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Valent P, Orfao A, Kubicek S, Staber P, Haferlach T, Deininger M, Kollmann K, Lion T, Virgolini I, Winter G, Hantschel O, Kenner L, Zuber J, Grebien F, Moriggl R, Hoermann G, Hermine O, Andreeff M, Bock C, Mughal T, Constantinescu SN, Kralovics R, Sexl V, Skoda R, Superti-Furga G, Jäger U. Precision Medicine in Hematology 2021: Definitions, Tools, Perspectives, and Open Questions. Hemasphere 2021; 5:e536. [PMID: 33623882 PMCID: PMC7892291 DOI: 10.1097/hs9.0000000000000536] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
During the past few years, our understanding of molecular mechanisms and cellular interactions relevant to malignant blood cell disorders has improved substantially. New insights include a detailed knowledge about disease-initiating exogenous factors, endogenous (genetic, somatic, epigenetic) elicitors or facilitators of disease evolution, and drug actions and interactions that underlie efficacy and adverse event profiles in defined cohorts of patients. As a result, precision medicine and personalized medicine are rapidly growing new disciplines that support the clinician in making the correct diagnosis, in predicting outcomes, and in optimally selecting patients for interventional therapies. In addition, precision medicine tools are greatly facilitating the development of new drugs, therapeutic approaches, and new multiparametric prognostic scoring models. However, although the emerging roles of precision medicine and personalized medicine in hematology and oncology are clearly visible, several questions remain. For example, it remains unknown how precision medicine tools can be implemented in healthcare systems and whether all possible approaches are also affordable. In addition, there is a need to define terminologies and to relate these to specific and context-related tools and strategies in basic and applied science. To discuss these issues, a working conference was organized in September 2019. The outcomes of this conference are summarized herein and include a proposal for definitions, terminologies, and applications of precision and personalized medicine concepts and tools in hematologic neoplasms. We also provide proposals aimed at reducing costs, thereby making these applications affordable in daily practice.
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Affiliation(s)
- Peter Valent
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
| | - Alberto Orfao
- Servicio Central de Citometria, Centro de Investigacion del Cancer (IBMCC; CSIC/USAL), IBSAL, CIBERONC and Department of Medicine, University of Salamanca, Spain
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Staber
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
| | | | - Michael Deininger
- Division of Hematology and Hematologic Malignancies, University of Utah, Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Karoline Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Thomas Lion
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
- Children’s Cancer Research Institute, Vienna, Austria
| | - Irene Virgolini
- Department of Nuclear Medicine, Medical University of Innsbruck, Austria
| | - Georg Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Oliver Hantschel
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps-University of Marburg, Germany
| | - Lukas Kenner
- Pathology of Laboratory Animals, University of Veterinary Medicine, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, Unit for Functional Cancer Genomics, University of Veterinary Medicine Vienna, Austria
| | - Gregor Hoermann
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - Olivier Hermine
- Imagine Institute Université Paris Descartes, Sorbonne, Paris Cité, Paris, France
- Department of Hematology, Necker Hospital, Paris, France
| | - Michael Andreeff
- University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tariq Mughal
- Division of Hematology & Oncology, Tufts University Medical Center, Boston, Massachusetts, USA
| | - Stefan N. Constantinescu
- de Duve Institute and Ludwig Cancer Research Brussels, Université catholique de Louvain, Brussels, Belgium
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Austria
| | - Radek Skoda
- Departement of Biomedicine, University of Basel, Switzerland
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ulrich Jäger
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
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352
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A geospatiotemporal and causal inference epidemiological exploration of substance and cannabinoid exposure as drivers of rising US pediatric cancer rates. BMC Cancer 2021; 21:197. [PMID: 33632159 PMCID: PMC7908679 DOI: 10.1186/s12885-021-07924-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Age-adjusted US total pediatric cancer incidence rates (TPCIR) rose 49% 1975-2015 for unknown reasons. Prenatal cannabis exposure has been linked with several pediatric cancers which together comprise the majority of pediatric cancer types. We investigated whether cannabis use was related spatiotemporally and causally to TPCIR. METHODS State-based age-adjusted TPCIR data was taken from the CDC Surveillance, Epidemiology and End Results cancer database 2003-2017. Drug exposure was taken from the nationally-representative National Survey of Drug Use and Health, response rate 74.1%. Drugs included were: tobacco, alcohol, cannabis, opioid analgesics and cocaine. This was supplemented by cannabinoid concentration data from the Drug Enforcement Agency and ethnicity and median household income data from US Census. RESULTS TPCIR rose while all drug use nationally fell, except for cannabis which rose. TPCIR in the highest cannabis use quintile was greater than in the lowest (β-estimate = 1.31 (95%C.I. 0.82, 1.80), P = 1.80 × 10- 7) and the time:highest two quintiles interaction was significant (β-estimate = 0.1395 (0.82, 1.80), P = 1.00 × 10- 14). In robust inverse probability weighted additive regression models cannabis was independently associated with TPCIR (β-estimate = 9.55 (3.95, 15.15), P = 0.0016). In interactive geospatiotemporal models including all drug, ethnic and income variables cannabis use was independently significant (β-estimate = 45.67 (18.77, 72.56), P = 0.0009). In geospatial models temporally lagged to 1,2,4 and 6 years interactive terms including cannabis were significant. Cannabis interactive terms at one and two degrees of spatial lagging were significant (from β-estimate = 3954.04 (1565.01, 6343.09), P = 0.0012). The interaction between the cannabinoids THC and cannabigerol was significant at zero, 2 and 6 years lag (from β-estimate = 46.22 (30.06, 62.38), P = 2.10 × 10- 8). Cannabis legalization was associated with higher TPCIR (β-estimate = 1.51 (0.68, 2.35), P = 0.0004) and cannabis-liberal regimes were associated with higher time:TPCIR interaction (β-estimate = 1.87 × 10- 4, (2.9 × 10- 5, 2.45 × 10- 4), P = 0.0208). 33/56 minimum e-Values were > 5 and 6 were infinite. CONCLUSION Data confirm a close relationship across space and lagged time between cannabis and TPCIR which was robust to adjustment, supported by inverse probability weighting procedures and accompanied by high e-Values making confounding unlikely and establishing the causal relationship. Cannabis-liberal jurisdictions were associated with higher rates of TPCIR and a faster rate of TPCIR increase. Data inform the broader general consideration of cannabinoid-induced genotoxicity.
