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Hu Y, He Z, Liu S, Ying W, Chen Y, Zhao M, He M, Wu X, Tang Y, Gu W, Ying M, Wang J, Tao T. Patient-derived rhabdomyosarcoma cells recapitulate the genetic and transcriptomic landscapes of primary tumors. iScience 2024; 27:110862. [PMID: 39319271 PMCID: PMC11417342 DOI: 10.1016/j.isci.2024.110862] [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: 05/13/2024] [Revised: 07/29/2024] [Accepted: 08/29/2024] [Indexed: 09/26/2024] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in childhood and adolescence. The availability of appropriate and well-characterized preclinical models for RMS is limited, posing a challenge for investigating the molecular mechanisms and evaluating new targeted compounds in preclinical settings. Here, we collected 51 RMS specimens (referred to as ZJUCH-RMS cohort) and established 9 patient-derived cells (PDCs) and validated the identity of these cells by the expression of RMS-specific markers. Whole-transcriptome analysis identified high-confidence mutations in ZJUCH-RMS cohort including RAS, TP53, ARID1A, MYOD1, and MYCN. Further studies showed that RMS PDCs retained the genetic alterations and the expression of RMS hallmark and dependency genes in matched primary tumors and acted as valuable tools to assess drug responses and pharmacogenomic interactions. Our study provides unique PDCs that are available for preclinical studies of RMS and further advances the feasibility of RMS PDCs as valuable tools for developing personalized treatments for patients.
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Affiliation(s)
- Yuxiang Hu
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The First Clinical Institute, Zunyi Medical University, Zunyi 563000, China
| | - Ziqi He
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The First Clinical Institute, Zunyi Medical University, Zunyi 563000, China
| | - Shuangai Liu
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The First Clinical Institute, Zunyi Medical University, Zunyi 563000, China
| | - Wenwen Ying
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yifan Chen
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Manli Zhao
- Department of Pathology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Min He
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Xuan Wu
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Yinbing Tang
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Weizhong Gu
- Department of Pathology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Meidan Ying
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Jinhu Wang
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Key Laboratory of Diagnosis and Treatment of Neonatal Diseases of Zhejiang Province, Hangzhou 310052, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Ting Tao
- Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Department of Surgical Oncology, Children’s Hospital Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
- Key Laboratory of Diagnosis and Treatment of Neonatal Diseases of Zhejiang Province, Hangzhou 310052, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
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2
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Nokchan N, Suthapot P, Choochuen P, Khongcharoen N, Hongeng S, Anurathapan U, Surachat K, Sangkhathat S, Thai Pediatric Cancer Atlas Tpca Consortium. Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma. J Pers Med 2024; 14:950. [PMID: 39338204 PMCID: PMC11433071 DOI: 10.3390/jpm14090950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/26/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
Neuroblastoma is the most prevalent solid tumor in early childhood, with a 5-year overall survival rate of 40-60% in high-risk cases. Therefore, the identification of novel biomarkers for the diagnosis, prognosis, and therapy of neuroblastoma is crucial for improving the clinical outcomes of these patients. In this study, we conducted the whole-exome sequencing of 48 freshly frozen tumor samples obtained from the Biobank. Somatic variants were identified and selected using a bioinformatics analysis pipeline. The mutational signatures were determined using the Mutalisk online tool. Cancer driver genes and druggable mutations were predicted using the Cancer Genome Interpreter. The most common mutational signature was single base substitution 5. MUC4, MUC16, and FLG were identified as the most frequently mutated genes. Using the Cancer Genome Interpreter, we identified five recurrent cancer driver mutations spanning MUC16, MUC4, ALK, and CTNND1, with the latter being novel and containing a missense mutation, R439C. We also identified 11 putative actionable mutations including NF1 Q1798*, Q2616*, and S636X, ALK F1174L and R1275Q, SETD2 P10L and Q1829E, BRCA1 R612S, NOTCH1 D1670V, ATR S1372L, and FGFR1 N577K. Our findings provide a comprehensive overview of the novel information relevant to the underlying molecular pathogenesis and therapeutic targets of neuroblastoma.
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Affiliation(s)
- Natakorn Nokchan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Praewa Suthapot
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pongsakorn Choochuen
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Natthapon Khongcharoen
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Usanarat Anurathapan
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Surasak Sangkhathat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
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3
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van der Ham CG, Suurenbroek LC, Kleisman MM, Antić Ž, Lelieveld SH, Yeong M, Westera L, Sonneveld E, Hoogerbrugge PM, van der Velden VHJ, van Leeuwen FN, Kuiper RP. Mutational mechanisms in multiply relapsed pediatric acute lymphoblastic leukemia. Leukemia 2024:10.1038/s41375-024-02403-7. [PMID: 39232206 DOI: 10.1038/s41375-024-02403-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is marked by low mutational load at initial diagnosis, which increases at relapse. To determine which processes are active in (relapsed) ALL and how they behave during disease progression before and after therapy, we performed whole genome sequencing on 97 tumor samples of 29 multiply relapsed ALL patients. Mutational load increased upon relapse in 28 patients and upon every subsequent relapse in 22 patients. In addition to two clock-like mutational processes, we identified UV-like damage, APOBEC activity, reactive oxygen species, thiopurine-associated damage and an unknown therapy component as drivers of mutagenesis. Mutational processes often affected patients over longer time periods, but could also occur in isolated events, suggesting the requirement of additional triggers. Thiopurine exposure was the most prominent source of new mutations in relapse, affecting over half of the studied patients in first and/or later relapse and causing potential relapse-driving mutations in multiple patients. Our data demonstrate that multiple mutational processes frequently act in parallel as prominent secondary drivers with dynamic activity during ALL development and progression.
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Affiliation(s)
| | | | | | - Željko Antić
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Marley Yeong
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Liset Westera
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Peter M Hoogerbrugge
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | | | | | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Department of Genetics, Utrecht University Medical Center, Utrecht University, Utrecht, The Netherlands.
