O, John I, Panasiti RN, Ranganathan S, Santoro L, Grélaud D, Wu T, Buccoliero AM, Casanova M, Alaggio R, Surrey LF. Infantile inflammatory myofibroblastic tumors: clinicopathological and molecular characterization of 12 cases. Mod Pathol 2020; 33:576-590. [PMID: 31690781 DOI: 10.1038/s41379-019-0406-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 12/17/2022]
Abstract
Inflammatory myofibroblastic tumors arising in infants are rare, poorly investigated and mostly reported as isolated cases or as a part of larger series thus, their clinicopathological and molecular features are essentially unknown. Archival files from two large pediatric institutions and a tumor registry were queried for pediatric inflammatory myofibroblastic tumors. Available material from patients ≤12 months of age was reviewed. Additional immunostains (ALK-1, D240, WT1) and ALK-FISH studies were performed as needed. Targeted anchored multiplex PCR with next-generation sequencing was done in all cases. A total of 12 of 131 infantile cases (mean 5.5 months) were identified (M:F of 2:1). Anatomic locations included intestinal/mesenteric (n = 6), head/neck (n = 3), and viscera (n = 3). Half of tumors showed a hypocellular myxoid pattern, perivascular condensation, and prominent vasculature with vague glomeruloid structures present in four of them. The remaining cases exhibited a more cellular pattern with minimal myxoid component. ALK-1 immunohistochemistry was positive in most cases (11/12) with cytoplasmic-diffuse (n = 6), cytoplasmic-granular (n = 2), and dot-like (n = 3) staining patterns. ALK fusion partners identified in five cases included EML4, TPM4, RANBP2, and a novel KLC1. Three inflammatory myofibroblastic tumors showed fusions with other kinases including TFG-ROS1 and novel FN1-ROS1 and RBPMS-NTRK3 rearrangements. Favorable outcome was documented in most cases (10/11) with available follow-up (median 17 months) while three patients were successfully treated with crizotinib. In summary, infantile inflammatory myofibroblastic tumors are rare and can exhibit paucicellular, extensively myxoid/vascular morphology with peculiar immunophenotype mimicking other mesenchymal or vascular lesions. All tumors harbored kinase fusions involving ALK, ROS1, and NTRK3 including three novel fusion partners (KLC1, FN1, and RBPMS, respectively). A favorable response to crizotinib seen in three cases supports its potential use in infants as seen in older patients. Awareness of these unusual morphologic, immunophenotypic, and molecular features is critical for appropriate diagnosis and optimized targeted therapy.
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Affiliation(s)
| | - Ivy John
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,UPMC Presbyterian Shadyside Hospital, Pittsburgh, PA, USA
| | - Ryane N Panasiti
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarangarajan Ranganathan
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Diane Grélaud
- Department of Pathology, University and Regional Laboratories, Region Skåne, Lund, Sweden
| | - Tao Wu
- Department of Pathology, KingMed Diagnostics, Guangzhou, Guangdong, China
| | | | | | - Rita Alaggio
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA. .,University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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75
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Ryall S, Tabori U, Hawkins C. Pediatric low-grade glioma in the era of molecular diagnostics. Acta Neuropathol Commun 2020; 8:30. [PMID: 32164789 PMCID: PMC7066826 DOI: 10.1186/s40478-020-00902-z] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Low grade gliomas are the most frequent brain tumors in children and encompass a spectrum of histologic entities which are currently assigned World Health Organisation grades I and II. They differ substantially from their adult counterparts in both their underlying genetic alterations and in the infrequency with which they transform to higher grade tumors. Nonetheless, children with low grade glioma are a therapeutic challenge due to the heterogeneity in their clinical behavior – in particular, those with incomplete surgical resection often suffer repeat progressions with resultant morbidity and, in some cases, mortality. The identification of up-regulation of the RAS–mitogen-activated protein kinase (RAS/MAPK) pathway as a near universal feature of these tumors has led to the development of targeted therapeutics aimed at improving responses while mitigating patient morbidity. Here, we review how molecular information can help to further define the entities which fall under the umbrella of pediatric-type low-grade glioma. In doing so we discuss the specific molecular drivers of pediatric low grade glioma and how to effectively test for them, review the newest therapeutic agents and their utility in treating this disease, and propose a risk-based stratification system that considers both clinical and molecular parameters to aid clinicians in making treatment decisions.
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76
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Barwe SP, Gopalakrisnapillai A, Mahajan N, Druley TE, Kolb EA, Crowgey EL. Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples. Genomics Inform 2020; 18:e6. [PMID: 32224839 PMCID: PMC7120351 DOI: 10.5808/gi.2020.18.1.e6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023] Open
Abstract
Acute leukemia represents the most common pediatric malignancy comprising diverse subtypes with varying prognosis and treatment outcomes. New and targeted treatment options are warranted for this disease. Patient-derived xenograft (PDX) models are increasingly being used for preclinical testing of novel treatment modalities. A novel approach involving targeted error-corrected RNA sequencing using ArcherDX HemeV2 kit was employed to compare 25 primary pediatric acute leukemia samples and their corresponding PDX samples. A comparison of the primary samples and PDX samples revealed a high concordance between single nucleotide variants and gene fusions whereas other complex structural variants were not as consistent. The presence of gene fusions representing the major driver mutations at similar allelic frequencies in PDX samples compared to primary samples and over multiple passages confirms the utility of PDX models for preclinical drug testing. Characterization and tracking of these novel cryptic fusions and exonal variants in PDX models is critical in assessing response to potential new therapies.