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Patient-Derived Mutant Forms of NFE2L2/NRF2 Drive Aggressive Murine Hepatoblastomas. Cell Mol Gastroenterol Hepatol 2021; 12:199-228. [PMID: 33618031 PMCID: PMC8102178 DOI: 10.1016/j.jcmgh.2021.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB), the most common pediatric liver cancer, often bears β-catenin mutations and deregulates the Hippo tumor suppressor pathway. Murine HBs can be generated by co-expressing β-catenin mutants and the constitutively active Hippo effector YAPS127A. Some HBs and other cancers also express mutants of NFE2L2/NRF2 (NFE2L2), a transcription factor that tempers oxidative and electrophilic stress. In doing so, NFE2L2 either suppresses or facilitates tumorigenesis. METHODS We evaluated NFE2L2's role in HB pathogenesis by co-expressing all combinations of mutant β-catenin, YAPS127A, and the patient-derived NFE2L2 mutants L30P and R34P in murine livers. We evaluated growth, biochemical and metabolic profiles, and transcriptomes of the ensuing tumors. RESULTS In association with β-catenin+YAPS127A, L30P and R34P markedly accelerated HB growth and generated widespread cyst formation and necrosis, which are otherwise uncommon features. Surprisingly, any 2 members of the mutant β-catenin-YAPS127A-L30P/R34P triad were tumorigenic, thus directly establishing NFE2L2's oncogenicity. Each tumor group displayed distinct features but shared 22 similarly deregulated transcripts, 10 of which perfectly correlated with survival in human HBs and 17 of which correlated with survival in multiple adult cancers. One highly up-regulated transcript encoded serpin E1, a serine protease inhibitor that regulates fibrinolysis, growth, and extracellular matrix. Although the combination of mutant β-catenin, YAPS127A, and serpin E1 did not accelerate cystogenic tumor growth, it did promote the widespread necrosis associated with mutant β-catenin-YAPS127A-L30P/R34P tumors. CONCLUSIONS Our findings establish the direct oncogenicity of NFE2L2 mutants and key transcripts, including serpin E1, that drive specific HB features.
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Prognostic Gene Expression, Stemness and Immune Microenvironment in Pediatric Tumors. Cancers (Basel) 2021; 13:cancers13040854. [PMID: 33670534 PMCID: PMC7922568 DOI: 10.3390/cancers13040854] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Tumors in children and young adults are rare and diagnostically distinct from those occurring in older patients. They frequently arise from developing cells, resembling stem cells, which may explain some of the clinical and biologic differences observed. The aim of this retrospective transcriptome study was to investigate the prognostic landscape, immune tumor microenvironment (TME) and stemness in a cohort of 4068 transcriptomes of such tumors. We find that patients’ prognosis correlates with distinct gene expression patterns similar to adult tumor types. Stemness defined by a computational stemness score (mRNAsi) correlates with clinical and molecular parameters that is distinct for each tumor type. In Wilms tumors that recapitulate normal kidney development microscopically, stemness correlates with distinct patterns of immune cell infiltration by transcriptome analysis and by cell localization in tumor tissue. Abstract Pediatric tumors frequently arise from embryonal cells, often displaying a stem cell-like (“small round blue”) morphology in tissue sections. Because recently “stemness” has been associated with a poor immune response in tumors, we investigated the association of prognostic gene expression, stemness and the immune microenvironment systematically using transcriptomes of 4068 tumors occurring mostly at the pediatric and young adult age. While the prognostic landscape of gene expression (PRECOG) and infiltrating immune cell types (CIBERSORT) is similar to that of tumor entities occurring mainly in adults, the patterns are distinct for each diagnostic entity. A high stemness score (mRNAsi) correlates with clinical and morphologic subtype in Wilms tumors, neuroblastomas, synovial sarcomas, atypical teratoid rhabdoid tumors and germ cell tumors. In neuroblastomas, a high mRNAsi is associated with shortened overall survival. In Wilms tumors a high mRNAsi correlates with blastemal morphology, whereas tumors with predominant epithelial or stromal differentiation have a low mRNAsi and a high percentage of M2 type macrophages. This could be validated in Wilms tumor tissue (n = 78). Here, blastemal areas are low in M2 macrophage infiltrates, while nearby stromal differentiated areas contain abundant M2 macrophages, suggesting local microanatomic regulation of the immune response.