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4
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Li B, Zhao S, Li S, Li C, Liu W, Li L, Cui B, Liu X, Chen H, Zhang J, Ren Y, Liu F, Yang M, Jiang T, Liu Y, Qiu X. Novel molecular subtypes of intracranial germ cell tumors expand therapeutic opportunities. Neuro Oncol 2024; 26:1335-1351. [PMID: 38430549 PMCID: PMC11226877 DOI: 10.1093/neuonc/noae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Indexed: 03/04/2024] Open
Abstract
BACKGROUND Intracranial germ cell tumors (IGCTs) are a rare group of malignancies that are clinically classified as germinomas and nongerminomatous germ cell tumors (NGGCTs). Previous studies have found that somatic mutations involving the mitogen-activated protein kinase/mTOR signaling pathway are common early events. However, a comprehensive genomic understanding of IGCTs is still lacking. METHODS We established a cohort including over 100 IGCTs and conducted genomic and transcriptomic sequencing. RESULTS We identified novel recurrent driver genomic aberrations, including USP28 truncation mutations and high-level copy number amplification of KRAS and CRKL caused by replication of extrachromosomal DNA. Three distinct subtypes associated with unique genomic and clinical profiles were identified with transcriptome analysis: Immune-hot, MYC/E2F, and SHH. Both immune-hot and MYC/E2F were predominantly identified in germinomas and shared similar mutations involving the RAS/MAPK signaling pathway. However, the immune-hot group showed an older disease onset age and a significant immune response. MYC/E2F was characterized by a younger disease onset age and increased genomic instability, with a higher proportion of tumors showing whole-genome doubling. Additionally, the SHH subtype was mostly identified in NGGCTs. CONCLUSIONS Novel genomic aberrations and molecular subtypes were identified in IGCTs. These findings provide molecular basis for the potential introduction of new treatment strategies in this setting.
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Affiliation(s)
- Bo Li
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shouwei Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Liu
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Huiyuan Chen
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing Zhang
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yin Ren
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fei Liu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Jinan, China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoguang Qiu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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5
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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024; 56:281-293. [PMID: 38212634 PMCID: PMC10864188 DOI: 10.1038/s41588-023-01640-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie L Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Todd A Alonzo
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Zugbi S, Aschero R, Ganiewich D, Cancela MB, Winter U, Ottaviani D, Sampor C, Dinardi M, Torbidoni AV, Mena M, Balaguer-Lluna L, Lamas G, Sgroi M, Lagomarsino E, Lubieniecki F, Fandiño A, Radvanyi F, Abramson DH, Podhajcer O, Llera AS, Cafferata EG, Chantada G, Carcaboso AM, Schaiquevich P. Establishment and Comprehensive Characterization of a Novel Preclinical Platform of Metastatic Retinoblastoma for Therapeutic Developments. Invest Ophthalmol Vis Sci 2023; 64:27. [PMID: 38117242 PMCID: PMC10741097 DOI: 10.1167/iovs.64.15.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Purpose Although there have been improvements in the management of metastatic retinoblastoma, most patients do not survive, and all patients suffer from multiple short- and long-term treatment toxicities. Reliable and informative models to assist clinicians are needed. Thus we developed and comprehensively characterized a novel preclinical platform of primary cell cultures and xenograft models of metastatic retinoblastoma to provide insights into the molecular biology underlying metastases and to perform drug screening for the identification of hit candidates with the highest potential for clinical translation. Methods Orbital tumor, bone marrow, cerebrospinal fluid, and lymph node tumor infiltration specimens were obtained from seven patients with metastatic retinoblastoma at diagnosis, disease progression, or relapse. Tumor specimens were engrafted in immunodeficient animals, and primary cell lines were established. Genomic, immunohistochemical/immunocytochemical, and pharmacological analysis were performed. Results We successfully established five primary cell lines: two derived from leptomeningeal, two from orbital, and one from lymph node tumor dissemination. After the intravitreal or intraventricular inoculation of these cells, we established cell-derived xenograft models. Both primary cell lines and xenografts accurately retained the histological and genomic features of the tumors from which they were derived and faithfully recapitulated the dissemination patterns and pharmacological sensitivity observed in the matched patients. Conclusions Ours is an innovative and thoroughly characterized preclinical platform of metastatic retinoblastoma developed for the understanding of tumor biology of this highly aggressive tumor and has the potential to identify drug candidates to treat patients who currently lack effective treatment options.
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Affiliation(s)
- Santiago Zugbi
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Rosario Aschero
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Daiana Ganiewich
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir – Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires, Argentina
| | - María B. Cancela
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Ursula Winter
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Daniela Ottaviani
- Institut Curie; PSL Research University, Centre National de la Recherche Scientifique (CNRS); Equipe Ligue contre le cancer, Paris, France
| | - Claudia Sampor
- Hematology-Oncology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Milagros Dinardi
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Ana V. Torbidoni
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Marcela Mena
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir – Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires, Argentina
| | - Leire Balaguer-Lluna
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Gabriela Lamas
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Mariana Sgroi
- Ophthalmology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Eduardo Lagomarsino
- Pharmacy Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - Adriana Fandiño
- Ophthalmology Service, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
| | - François Radvanyi
- Institut Curie; PSL Research University, Centre National de la Recherche Scientifique (CNRS); Equipe Ligue contre le cancer, Paris, France
| | - David H. Abramson
- Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Osvaldo Podhajcer
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir – Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires, Argentina
| | - Andrea S. Llera
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir – Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires, Argentina
| | - Eduardo G. Cafferata
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir – Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires, Argentina
| | - Guillermo Chantada
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Angel M. Carcaboso
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Paula Schaiquevich
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires, Argentina
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
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7
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Skitchenko R, Modrusan Z, Loboda A, Kopp JB, Winkler CA, Sergushichev A, Gupta N, Stevens C, Daly MJ, Shaw A, Artomov M. CR1 variants contribute to FSGS susceptibility across multiple populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.20.23298462. [PMID: 38076851 PMCID: PMC10705641 DOI: 10.1101/2023.11.20.23298462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a common cause of nephrotic syndrome with an annual incidence in the United States in African-Americans compared to European-Americans of 24 cases and 5 cases per million, respectively. Among glomerular diseases in Europe and Latin-America, FSGS was the second most frequent diagnosis, and in Asia the fifth. We expand previous efforts in understanding genetics of FSGS by performing a case-control study involving ethnically-diverse groups FSGS cases (726) and a pool of controls (13,994), using panel sequencing of approximately 2,500 podocyte-expressed genes. Through rare variant association tests, we replicated known risk genes - KANK1, COL4A4, and APOL1. A novel significant association was observed for the gene encoding complement receptor 1 (CR1). High-risk rare variants in CR1 in the European-American cohort were commonly observed in Latin- and African-Americans. Therefore, a combined rare and common variant analysis was used to replicate the CR1 association in non-European populations. The CR1 risk variant, rs17047661, gives rise to the Sl1/Sl2 (R1601G) allele that was previously associated with protection against cerebral malaria. Pleiotropic effects of rs17047661 may explain the difference in allele frequencies across continental ancestries and suggest a possible role for genetically-driven alterations of adaptive immunity in the pathogenesis of FSGS.