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Affiliation(s)
- Sonali P. Barwe
- Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | | | - Nitin Mahajan
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd E. Druley
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - E. Anders Kolb
- Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Erin L. Crowgey
- Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
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77
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MacFarland SP, Zelley K, Surrey LF, Gallo D, Luo M, Raman P, Wertheim G, Hunger SP, Li MM, Brodeur GM. Pediatric Somatic Tumor Sequencing Identifies Underlying Cancer Predisposition. JCO Precis Oncol 2019; 3. [PMID: 32783018 DOI: 10.1200/po.19.00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The diagnosis of cancer predisposition in pediatric patients with cancer is vital for treatment decisions, surveillance, and management of at-risk family members. Somatic tumor testing can identify potential underlying constitutional variants that confer increased cancer risk. Here, we report the characteristics of constitutional variants identified through tumor testing. MATERIALS AND METHODS Data were abstracted from medical record review of 1,023 patients who received inhouse somatic tumor testing over a 28-month period. Patients were identified for testing using referral criteria developed as a collaboration between genomic diagnostics, pathology, and oncology. Characteristics of patients who underwent constitutional testing, including family history and variant loss of heterozygosity, were tracked. RESULTS From 1,023 patients who underwent somatic tumor sequencing in a 28-month period, 210 variants were identified in 141 patients (13.8%) that were concerning for cancer predisposition syndromes requiring intervention. A total of 73 variants in 41 patients have undergone clinical confirmatory testing thus far. Of these, 26 variants were confirmed to be constitutionally present (35.6%). Among patients tested, 23 (56.1%) of 41 total patients were diagnosed with a cancer predisposition syndrome. CONCLUSION Our data demonstrate that more than one third of variants in tumor somatic sequencing that were concerning for underlying cancer predisposition were constitutionally confirmed. Overall, somatic tumor testing identified potential cancer predisposition syndromes in pediatric patients, and some would not have been identified on the basis of clinical history alone.
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Affiliation(s)
- Suzanne P MacFarland
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Daniel Gallo
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stephen P Hunger
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Garrett M Brodeur
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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78
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Surrey LF, Jain P, Zhang B, Straka J, Zhao X, Harding BN, Resnick AC, Storm PB, Buccoliero AM, Genitori L, Li MM, Waanders AJ, Santi M. Genomic Analysis of Dysembryoplastic Neuroepithelial Tumor Spectrum Reveals a Diversity of Molecular Alterations Dysregulating the MAPK and PI3K/mTOR Pathways. J Neuropathol Exp Neurol 2019; 78:1100-1111. [DOI: 10.1093/jnen/nlz101] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AbstractDysembryoplastic neuroepithelial tumors (DNT) lacking key diagnostic criteria are challenging to diagnose and sometimes fall into the broader category of mixed neuronal-glial tumors (MNGT) or the recently described polymorphous low-grade neuroepithelial tumor of the young (PLNTY). We examined 41 patients with DNT, MNGT, or PLNTY for histologic features, genomic findings, and progression-free survival (PFS). Genomic analysis included sequence and copy number variants and RNA-sequencing. Classic DNT (n = 26) was compared with those with diffuse growth without cortical nodules (n = 15), 6 of which exhibited impressive CD34 staining classifying them as PLNTY. Genomic analysis was complete in 33, with sequence alterations recurrently identified in BRAF, FGFR1, NF1, and PDGFRA, as well as 7 fusion genes involving FGFR2, FGFR1, NTRK2, and BRAF. Genetic alterations did not distinguish between MNGTs, DNTs, or PLNTYs; however, FGFR1 alterations were confined to DNT, and PLNTYs contained BRAF V600E or FGFR2 fusion genes. Analysis of PFS showed no significant difference by histology or genetic alteration; however, numbers were small and follow-up time short. Further molecular characterization of a PLNTY-related gene fusion, FGFR2-CTNNA3, demonstrated oncogenic potential via MAPK/PI3K/mTOR pathway activation. Overall, DNT-MNGT spectrum tumors exhibit diverse genomic alterations, with more than half (19/33) leading to MAPK/PI3K pathway alterations.
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Affiliation(s)
- Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia
| | - Payal Jain
- Perelman School of Medicine, University of Pennsylvania
| | - Bo Zhang
- Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia
| | - Joshua Straka
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Adam C Resnick
- Department of Pediatrics, Feinberg School of Medicine Northwestern University
| | - Phillip B Storm
- Department of Pediatrics, Feinberg School of Medicine Northwestern University
| | - Anna Maria Buccoliero
- Division of Hematology, Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Lorenzo Genitori
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia
| | - Angela J Waanders
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia
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