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355
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Simovic M, Ernst A. Chromothripsis, DNA repair and checkpoints defects. Semin Cell Dev Biol 2021; 123:110-114. [PMID: 33589336 DOI: 10.1016/j.semcdb.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/05/2021] [Indexed: 11/28/2022]
Abstract
Chromothripsis is a unique form of genome instability characterized by tens to hundreds of DNA double-strand breaks on one or very few chromosomes, followed by error-prone repair. The derivative chromosome(s) display massive rearrangements, which lead to the loss of tumor suppressor function and to the activation of oncogenes. Chromothripsis plays a major role in cancer as well as in other conditions, such as congenital diseases. In this review, we discuss the repair processes involved in the rejoining of the chromosome fragments, the role of DNA repair and checkpoint defects as a cause for chromothripsis as well as DNA repair defects resulting from chromothripsis. Finally, we consider clinical implications and potential therapeutic vulnerabilities that could be utilized to eliminate tumor cells with chromothripsis.
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Affiliation(s)
- Milena Simovic
- Group Genome Instability in Tumors, German Cancer Research Centre (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
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356
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Davies HR, Broad KD, Onadim Z, Price EA, Zou X, Sheriff I, Karaa EK, Scheimberg I, Reddy MA, Sagoo MS, Ohnuma SI, Nik-Zainal S. Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature. Cancers (Basel) 2021; 13:754. [PMID: 33670346 PMCID: PMC7918943 DOI: 10.3390/cancers13040754] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought RB1 and other driver mutations and investigated mutational signatures. At least one RB1 mutation was identified in all retinoblastomas, including new mutations in addition to those previously identified by clinical screening. Ten tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. Mutational signature analysis showed predominance of signatures associated with cell division, an absence of ultraviolet-related DNA damage and a profound platinum-related mutational signature in a chemotherapy-exposed tumour. Most RB1 mutations are identifiable by clinical screening. However, the increased resolution and ability to detect otherwise elusive rearrangements by WGS have important repercussions on clinical management and advice on recurrence risks.
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Affiliation(s)
- Helen R. Davies
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Kevin D. Broad
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Elizabeth A. Price
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Xueqing Zou
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Ibrahim Sheriff
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
| | - Esin Kotiloğlu Karaa
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - Irene Scheimberg
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - M. Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Shin-ichi Ohnuma
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
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Rosales-Rodríguez B, Núñez-Enríquez JC, Velázquez-Wong AC, González-Torres C, Gaytán-Cervantes J, Jiménez-Hernández E, Martín-Trejo JA, Campo-Martínez MDLÁD, Medina-Sanson A, Flores-Lujano J, Flores-Villegas LV, Peñaloza-González JG, Torres-Nava JR, Espinosa-Elizondo RM, Amador-Sánchez R, Miranda-Madrazo MR, Santillán-Juárez JD, Pérez-Saldívar ML, Gurrola-Silva A, Orozco-Ruiz D, Solís-Labastida KA, Velázquez-Aviña MM, Duarte-Rodríguez DA, Mata-Rocha M, Sepúlveda-Robles OA, Ortiz-Maganda M, Bekker-Méndez VC, Jiménez-Morales S, Mejía-Aranguré JM, Rosas-Vargas H. Copy Number Alterations are Associated with the Risk of Very Early Relapse in Pediatric B-lineage Acute Lymphoblastic Leukemia: A Nested Case-control MIGICCL Study. Arch Med Res 2021; 52:414-422. [PMID: 33541741 DOI: 10.1016/j.arcmed.2020.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Refining risk stratification to avoid very early relapses (VER) in Mexican patients with B-lineage acute lymphoblastic leukemia (B-ALL) could lead to better survival rates in our population. AIM OF THE STUDY The purpose of this study was to investigate the association between the United Kingdom ALL (UKALL)-CNA classifier and VER risk in Mexican patients with childhood B-ALL. METHODS A nested case-control study of 25 cases with VER and 38 frequency-matched controls without relapse was conducted within the MIGICCL study cohort. They were grouped into the categories of the UKALL-CNA risk classifier (good [reference], intermediate and poor), according to the results obtained by multiplex ligation dependent probe amplification. Overall and disease-free survival (DFS) were estimated using the Kaplan-Meier method. Univariate and multivariate Cox proportional hazards analyses were conducted. RESULTS The CDKN2A/B genes were most frequently deleted in the group with relapse. According to UKALL-CNA classifier, 33 (52.4%) patients were classified as good, 21 (33.3%) intermediate and 9 (14.3%) poor-risk B-ALL. The intermediate and poor risk groups were associated with an increased risk of VER (HR = 4.94, 95% CI = 1.87-13.07 and HR = 7.42, 95% CI = 2.37-23.26, respectively) in comparison to the good-risk patients. After adjusting by NCI risk classification and chemotherapy scheme in a multivariate model, the risks remained significant. CONCLUSIONS Our data support the clinical utility of profiling CNAs to potentially refine current risk stratification strategies of patients with B-ALL.