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Affiliation(s)
- Rostislav Skitchenko
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Zora Modrusan
- Research Biology, Genentech Inc., San Francisco, CA, USA
| | - Alexander Loboda
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Centre, St. Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
| | - Jeffrey B. Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Cheryl A. Winkler
- Molecular Genetic Epidemiology Studies Section, National Cancer Institute (NCI), Frederick, Maryland, USA
| | | | | | | | - Mark J. Daly
- Broad Institute, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Andrey Shaw
- Research Biology, Genentech Inc., San Francisco, CA, USA
| | - Mykyta Artomov
- Broad Institute, Cambridge, MA, USA
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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8
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Chen C, Qin N, Wang M, Dong Q, Tithi SS, Hui Y, Chen W, Wu G, Kennetz D, Edmonson MN, Rusch MC, Thrasher A, Easton J, Mulder HL, Song N, Plonski NM, Shelton K, Im C, Ehrhardt MJ, Nichols KE, Leisenring WM, Stratton KL, Howell R, Yasui Y, Bhatia S, Armstrong GT, Ness KK, Hudson MM, Zhang J, Wang H, Srivastava DK, Robison LL, Wang Z. Cancer germline predisposing variants and late mortality from subsequent malignant neoplasms among long-term childhood cancer survivors: a report from the St Jude Lifetime Cohort and the Childhood Cancer Survivor Study. Lancet Oncol 2023; 24:1147-1156. [PMID: 37797633 PMCID: PMC10712938 DOI: 10.1016/s1470-2045(23)00403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Carriers of cancer predisposing variants are at an increased risk of developing subsequent malignant neoplasms among those who have survived childhood cancer. We aimed to investigate whether cancer predisposing variants contribute to the risk of subsequent malignant neoplasm-related late mortality (5 years or more after diagnosis). METHODS In this analysis, data were included from two retrospective cohort studies, St Jude Lifetime Cohort (SJLIFE) and the Childhood Cancer Survivor Study (CCSS), with prospective follow-up of patients who were alive for at least 5 years after diagnosis with childhood cancer (ie, long-term childhood cancer survivors) with corresponding germline whole genome or whole exome sequencing data. Cancer predisposing variants affecting 60 genes associated with well-established autosomal-dominant cancer-predisposition syndromes were characterised. Subsequent malignant neoplasms were graded using the National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE) version 4.03 with modifications. Cause-specific late mortality was based on linkage with the US National Death Index and systematic cohort follow up. Fine-Gray subdistribution hazard models were used to estimate subsequent malignant neoplasm-related late mortality starting from the first biospecimen collection, treating non-subsequent malignant neoplasm-related deaths as a competing risk, adjusting for genetic ancestry, sex, age at diagnosis, and cancer treatment exposures. SJLIFE (NCT00760656) and CCSS (NCT01120353) are registered with ClinicalTrials.gov. FINDINGS 12 469 (6172 male and 6297 female) participants were included, 4402 from the SJLIFE cohort (median follow-up time since collection of the first biospecimen 7·4 years [IQR 3·1-9·4]) and 8067 from the CCSS cohort (median follow-up time since collection of the first biospecimen 12·6 years [2·2-16·6]). 641 (5·1%) of 12 469 participants carried cancer predisposing variants (294 [6·7%] in the SJLIFE cohort and 347 [4·3%] in the CCSS cohort), which were significantly associated with an increased severity of subsequent malignant neoplasms (CTCAE grade ≥4 vs grade <4: odds ratio 2·15, 95% CI 1·18-4·19, p=0·0085). 263 (2·1%) subsequent malignant neoplasm-related deaths (44 [1·0%] in the SJLIFE cohort; and 219 [2·7%] in the CCSS cohort) and 426 (3·4%) other-cause deaths (103 [2·3%] in SJLIFE; and 323 [4·0%] in CCSS) occurred. Cumulative subsequent malignant neoplasm-related mortality at 10 years after the first biospecimen collection in carriers of cancer predisposing variants was 3·7% (95% CI 1·2-8·5) in SJLIFE and 6·9% (4·1-10·7) in CCSS versus 1·5% (1·0-2·1) in SJLIFE and 2·1% (1·7-2·5) in CCSS in non-carriers. Carrying a cancer predisposing variant was associated with an increased risk of subsequent malignant neoplasm-related mortality (SJLIFE: subdistribution hazard ratio 3·40 [95% CI 1·37-8·43]; p=0·0082; CCSS: 3·58 [2·27-5·63]; p<0·0001). INTERPRETATION Identifying participants at increased risk of subsequent malignant neoplasms via genetic counselling and clinical genetic testing for cancer predisposing variants and implementing early personalised cancer surveillance and prevention strategies might reduce the substantial subsequent malignant neoplasm-related mortality burden. FUNDING American Lebanese Syrian Associated Charities and US National Institutes of Health.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mingjuan Wang
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Saima Sultana Tithi
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yawei Hui
- High-Performance Computing Facility, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenan Chen
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dennis Kennetz
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael N Edmonson
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael C Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew Thrasher
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nan Song
- College of Pharmacy, Chungbuk National University, Cheongju, South Korea
| | - Noel-Marie Plonski
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kyla Shelton
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Cindy Im
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Matthew J Ehrhardt
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kim E Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Wendy M Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kayla L Stratton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rebecca Howell
- Department of Radiation Physics, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA; Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deo Kumar Srivastava
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA; Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Skitchenko R, Dinikina Y, Smirnov S, Krapivin M, Smirnova A, Morgacheva D, Artomov M. Case report: Somatic mutations in microtubule dynamics-associated genes in patients with WNT-medulloblastoma tumors. Front Oncol 2023; 12:1085947. [PMID: 36713498 PMCID: PMC9877404 DOI: 10.3389/fonc.2022.1085947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/07/2022] [Indexed: 01/14/2023] Open
Abstract
Medulloblastoma (MB) is the most common pediatric brain tumor which accounts for about 20% of all pediatric brain tumors and 63% of intracranial embryonal tumors. MB is considered to arise from precursor cell populations present during an early brain development. Most cases (~70%) of MB occur at the age of 1-4 and 5-9, but are also infrequently found in adults. Total annual frequency of pediatric tumors is about 5 cases per 1 million children. WNT-subtype of MB is characterized by a high probability of remission, with a long-term survival rate of about 90%. However, in some rare cases there may be increased metastatic activity, which dramatically reduces the likelihood of a favorable outcome. Here we report two cases of MB with a histological pattern consistent with desmoplastic/nodular (DP) and classic MB, and genetically classified as WNT-MB. Both cases showed putative causal somatic protein truncating mutations identified in microtubule-associated genes: ARID2, TUBB4A, and ANK3.