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Affiliation(s)
- Beatriz Rosales-Rodríguez
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México; Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Ana Claudia Velázquez-Wong
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Carolina González-Torres
- Laboratorio de Secuenciación, División de Desarrollo de la Investigación, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Javier Gaytán-Cervantes
- Laboratorio de Secuenciación, División de Desarrollo de la Investigación, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Elva Jiménez-Hernández
- Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México; Servicio de Hematología Pediátrica, Hospital General Gaudencio González Garza, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología, Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - María de Los Ángeles Del Campo-Martínez
- Servicio de Hematología Pediátrica, Hospital General Gaudencio González Garza, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Aurora Medina-Sanson
- Servicio de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Secretaria de Salud, Ciudad de México, México
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Ciudad de México, México
| | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico Moctezuma, Secretaría de Salud de la Ciudad de México, Ciudad de México, México
| | | | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, Hospital General Regional No. 1 Dr. Carlos MacGregor Sánchez Navarro, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - María Raquel Miranda-Madrazo
- Servicio de Hematología Pediátrica, Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Ciudad de México, México
| | - Jessica Denise Santillán-Juárez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1° de Octubre, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Ciudad de México, México
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Alma Gurrola-Silva
- Servicio de Pediatría, Hospital Regional Tipo B de Alta Especialidad Bicentenario de la Independencia, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Ciudad de México, México
| | - Darío Orozco-Ruiz
- Servicio de Oncología, Hospital Pediátrico Moctezuma, Secretaría de Salud de la Ciudad de México, Ciudad de México, México
| | - Karina Anastacia Solís-Labastida
- Servicio de Hematología, Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México; Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México; Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Mónica Ortiz-Maganda
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología Dr. Daniel Méndez Hernández, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología Dr. Daniel Méndez Hernández, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Juan Manuel Mejía-Aranguré
- Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.
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Hanemaaijer ES, Margaritis T, Sanders K, Bos FL, Candelli T, Al-Saati H, van Noesel MM, Meyer-Wentrup FAG, van de Wetering M, Holstege FCP, Clevers H. Single-cell atlas of developing murine adrenal gland reveals relation of Schwann cell precursor signature to neuroblastoma phenotype. Proc Natl Acad Sci U S A 2021; 118:e2022350118. [PMID: 33500353 PMCID: PMC7865168 DOI: 10.1073/pnas.2022350118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor and accounts for ∼10% of pediatric cancer-related deaths. The exact cell of origin has yet to be elucidated, but it is generally accepted that neuroblastoma derives from the neural crest and should thus be considered an embryonal malignancy. About 50% of primary neuroblastoma tumors arise in the adrenal gland. Here, we present an atlas of the developing mouse adrenal gland at a single-cell level. Five main cell cluster groups (medulla, cortex, endothelial, stroma, and immune) make up the mouse adrenal gland during fetal development. The medulla group, which is of neural crest origin, is further divided into seven clusters. Of interest is the Schwann cell precursor ("SCP") and the "neuroblast" cluster, a highly cycling cluster that shares markers with sympathoblasts. The signature of the medullary SCP cluster differentiates neuroblastoma patients based on disease phenotype: The SCP signature score anticorrelates with ALK and MYCN expression, two indicators of poor prognosis. Furthermore, a high SCP signature score is associated with better overall survival rates. This study provides an insight into the developing adrenal gland and introduces the SCP gene signature as being of interest for further research in understanding neuroblastoma phenotype.
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Affiliation(s)
- Evelyn S Hanemaaijer
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Karin Sanders
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Frank L Bos
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Hanin Al-Saati
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | | | - Marc van de Wetering
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands;
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584 CT Utrecht, The Netherlands
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359
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Antić Ž, Lelieveld SH, van der Ham CG, Sonneveld E, Hoogerbrugge PM, Kuiper RP. Unravelling the Sequential Interplay of Mutational Mechanisms during Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia. Genes (Basel) 2021; 12:genes12020214. [PMID: 33540666 PMCID: PMC7913080 DOI: 10.3390/genes12020214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 11/16/2022] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and is characterized by clonal heterogeneity. Genomic mutations can increase proliferative potential of leukemic cells and cause treatment resistance. However, mechanisms driving mutagenesis and clonal diversification in ALL are not fully understood. In this proof of principle study, we performed whole genome sequencing of two cases with multiple relapses in order to investigate whether groups of mutations separated in time show distinct mutational signatures. Based on mutation allele frequencies at diagnosis and subsequent relapses, we clustered mutations into groups and performed cluster-specific mutational profile analysis and de novo signature extraction. In patient 1, who experienced two relapses, the analysis unraveled a continuous interplay of aberrant activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) activity. The associated signatures SBS2 and SBS13 were present already at diagnosis, and although emerging mutations were lost in later relapses, the process remained active throughout disease evolution. Patient 2 had three relapses. We identified episodic mutational processes at diagnosis and first relapse leading to mutations resembling ultraviolet light-driven DNA damage, and thiopurine-associated damage at first relapse. In conclusion, our data shows that investigation of mutational processes in clusters separated in time may aid in understanding the mutational mechanisms and discovery of underlying causes.
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Affiliation(s)
- Željko Antić
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
| | - Stefan H. Lelieveld
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
| | - Cédric G. van der Ham
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
- Dutch Childhood Oncology Group, 3584 CS Utrecht, The Netherlands
| | - Peter M. Hoogerbrugge
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
- Dutch Childhood Oncology Group, 3584 CS Utrecht, The Netherlands
| | - Roland P. Kuiper
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-88-97-252-12
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360
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Abstract
PURPOSE OF REVIEW Recent genetic and molecular findings have impacted the diagnosis, prognosis, and in some instances, treatment strategies for children with pediatric central nervous system tumors. Herein, we review the most up-to-date molecular findings and how they have impacted tumor classification and clinical care. RECENT FINDINGS It is now recognized that aberrations of the mitogen-activated protein kinase pathway are present in the majority of pediatric low-grade glioma. Also, there has been the identification of recurrent histone H3 K27M mutations in diffuse intrinsic pontine and other midline gliomas. Medulloblastoma is now divided into four molecular subgroups with distinct characteristics and prognoses. The classification of other unique embryonal tumors is also highlighted. Finally, we present the newest classification of ependymoma; supratentorial ependymomas comprise two subtypes based on expression of the chromosome 11 Open Reading Frame 95-reticuloendotheliosis Viral Oncogene Homolog A or yes-associated protein 1 fusion, whereas posterior fossa ependymomas are divided into two distinct molecular subgroups, posterior fossa-A and posterior fossa-B. SUMMARY These advances in the molecular classification of pediatric central nervous system tumors have not only assisted in diagnoses, but they have led to a new era of tumor classification and prognostication. They also have served as drivers for the evaluation of new targeted therapies based upon molecular aberrations with the hope for improved survival outcomes for our patients.
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361
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Ginsburg O, Ashton-Prolla P, Cantor A, Mariosa D, Brennan P. The role of genomics in global cancer prevention. Nat Rev Clin Oncol 2021; 18:116-128. [PMID: 32973296 DOI: 10.1038/s41571-020-0428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
Abstract
Despite improvements in the understanding of cancer causation, much remains unknown regarding the mechanisms by which genomic and non-genomic factors initiate carcinogenesis, drive cell invasion and metastasis, and enable cancer to develop. Technological advances have enabled the analysis of whole genomes, comprising thousands of tumours across populations worldwide, with the aim of identifying mutation signatures associated with particular tumour types. Large collaborative efforts have resulted in the identification and improved understanding of causal factors, and have shed light on new opportunities to prevent cancer. In this new era in cancer genomics, discoveries from studies conducted on an international scale can inform evidence-based strategies in cancer control along the cancer care continuum, from prevention to treatment. In this Review, we present the relevant history and emerging frontiers of cancer genetics and genomics from the perspective of global cancer prevention. We highlight the importance of local context in the adoption of new technologies and emergent evidence, with illustrative examples from worldwide. We emphasize the challenges in implementing important genomic findings in clinical settings with disparate resource availability and present a conceptual framework for the translation of such findings into clinical practice, and evidence-based policies in order to maximize the utility for a population.
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Affiliation(s)
- Ophira Ginsburg
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Section for Global Health, Division of Health and Behavior, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA.
| | - Patricia Ashton-Prolla
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre and Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anna Cantor
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
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362
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Johann PD. Invited Review: Dysregulation of chromatin remodellers in paediatric brain tumours - SMARCB1 and beyond. Neuropathol Appl Neurobiol 2021; 46:57-72. [PMID: 32307752 DOI: 10.1111/nan.12616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/21/2020] [Indexed: 12/13/2022]
Abstract
Mutations in chromatin remodelling genes occur in approximately 25% of all human tumours (Kadoch et al. Nat Genet 45: 592-601, 2013). The spectrum of alterations is broad and comprises single nucleotide variants, insertion/deletions and more complex structural variations. The single most often affected remodelling complex is the SWI/SNF complex (SWItch/sucrose non-fermentable). In the field of paediatric neuro-oncology, the spectrum of affected genes implicated in epigenetic remodelling is narrower with SMARCB1 and SMARCA4 being the most frequent. The low mutation frequencies in many of the SWI/SNF mutant entities underline the fact that perturbed chromatin remodelling is the most salient factor in tumourigenesis and could thus be a potential therapeutic opportunity. Here, I review the genetic basis of aberrant chromatin remodelling in paediatric brain tumours and discuss their impact on the epigenome in the respective entities, mainly medulloblastomas and rhabdoid tumours.