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Affiliation(s)
- Rostislav Skitchenko
- Almazov National Medical Research Centre, St. Petersburg, Russia,Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Yulia Dinikina
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Sergey Smirnov
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Mikhail Krapivin
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Anna Smirnova
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Daria Morgacheva
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Mykyta Artomov
- Almazov National Medical Research Centre, St. Petersburg, Russia,Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia,The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States,Department of Pediatrics, Ohio State University, Columbus, OH, United States,*Correspondence: Mykyta Artomov,
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10
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Brady SW, Roberts KG, Gu Z, Shi L, Pounds S, Pei D, Cheng C, Dai Y, Devidas M, Qu C, Hill AN, Payne-Turner D, Ma X, Iacobucci I, Baviskar P, Wei L, Arunachalam S, Hagiwara K, Liu Y, Flasch DA, Liu Y, Parker M, Chen X, Elsayed AH, Pathak O, Li Y, Fan Y, Michael JR, Rusch M, Wilkinson MR, Foy S, Hedges DJ, Newman S, Zhou X, Wang J, Reilly C, Sioson E, Rice SV, Pastor Loyola V, Wu G, Rampersaud E, Reshmi SC, Gastier-Foster J, Guidry Auvil JM, Gesuwan P, Smith MA, Winick N, Carroll AJ, Heerema NA, Harvey RC, Willman CL, Larsen E, Raetz EA, Borowitz MJ, Wood BL, Carroll WL, Zweidler-McKay PA, Rabin KR, Mattano LA, Maloney KW, Winter SS, Burke MJ, Salzer W, Dunsmore KP, Angiolillo AL, Crews KR, Downing JR, Jeha S, Pui CH, Evans WE, Yang JJ, Relling MV, Gerhard DS, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric acute lymphoblastic leukemia. Nat Genet 2022; 54:1376-1389. [PMID: 36050548 PMCID: PMC9700506 DOI: 10.1038/s41588-022-01159-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL, we find that, despite a generally low mutation burden, ALL cases harbor a median of four putative somatic driver alterations per sample, with 376 putative driver genes identified varying in prevalence across ALL subtypes. Most samples harbor at least one rare gene alteration, including 70 putative cancer driver genes associated with ubiquitination, SUMOylation, noncoding transcripts and other functions. In hyperdiploid B-ALL, chromosomal gains are acquired early and synchronously before ultraviolet-induced mutation. By contrast, ultraviolet-induced mutations precede chromosomal gains in B-ALL cases with intrachromosomal amplification of chromosome 21. We also demonstrate the prognostic significance of genetic alterations within subtypes. Intriguingly, DUX4- and KMT2A-rearranged subtypes separate into CEBPA/FLT3- or NFATC4-expressing subgroups with potential clinical implications. Together, these results deepen understanding of the ALL genomic landscape and associated outcomes.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yunfeng Dai
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ashley N Hill
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pradyuamna Baviskar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sasi Arunachalam
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diane A Flasch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abdelrahman H Elsayed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Omkar Pathak
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J Robert Michael
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark R Wilkinson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dale J Hedges
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Victor Pastor Loyola
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shalini C Reshmi
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Jaime M Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Office of Data Sharing, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malcolm A Smith
- Cancer Therapeutics Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Naomi Winick
- Department of Pediatric Hematology Oncology and Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Richard C Harvey
- Department of Pathology, University of New Mexico Cancer Center, Albuquerque, NM, USA
| | | | - Eric Larsen
- Department of Pediatrics, Maine Children's Cancer Program, Scarborough, ME, USA
| | - Elizabeth A Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Michael J Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - William L Carroll
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | | | - Karen R Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Kelly W Maloney
- Department of Pediatrics and Children's Hospital Colorado, University of Colorado, Aurora, CO, USA
| | - Stuart S Winter
- Children's Minnesota Research Institute and Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Michael J Burke
- Division of Pediatric Hematology-Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wanda Salzer
- Uniformed Services University, School of Medicine, Bethesda, MD, USA
| | | | | | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Li J, Miao B, Wang S, Dong W, Xu H, Si C, Wang W, Duan S, Lou J, Bao Z, Zeng H, Yang Z, Cheng W, Zhao F, Zeng J, Liu XS, Wu R, Shen Y, Chen Z, Chen S, Wang M. Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization. Brief Bioinform 2022; 23:6620876. [PMID: 35788820 DOI: 10.1093/bib/bbac261] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/18/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud- and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multi-user plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.
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Affiliation(s)
- Jianfeng Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Benben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Shixiang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Dong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Houshi Xu
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenchen Si
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wang
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Songqi Duan
- College of Food Science, Sichuan Agricultural University, Yaan, China
| | - Jiacheng Lou
- Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhiwei Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hailuan Zeng
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan Institute for Metabolic Diseases, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Zengzeng Yang
- Qinghai Academy of Animal and Veterinary Science, State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland Qinghai University, Xining, China
| | - Wenyan Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jianming Zeng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Renxie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yang Shen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingjie Wang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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Xie R, Wu J, Shang B, Cao C, Bi X, Shi H, Shou J, Guan Y. Transmembrane Transporter Sema3D Serves as a Tumor Suppressor in Localized Clear Cell Renal Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:3204189. [PMID: 35813868 PMCID: PMC9262505 DOI: 10.1155/2022/3204189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Background The transmembrane transporter Sema3D is a vital molecule involved in axon guidance and carcinogenesis of variant malignancies. However, the relationship between Sema3D and clear cell renal cell carcinoma (ccRCC) is barely reported and remains unclear. Methods Sema3D expression and the connection of clinical and histological characteristics were first analyzed with transcriptome data in the TCGA repository. We then located and examined the Sema3D expression in ccRCC patients by using immunofluorescence staining in the tissue microarray. The prognostic value of Sema3D in localized ccRCC was evaluated by Cox proportional hazard analysis. Functional and gene set enrichment analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to describe the potential mechanisms of Sema3D in ccRCC. Correlation analysis between Sema3D and tumor-infiltrating lymphocytes was calculated by ssGSEA. Results In 86 ccRCC patients, Sema3D mRNA and protein expression were downregulated in tumor tissues than the para-tumor tissues, and Sema3D was dominantly expressed in the extracellular space. Low expression of Sema3D was associated with advanced tumor stage, advanced histological grade, and poor prognosis in ccRCC. In the subgroup analysis of 81 localized ccRCC patients, Sema3D expression level was an independent protective prognostic factor for overall survival (OS) (HR = 0.125, p=0.043). Coagulation, complement, estrogen response, and KRAS signaling hallmark gene sets were identified as Sema3D-related signaling pathways. The expression level of Sema3D was significantly correlated with a high abundance of several immune cells (neutrophils, eosinophils, and T helper cells). Conclusions Transmembrane transporter Sema3D is an efficient prognostic biomarker for localized ccRCC patients, by playing the role of tumor suppressor in ccRCC. Sema3D can be a novel therapeutic target for ccRCC.