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Affiliation(s)
- P D Johann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany.,Department of Paediatric Haematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
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363
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Samoyedny A, Srinivasan A, States L, Mosse YP, Alai E, Pawel B, Pogoriler J, Shellikeri S, Vatsky S, Acord M, Escobar F, Edgar JC, Maris JM, Cahill AM. Image-Guided Biopsy for Relapsed Neuroblastoma: Focus on Safety, Adequacy for Genetic Sequencing, and Correlation of Tumor Cell Percent With Quantitative Lesion MIBG Uptake. JCO Precis Oncol 2021; 5:PO.20.00171. [PMID: 34250393 DOI: 10.1200/po.20.00171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Many novel therapies for relapsed and refractory neuroblastoma require tumor tissue for genomic sequencing. We analyze our experience with image-guided biopsy in these patients, focusing on safety, yield, adequacy for next-generation sequencing (NGS), and correlation of tumor cell percent (TC%) with quantitative uptake on 123I-meta-iodobenzylguanidine (MIBG) single-photon emission computed tomography with computed tomography (SPECT/CT). MATERIALS AND METHODS An 11-year retrospective review of image-guided biopsy on 66 patients (30 female), with a median age of 8.7 years (range, 0.9-49 years), who underwent 95 biopsies (55 bone and 40 soft tissue) of relapsed or refractory neuroblastoma lesions was performed. RESULTS There were seven minor complications (7%) and one major complication (1%). Neuroblastoma was detected in 88% of MIBG- or fluorodeoxyglucose-avid foci. The overall NGS adequacy was 69% (64% in bone and 74% in soft tissue, P = .37). NGS adequacy within neuroblastoma-positive biopsies was 88% (82% bone and 96% soft tissue, P = .11). NGS-adequate biopsies had a greater mean TC% than inadequates (51% v 18%, P = .03). NGS-adequate biopsies had a higher mean number of needle passes (7.5 v 3.4, P = .0002). The mean tissue volume from NGS-adequate soft-tissue lesions was 0.16 cm3 ± 0.12. Lesion:liver and lesion:psoas MIBG uptake ratios correlated with TC% (r = 0.74, r = 0.72, and n = 14). Mean TC% in NGS-adequate samples was 51%, corresponding to a lesion:liver ratio of 2.9 and a lesion:psoas ratio of 9.0. Thirty percent of biopsies showed an actionable ALK mutation or other therapeutically relevant variant. CONCLUSION Image-guided biopsy for relapsed or refractory neuroblastoma was safe and likely to provide NGS data to guide therapy decisions. A lesion:liver MIBG uptake ratio of ≥ 3 or a lesion:psoas ratio of > 9 was associated with a TC% sufficient to deliver NGS results.
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Affiliation(s)
- Andrew Samoyedny
- Children's Hospital of Philadelphia, Philadelphia, PA.,Drexel University College of Medicine, Philadelphia, PA
| | - Abhay Srinivasan
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Lisa States
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yael P Mosse
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Emma Alai
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bruce Pawel
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jennifer Pogoriler
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | - Seth Vatsky
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Michael Acord
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Fernando Escobar
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | - John M Maris
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Anne Marie Cahill
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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364
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Support of BCP-ALL-cells by autologous bone marrow Th-cells involves induction of AID expression but not widespread AID off-target mutagenesis. Cancer Immunol Immunother 2021; 70:2275-2289. [PMID: 33507341 PMCID: PMC8289808 DOI: 10.1007/s00262-020-02835-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/17/2020] [Indexed: 12/22/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common childhood malignancy. The two-step BCP-ALL pathogenesis requires in utero-induced chromosomal aberrations and additional mutagenic events for overt leukemia. In mouse models, activation-induced cytidine deaminase (AID/AICDA) was suggested to contribute to BCP-ALL pathogenesis by off-target mutagenic activity. The role of AID in patients, however, remains unclear. Moreover, AID is usually not expressed in precursor B-cells but in germinal center B-cells, where it is induced upon T-helper (Th) cell stimulation. We have previously demonstrated that autologous Th-cells supportively interacted with BCP-ALL-cells. Here, we hypothesize that this interaction additionally induces AID expression in BCP-ALL-cells, leading to off-target mutagenic activity. We show that co-culture with autologous bone marrow Th-cells induced high AICDA expression in primary BCP-ALL-cells. This induction was mediated by a mechanism similar to the induction in mature B-cells involving IL-13/Stat6, CD40L/NF-κB and TGFβ/Smad2/3 signaling. Even though Th-cell-induced AID seemed to be active in vitro in a BCP-ALL reporter cell line, extensive mutational signature analysis revealed no major contribution of AID activity to the mutational landscape in BCP-ALL patients. AID activity was neither detected in mutation clusters nor in known AID targets. Moreover, no recurrently mutated gene showed a relevant enrichment of mutations in the AID motif. Together, the lack of AID-induced mutational consequences argues towards a Th-cell-promoted yet AID-independent BCP-ALL pathogenesis and favors therapeutic research focusing on Th-cell-derived support of BCP-ALL-cells rather than AID-induced effects.
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365
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Portals for Exploring Noncoding Variants in Pediatric Cancer. Trends Genet 2021; 37:297-298. [PMID: 33494957 DOI: 10.1016/j.tig.2021.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 11/22/2022]
Abstract
Zhou et al. present GenomePaint, a dynamic web-based data portal for exploring noncoding somatic alterations in cancer by genomic location. Multiple omics platforms - including whole-genome, whole-exome, transcriptome, and epigenome - can be visualized together. The portal incorporates data from >3800 pediatric tumors, and users may upload their own data.
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366
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Yang J, Li Q, Noureen N, Fang Y, Kurmasheva R, Houghton PJ, Wang X, Zheng S. PCAT: an integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models. Nucleic Acids Res 2021; 49:D1321-D1327. [PMID: 32810235 PMCID: PMC7778893 DOI: 10.1093/nar/gkaa698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/30/2022] Open
Abstract
Although cancer is the leading cause of disease-related mortality in children, the relative rarity of pediatric cancers poses a significant challenge for developing novel therapeutics to further improve prognosis. Patient-derived xenograft (PDX) models, which are usually developed from high-risk tumors, are a useful platform to study molecular driver events, identify biomarkers and prioritize therapeutic agents. Here, we develop PDX for Childhood Cancer Therapeutics (PCAT), a new integrated portal for pediatric cancer PDX models. Distinct from previously reported PDX portals, PCAT is focused on pediatric cancer models and provides intuitive interfaces for querying and data mining. The current release comprises 324 models and their associated clinical and genomic data, including gene expression, mutation and copy number alteration. Importantly, PCAT curates preclinical testing results for 68 models and 79 therapeutic agents manually collected from individual agent testing studies published since 2008. To facilitate comparisons of patterns between patient tumors and PDX models, PCAT curates clinical and molecular data of patient tumors from the TARGET project. In addition, PCAT provides access to gene fusions identified in nearly 1000 TARGET samples. PCAT was built using R-shiny and MySQL. The portal can be accessed at http://pcat.zhenglab.info or http://www.pedtranscriptome.org.
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Affiliation(s)
- Juechen Yang
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Qilin Li
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Nighat Noureen
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Yanbing Fang
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,School of Natural Science, University of Texas at Austin, Austin, TX 78712, USA
| | - Raushan Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Xiaojing Wang
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Population Health Sciences, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.,Department of Population Health Sciences, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
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367
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Nishii R, Baskin-Doerfler R, Yang W, Oak N, Zhao X, Yang W, Hoshitsuki K, Bloom M, Verbist K, Burns M, Li Z, Lin TN, Qian M, Moriyama T, Gastier-Foster JM, Rabin KR, Raetz E, Mullighan C, Pui CH, Yeoh AEJ, Zhang J, Metzger ML, Klco JM, Hunger SP, Newman S, Wu G, Loh ML, Nichols KE, Yang JJ. Molecular basis of ETV6-mediated predisposition to childhood acute lymphoblastic leukemia. Blood 2021; 137:364-373. [PMID: 32693409 PMCID: PMC7819760 DOI: 10.1182/blood.2020006164] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/03/2020] [Indexed: 12/24/2022] Open
Abstract
There is growing evidence supporting an inherited basis for susceptibility to acute lymphoblastic leukemia (ALL) in children. In particular, we and others reported recurrent germline ETV6 variants linked to ALL risk, which collectively represent a novel leukemia predisposition syndrome. To understand the influence of ETV6 variation on ALL pathogenesis, we comprehensively characterized a cohort of 32 childhood leukemia cases arising from this rare syndrome. Of 34 nonsynonymous germline ETV6 variants in ALL, we identified 22 variants with impaired transcription repressor activity, loss of DNA binding, and altered nuclear localization. Missense variants retained dimerization with wild-type ETV6 with potentially dominant-negative effects. Whole-transcriptome and whole-genome sequencing of this cohort of leukemia cases revealed a profound influence of germline ETV6 variants on leukemia transcriptional landscape, with distinct ALL subsets invoking unique patterns of somatic cooperating mutations. 70% of ALL cases with damaging germline ETV6 variants exhibited hyperdiploid karyotype with characteristic recurrent mutations in NRAS, KRAS, and PTPN11. In contrast, the remaining 30% cases had a diploid leukemia genome and an exceedingly high frequency of somatic copy-number loss of PAX5 and ETV6, with a gene expression pattern that strikingly mirrored that of ALL with somatic ETV6-RUNX1 fusion. Two ETV6 germline variants gave rise to both acute myeloid leukemia and ALL, with lineage-specific genetic lesions in the leukemia genomes. ETV6 variants compromise its tumor suppressor activity in vitro with specific molecular targets identified by assay for transposase-accessible chromatin sequencing profiling. ETV6-mediated ALL predisposition exemplifies the intricate interactions between inherited and acquired genomic variations in leukemia pathogenesis.