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Affiliation(s)
- Ruiyang Xie
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Jie Wu
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Bingqing Shang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Chuanzhen Cao
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Xingang Bi
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Hongzhe Shi
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Jianzhong Shou
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
| | - Youyan Guan
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Chaoyang District, Beijing, China
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13
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Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:194-207. [PMID: 35176137 PMCID: PMC9780084 DOI: 10.1158/2643-3230.bcd-21-0160] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 08/27/2021] [Accepted: 01/24/2022] [Indexed: 01/21/2023] Open
Abstract
The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML. SIGNIFICANCE We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Benjamin J. Huang
- Department of Pediatrics, University of California, Benioff Children's Hospital, San Francisco, California
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juan M. Barajas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Melvin E. Thomas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott G. Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew B. Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Bengsheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jenny L. Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan Parganas
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan Miller
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Todd A. Alonzo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James R. Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M. Madan Babu
- Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
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14
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Drosos Y, Myers JA, Xu B, Mathias KM, Beane EC, Radko-Juettner S, Mobley RJ, Larsen ME, Piccioni F, Ma X, Low J, Hansen BS, Peters ST, Bhanu NV, Dhanda SK, Chen T, Upadhyaya SA, Pruett-Miller SM, Root DE, Garcia BA, Partridge JF, Roberts CW. NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition. Mol Cell 2022; 82:2472-2489.e8. [DOI: 10.1016/j.molcel.2022.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
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15
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Distinct genomic landscape of Chinese pediatric acute myeloid leukemia impacts clinical risk classification. Nat Commun 2022; 13:1640. [PMID: 35347147 PMCID: PMC8960760 DOI: 10.1038/s41467-022-29336-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
Studies have revealed key genomic aberrations in pediatric acute myeloid leukemia (AML) based on Western populations. It is unknown to what extent the current genomic findings represent populations with different ethnic backgrounds. Here we present the genomic landscape of driver alterations of Chinese pediatric AML and discover previously undescribed genomic aberrations, including the XPO1-TNRC18 fusion. Comprehensively comparing between the Chinese and Western AML cohorts reveal a substantially distinct genomic alteration profile. For example, Chinese AML patients more commonly exhibit mutations in KIT and CSF3R, and less frequently mutated of genes in the RAS signaling pathway. These differences in mutation frequencies lead to the detection of previously uncharacterized co-occurring mutation pairs. Importantly, the distinct driver profile is clinical relevant. We propose a refined prognosis risk classification model which better reflected the adverse event risk for Chinese AML patients. These results emphasize the importance of genetic background in precision medicine. The genomic landscape of pediatric acute myeloid leukemia (AML) has mostly been characterised for Western populations. Here, the authors identify potential driver alterations in Chinese pediatric AML, which differ from Western populations, and propose a prognostic risk classification model.
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16
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Gómez-Flores-Ramos L, Barraza-Arellano AL, Mohar A, Trujillo-Martínez M, Grimaldo L, Ortiz-Lopez R, Treviño V. Germline Variants in Cancer Genes from Young Breast Cancer Mexican Patients. Cancers (Basel) 2022; 14:cancers14071647. [PMID: 35406420 PMCID: PMC8997148 DOI: 10.3390/cancers14071647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is one of the most frequent cancer types in women worldwide. About 7% is diagnosed in young women (YBC) less than 40 years old. In Mexico, however, YBC reaches 15% suggesting a higher genetic susceptibility. There have been some reports of germline variants in YBC across the world. However, there is only one report from a Mexican population, which is not restricted by age and limited to a panel of 143 genes resulting in 15% of patients carrying putatively pathogenic variants. Nevertheless, expanding the analysis to whole exome involves using more complex tools to determine which genes and variants could be pathogenic. We used germline whole exome sequencing combined with the PeCanPie tool to analyze exome variants in 115 YBC patients. Our results showed that we were able to identify 49 high likely pathogenic variants involving 40 genes on 34% of patients. We noted many genes already reported in BC and YBC worldwide, such as BRCA1, BRCA2, ATM, CHEK2, PALB2, and POLQ, but also others not commonly reported in YBC in Latin America, such as CLTCL1, DDX3X, ERCC6, FANCE, and NFKBIE. We show further supporting and controversial evidence for some of these genes. We conclude that exome sequencing combined with robust annotation tools and further analysis, can identify more genes and more patients affected by germline mutations in cancer.
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Affiliation(s)
- Liliana Gómez-Flores-Ramos
- CONACYT/Center for Population Health Research, National Institute of Public Health, Universidad No. 655, Cuernavaca 62100, Morelos, Mexico; (L.G.-F.-R.); (L.G.)
| | - Angélica Leticia Barraza-Arellano
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
| | - Alejandro Mohar
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Dirección de Investigación, Instituto Nacional de Cancerología, Av. San Fernando #22, Col. Sección XVI, Delegación Tlalpan, Mexico City 14080, Mexico;
| | - Miguel Trujillo-Martínez
- Instituto Mexicano del Seguro Social, Hospital General de Zona con Medicina Familiar No. 7, Cuautla 62780, Morelos, Mexico;
| | - Lizbeth Grimaldo
- CONACYT/Center for Population Health Research, National Institute of Public Health, Universidad No. 655, Cuernavaca 62100, Morelos, Mexico; (L.G.-F.-R.); (L.G.)
| | - Rocío Ortiz-Lopez
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
- The Institute for Obesity Research, Tecnologico de Monterrey, Eugenio Garza Sada Av 2501, Monterrey 64849, Nuevo Leon, Mexico
| | - Víctor Treviño
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
- The Institute for Obesity Research, Tecnologico de Monterrey, Eugenio Garza Sada Av 2501, Monterrey 64849, Nuevo Leon, Mexico
- Correspondence:
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17
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Immunotherapy for SMARCB1-Deficient Sarcomas: Current Evidence and Future Developments. Biomedicines 2022; 10:biomedicines10030650. [PMID: 35327458 PMCID: PMC8945563 DOI: 10.3390/biomedicines10030650] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
Mutations in subunits of the SWItch Sucrose Non-Fermentable (SWI/SNF) complex occur in 20% of all human tumors. Among these, the core subunit SMARCB1 is the most frequently mutated, and SMARCB1 loss represents a founder driver event in several malignancies, such as malignant rhabdoid tumors (MRT), epithelioid sarcoma, poorly differentiated chordoma, and renal medullary carcinoma (RMC). Intriguingly, SMARCB1-deficient pediatric MRT and RMC have recently been reported to be immunogenic, despite their very simple genome and low tumor mutational burden. Responses to immune checkpoint inhibitors have further been reported in some SMARCB1-deficient diseases. Here, we will review the preclinical data and clinical data that suggest that immunotherapy, including immune checkpoint inhibitors, may represent a promising therapeutic strategy for SMARCB1-defective tumors. We notably discuss the heterogeneity that exists among the spectrum of malignancies driven by SMARCB1-loss, and highlight challenges that are at stake for developing a personalized immunotherapy for these tumors, notably using molecular profiling of the tumor and of its microenvironment.
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18
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Chang TC, Xu K, Cheng Z, Wu G. Somatic and Germline Variant Calling from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:37-54. [DOI: 10.1007/978-3-030-91836-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Zhu H, Dong B, Zhang Y, Wang M, Rao J, Cui B, Liu Y, Jiang Q, Wang W, Yang L, Yu A, Li Z, Liu C, Zhang L, Huang X, Zhu X, Wu H. Integrated genomic analyses identify high-risk factors and actionable targets in T-cell acute lymphoblastic leukemia. BLOOD SCIENCE 2022; 4:16-28. [PMID: 35399540 PMCID: PMC8974951 DOI: 10.1097/bs9.0000000000000102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy often associated with poor outcomes. To identify high-risk factors and potential actionable targets for T-ALL, we perform integrated genomic and transcriptomic analyses on samples from 165 Chinese pediatric and adult T-ALL patients, of whom 85% have outcome information. The genomic mutation landscape of this Chinese cohort is very similar to the Western cohort published previously, except that the rate of NOTCH1 mutations is significant lower in the Chinese T-ALL patients. Among 47 recurrently mutated genes in 7 functional categories, we identify RAS pathway and PTEN mutations as poor survival factors for non-TAL and TAL subtypes, respectively. Mutations in the PI3K pathway are mutually exclusive with mutations in the RAS and NOTCH1 pathways as well as transcription factors. Further analysis demonstrates that approximately 43% of the high-risk patients harbor at least one potential actionable alteration identified in this study, and T-ALLs with RAS pathway mutations are hypersensitive to MEKi in vitro and in vivo. Thus, our integrated genomic analyses not only systematically identify high-risk factors but suggest that these high-risk factors are promising targets for T-ALL therapies.
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Affiliation(s)
- Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Current address: Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Hubei 430081, China
| | - Bingjie Dong
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mei Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
| | - Qian Jiang
- Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Weitao Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Anqi Yu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zongru Li
- Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Chao Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Leping Zhang
- Department of Pediatrics, Peking University People's Hospital, Beijing 100044, China
| | - Xiaojun Huang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
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20
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Diffuse leptomeningeal glioneuronal tumour (DLGNT) in children: the emerging role of genomic analysis. Acta Neuropathol Commun 2021; 9:147. [PMID: 34493325 PMCID: PMC8422739 DOI: 10.1186/s40478-021-01248-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 11/10/2022] Open
Abstract
Diffuse leptomeningeal glioneuronal tumours (DLGNT) represent rare enigmatic CNS tumours of childhood. Most patients with this disease share common radiological and histopathological features but the clinical course of this disease is variable. A radiological hallmark of this disease is widespread leptomeningeal enhancement that may involve the entire neuroaxis with predilection for the posterior fossa and spine. The classic pathologic features include low- to moderate-density cellular lesions with OLIG2 expression and evidence of ‘oligodendroglioma-like’ appearance. The MAPK/ERK signaling pathway has recently been reported as a potential driver of tumourigenesis in up to 80% of DLGNT with KIAA1549:BRAF fusions being the most common event seen. Until now, limited analysis of the biological drivers of tumourigenesis has been undertaken via targeted profiling, chromosomal analysis and immunohistochemistry. Our study represents the first examples of comprehensive genomic sequencing in DLGNT and shows that it is not only feasible but crucial to our understanding of this rare disease. Moreover, we demonstrate that DLGNT may be more genomically complex than single-event MAPK/ERK signaling pathway tumours.
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21
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Newman S, Nakitandwe J, Kesserwan CA, Azzato EM, Wheeler DA, Rusch M, Shurtleff S, Hedges DJ, Hamilton KV, Foy SG, Edmonson MN, Thrasher A, Bahrami A, Orr BA, Klco JM, Gu J, Harrison LW, Wang L, Clay MR, Ouma A, Silkov A, Liu Y, Zhang Z, Liu Y, Brady SW, Zhou X, Chang TC, Pande M, Davis E, Becksfort J, Patel A, Wilkinson MR, Rahbarinia D, Kubal M, Maciaszek JL, Pastor V, Knight J, Gout AM, Wang J, Gu Z, Mullighan CG, McGee RB, Quinn EA, Nuccio R, Mostafavi R, Gerhardt EL, Taylor LM, Valdez JM, Hines-Dowell SJ, Pappo AS, Robinson G, Johnson LM, Pui CH, Ellison DW, Downing JR, Zhang J, Nichols KE. Genomes for Kids: The scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing. Cancer Discov 2021; 11:3008-3027. [PMID: 34301788 DOI: 10.1158/2159-8290.cd-20-1631] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022]
Abstract
Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole genome (WGS), exome, and RNA sequencing, to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically-relevant (25%), and/or cancer predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors) and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers.
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Affiliation(s)
- Scott Newman
- Computational Biology, St. Jude Children's Research Hospital
| | - Joy Nakitandwe
- Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | | | | | | | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | - Dale J Hedges
- Computational Biology, St. Jude Children's Research Hospital
| | - Kayla V Hamilton
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Scott G Foy
- Computational Biology, St. Jude Children's Research Hospital
| | | | - Andrew Thrasher
- Computational Biology, St. Jude Children's Research Hospital
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital
| | - Brent A Orr
- Pathology, St. Jude Children's Research Hospital
| | | | - Jiali Gu
- Department of Pathology, St. Jude Children's Research Hospital
| | - Lynn W Harrison
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Lu Wang
- Pathology, St. Jude Children's Research Hospital
| | | | - Annastasia Ouma
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Antonina Silkov
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | | | - Yu Liu
- Computational Biology, St. Jude Children's Research Hospital
| | - Samuel W Brady
- Computational Biology, St. Jude Children's Research Hospital
| | - Xin Zhou
- St. Jude Children's Research Hospital
| | - Ti-Cheng Chang
- Computational Biology, St. Jude Children's Research Hospital
| | - Manjusha Pande
- Department of Computational Biology, St. Jude Children's Research Hospital
| | - Eric Davis
- Department of Computational Biology, St. Jude Children's Research Hospital
| | - Jared Becksfort
- Computational Biology, St. Jude Children's Research Hospital
| | - Aman Patel
- Computational Biology, St. Jude Children's Research Hospital
| | | | | | - Manish Kubal
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | | | - Jay Knight
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | | | | | - Emily A Quinn
- Pharmacy and Health Sciences, Keck Graduate Institute
| | - Regina Nuccio
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | - Elsie L Gerhardt
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Leslie M Taylor
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | | | | | | | - Liza-Marie Johnson
- Division of Quality of Life and Palliative Care, St. Jude Children's Research Hospital
| | | | | | | | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital
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22
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Gout AM, Arunachalam S, Finkelstein DB, Zhang J. Data-driven approaches to advance research and clinical care for pediatric cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188571. [PMID: 34051287 DOI: 10.1016/j.bbcan.2021.188571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022]
Abstract
Pediatric cancer is a rare disease with a distinct etiology and mutational landscape compared with adult cancer. Multi-omics profiling of retrospective and prospective cohorts coupled with innovative computational analysis have been instrumental in uncovering mechanisms of tumorigenesis and drug resistance that are now informing pediatric cancer clinical therapy. In this review we present the major data resources of pediatric cancer and actionable insights into pediatric cancer etiology stemming from the identification of oncogenic gene fusions, mutational signature analysis, systems biology, cancer predisposition and survivorship studies - that have led to improved clinical diagnosis, discovery of new drug-targets, pharmacological therapy, and screening for genetic predisposition. Ultimately, integration of large-scale omics datasets generated through international collaboration is required to maximize the power of data-driven approaches to advance pediatric cancer research informing clinical therapy.
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Affiliation(s)
- Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sasi Arunachalam
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David B Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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23
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McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, Macias M, Birch K, Finkelstein D, Sunny J, Mudunuri R, Orr BA, Treadway M, Davidson B, Ard TK, Chiao A, Swistak A, Wiggins S, Foy S, Wang J, Sioson E, Wang S, Michael JR, Liu Y, Ma X, Patel A, Edmonson MN, Wilkinson MR, Frantz AM, Chang TC, Tian L, Lei S, Islam SMA, Meyer C, Thangaraj N, Tater P, Kandali V, Ma S, Nguyen T, Serang O, McGuire I, Robison N, Gentry D, Tang X, Palmer LE, Wu G, Suh E, Tanner L, McMurry J, Lear M, Pappo AS, Wang Z, Wilson CL, Cheng Y, Meshinchi S, Alexandrov LB, Weiss MJ, Armstrong GT, Robison LL, Yasui Y, Nichols KE, Ellison DW, Bangur C, Mullighan CG, Baker SJ, Dyer MA, Miller G, Newman S, Rusch M, Daly R, Perry K, Downing JR, Zhang J. St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem. Cancer Discov 2021; 11:1082-1099. [PMID: 33408242 DOI: 10.1158/2159-8290.cd-20-1230] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Effective data sharing is key to accelerating research to improve diagnostic precision, treatment efficacy, and long-term survival in pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a cloud-based data-sharing ecosystem for accessing, analyzing, and visualizing genomic data from >10,000 pediatric patients with cancer and long-term survivors, and >800 pediatric sickle cell patients. Harmonized genomic data totaling 1.25 petabytes are freely available, including 12,104 whole genomes, 7,697 whole exomes, and 2,202 transcriptomes. The resource is expanding rapidly, with regular data uploads from St. Jude's prospective clinical genomics programs. Three interconnected apps within the ecosystem-Genomics Platform, Pediatric Cancer Knowledgebase, and Visualization Community-enable simultaneously performing advanced data analysis in the cloud and enhancing the Pediatric Cancer knowledgebase. We demonstrate the value of the ecosystem through use cases that classify 135 pediatric cancer subtypes by gene expression profiling and map mutational signatures across 35 pediatric cancer subtypes. SIGNIFICANCE: To advance research and treatment of pediatric cancer, we developed St. Jude Cloud, a data-sharing ecosystem for accessing >1.2 petabytes of raw genomic data from >10,000 pediatric patients and survivors, innovative analysis workflows, integrative multiomics visualizations, and a knowledgebase of published data contributed by the global pediatric cancer community.This article is highlighted in the In This Issue feature, p. 995.
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Affiliation(s)
- Clay McLeod
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew Thrasher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Macias
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kirby Birch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jobin Sunny
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rahul Mudunuri
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Madison Treadway
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Arthur Chiao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew Swistak
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephanie Wiggins
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shuoguo Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - J Robert Michael
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Aman Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mark R Wilkinson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew M Frantz
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ti-Cheng Chang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shaohua Lei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | | | | | | | | | | | | | | | - Irina McGuire
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nedra Robison
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Darrell Gentry
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xing Tang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lance E Palmer
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ed Suh
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Leigh Tanner
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - James McMurry
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Matthew Lear
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alberto S Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center Professor of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Keith Perry
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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24
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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25
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Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics 2020; 36:1382-1390. [PMID: 31593214 DOI: 10.1093/bioinformatics/btz753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Reliable identification of expressed somatic insertions/deletions (indels) is an unmet need due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor transcriptome. RESULTS We present RNAIndel, a tool for predicting somatic, germline and artifact indels from tumor RNA-Seq data. RNAIndel leverages features derived from indel sequence context and biological effect in a machine-learning framework. Except for tumor samples with microsatellite instability, RNAIndel robustly predicts 88-100% of somatic indels in five diverse test datasets of pediatric and adult cancers, even recovering subclonal (VAF range 0.01-0.15) driver indels missed by targeted deep-sequencing, outperforming the current best-practice for RNA-Seq variant calling which had 57% sensitivity but with 14 times more false positives. AVAILABILITY AND IMPLEMENTATION RNAIndel is freely available at https://github.com/stjude/RNAIndel. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kohei Hagiwara
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael N Edmonson
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen V Rice
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott Newman
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Juncheng Dai
- Department of Epidemiology, Nanjing Medical University School of Public Health, Jiangning District, Nanjing, 211166, People's Republic of China
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Michael Rusch
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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26
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Pre-Existing Tumoral B Cell Infiltration and Impaired Genome Maintenance Correlate with Response to Chemoradiotherapy in Locally Advanced Rectal Cancer. Cancers (Basel) 2020; 12:cancers12082227. [PMID: 32784964 PMCID: PMC7464257 DOI: 10.3390/cancers12082227] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Locally advanced rectal cancer (LARC) remains a medical challenge. Reliable biomarkers to predict which patients will significantly respond to neoadjuvant chemoradiotherapy (nCRT) have not been identified. We evaluated baseline genomic and transcriptomic features to detect differences that may help predict response to nCRT. Eligible LARC patients received nCRT (3D-LCRT 50.4 Gy plus capecitabine 825 mg/m2/bid), preceded by three cycles of CAPOX in high systemic-relapse risk tumors, and subsequent surgery. Frozen tumor biopsies at diagnosis were sequenced using a colorectal cancer panel. Transcriptomic data was used for pathway and cell deconvolution inferential algorithms, coupled with immunohistochemical validation. Clinical and molecular data were analyzed according to nCRT outcome. Pathways related to DNA repair and proliferation (p < 0.005), and co-occurrence of RAS and TP53 mutations (p = 0.001) were associated with poor response. Enrichment of expression signatures related to enhanced immune response, particularly B cells and interferon signaling (p < 0.005), was detected in good responders. Immunohistochemical analysis of CD20+ cells validated the association of good response with B cell infiltration (p = 0.047). Findings indicate that the presence of B cells is associated with successful tumor regression following nCRT in LARC. The prevalence of simultaneous RAS and TP53 mutations along with a proficient DNA repair system that may counteract chemoradio-induced DNA damage was associated with poor response.
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27
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Wojcicki AV, Kasowski MM, Sakamoto KM, Lacayo N. Metabolomics in acute myeloid leukemia. Mol Genet Metab 2020; 130:230-238. [PMID: 32457018 DOI: 10.1016/j.ymgme.2020.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022]
Abstract
Acute myeloid leukemia (AML) is a complex, heterogenous hematological malignancy caused by mutations in myeloid differentiation and proliferation. Response to therapy and long-term outcomes vary widely based on chromosomal and molecular aberrations. Many platforms have been used to characterize and stratify AML. Metabolomics, the global profiling of small molecules in a biological sample, has emerged in the last decade as an important tool for studying the metabolic dependency of cancer cells. Metabolic reprogramming is not only an important manifestation of AML but clinically relevant for diagnosis, risk stratification and targeted drug development. In this review, we discuss notable metabolic studies of the last decade and their application to novel therapies.
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Affiliation(s)
- Anna V Wojcicki
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Maya M Kasowski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathleen M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Norman Lacayo
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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28
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Alsultan A, Essa M, Aljefri A, Ayas M, Alharbi M, Alkhayat N, Al-Anzi F, Yassin F, Alkasim F, Alharbi Q, Abdullah S, Jastaniah W. Frequency of pathogenic/likely pathogenic germline variants in cancer-related genes among children with acute leukemia in Saudi Arabia. Pediatr Blood Cancer 2020; 67:e28340. [PMID: 32359129 DOI: 10.1002/pbc.28340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND The frequency of pathogenic/likely pathogenic (P/LP) germline mutations in cancer-related genes among children with cancer in highly consanguineous populations is not well studied. METHODS Whole-exome sequencing of germline DNA was performed in 60 children with acute leukemia. We used the St. Jude Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) data portal for the classification of germline variants by the St. Jude Medal Ceremony pipeline. RESULTS Fifty-seven patients had acute lymphoblastic leukemia (ALL) and three patients had acute myeloid leukemia. Parental consanguinity was present in 27 (45%) patients. All patients were of Arab ancestry. Three patients (5%) had a history of cancer in their siblings. Five patients (8.3%) had P/LP germline mutations in cancer-related genes. Three patients with B-ALL had heterozygous pathogenic mutations in TP53, BRCA1, and BRCA2; one patient with B-ALL had homozygous pathogenic mutation in PMS2; and one patient with T-ALL had LP homozygous mutation in AK2 that was associated with reticular dysgenesis. Among patients who had history of parental consanguinity, three (11%) had P/LP germline mutations compared with two (8%) in the absence of parental consanguinity. Fourteen (23%) patients had gold medal variants in cancer-related genes, 13 were heterozygous, and one was homozygous. Silver medal variants were present in 35 (58%) patients; all were heterozygous except one homozygous. CONCLUSIONS Children with acute leukemia in Saudi Arabia had low frequency of P/LP mutations in cancer-related genes despite the high rate of consanguinity. Larger studies using whole-genome sequencing are needed to further explore the heritability of childhood leukemia.
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Affiliation(s)
- Abdulrahman Alsultan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Essa
- Department of Pediatric Hematology/Oncology, King Abdullah Specialist Children's Hospital, Riyadh, Saudi Arabia.,College of Medicine, Ministry of National Guard Health Affairs, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdullah Aljefri
- Department of Pediatric Hematology/Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mouhab Ayas
- Department of Pediatric Hematology/Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Musa Alharbi
- Department of Pediatric Hematology/Oncology, Cancer Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Nawaf Alkhayat
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Faisal Al-Anzi
- Prince Faisal Bin Bandar Cancer Center, Qassim, Saudi Arabia
| | - Fawwaz Yassin
- Department of Pediatric Hematology/Oncology, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | | | - Qasim Alharbi
- Department of Pediatric Hematology/Oncology, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Shaker Abdullah
- Department of Oncology, Princess Noorah Oncology Center, King Saud Bin Abdulaziz University and King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Wasil Jastaniah
- Department of Oncology, Princess Noorah Oncology Center, King Saud Bin Abdulaziz University and King Abdulaziz Medical City, Jeddah, Saudi Arabia.,Department of Pediatrics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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