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Affiliation(s)
| | | | | | - Ninad Oak
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xujie Zhao
- Department of Pharmaceutical Sciences and
| | | | | | - Mackenzie Bloom
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Katherine Verbist
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Melissa Burns
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Zhenhua Li
- Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | | | - Maoxiang Qian
- Department of Pharmaceutical Sciences and
- Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | | | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
- Department of Pathology and
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Karen R Rabin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Elizabeth Raetz
- Department of Pediatrics, NYU Langone Medical Center, New York, NY
| | - Charles Mullighan
- Department of Pathology and
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Allen Eng-Juh Yeoh
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
- VIVA-NUS Center for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Monika L Metzger
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Jeffery M Klco
- Department of Pathology and
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Stephen P Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | | | - Gang Wu
- Department of Computational Biology and
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA; and
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences and
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
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368
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Rodrigues GOL, Cramer SD, Winer HY, Hixon JA, Li W, Yunes JA, Durum SK. Mutations that collaborate with IL-7Ra signaling pathways to drive ALL. Adv Biol Regul 2021; 80:100788. [PMID: 33578108 DOI: 10.1016/j.jbior.2021.100788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
Abstract
The IL-7 pathway is required for normal T cell development and survival. In recent years the pathway has been shown to be a major driver of acute lymphoblastic leukemia (ALL), the most common cancer in children. Gain-of-function mutations in the alpha chain of the IL-7 receptor found in ALL patients clearly demonstrated that this pathway was a driver. However mutant IL-7R alone was insufficient to transform primary T cell progenitors, indicating that cooperating mutations were required. Here we review evidence for additional oncogenic mutations in the IL-7 pathway. We discuss several oncogenes, loss of tumor suppressor genes and epigenetic effects that can cooperate with mutant IL-7 receptor. These include NRas, HOXA, TLX3, Notch 1, Arf, PHF6, WT1, PRC, PTPN2 and CK2. As new therapeutics targeting the IL-7 pathway are developed, combination with agents directed to cooperating pathways offer hope for novel therapies for ALL.
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Affiliation(s)
- Gisele O L Rodrigues
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute, National Institutes of Health (NIH), Frederick, MD, USA; Molecular Biology Laboratory, Boldrini Children's Center, Campinas, Brazil; Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Sarah D Cramer
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute, National Institutes of Health (NIH), Frederick, MD, USA; Comparative Biomedical Scientist Training Program, NIH, Bethesda, MD, USA; Department of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Hila Y Winer
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute, National Institutes of Health (NIH), Frederick, MD, USA
| | - Julie A Hixon
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute, National Institutes of Health (NIH), Frederick, MD, USA
| | - WenQing Li
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute, National Institutes of Health (NIH), Frederick, MD, USA
| | - José Andres Yunes
- Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Scott K Durum
- Cytokines and Immunity Section, Laboratory of Cancer Immunometabolism, National Cancer Institute, National Institutes of Health (NIH), Frederick, MD, USA.
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369
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Williams J, Xu B, Putnam D, Thrasher A, Li C, Yang J, Chen X. MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors. Genome Biol 2021; 22:24. [PMID: 33461601 PMCID: PMC7814737 DOI: 10.1186/s13059-020-02220-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/06/2020] [Indexed: 12/12/2022] Open
Abstract
Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive. Here we present MethylationToActivity (M2A), a machine learning framework that uses convolutional neural networks to infer promoter activities based on H3K4me3 and H3K27ac enrichment, from DNA methylation patterns for individual genes. Using publicly available datasets in real-world test scenarios, we demonstrate that M2A is highly accurate and robust in revealing promoter activity landscapes in various pediatric and adult cancers, including both solid and hematologic malignant neoplasms.
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Affiliation(s)
- Justin Williams
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Putnam
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN, 38105, USA
| | - Andrew Thrasher
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN, 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1135, Memphis, TN, 38105, USA.
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370
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Zhou X, Wang J, Patel J, Valentine M, Shao Y, Newman S, Sioson E, Tian L, Liu Y, Brady SW, Flasch D, Ma X, Liu Y, Paul R, Edmonson MN, Rusch MC, Li C, Baker SJ, Easton J, Zhang J. Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint. Cancer Cell 2021; 39:83-95.e4. [PMID: 33434514 PMCID: PMC7884056 DOI: 10.1016/j.ccell.2020.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 10/13/2020] [Accepted: 12/10/2020] [Indexed: 12/14/2022]
Abstract
GenomePaint (https://genomepaint.stjude.cloud/) is an interactive visualization platform for whole-genome, whole-exome, transcriptome, and epigenomic data of tumor samples. Its design captures the inter-relatedness between DNA variations and RNA expression, supporting in-depth exploration of both individual cancer genomes and full cohorts. Regulatory non-coding variants can be inspected and analyzed along with coding variants, and their functional impact further explored by examining 3D genome data from cancer cell lines. Further, GenomePaint correlates mutation and expression patterns with patient outcomes, and supports custom data upload. We used GenomePaint to unveil aberrant splicing that disrupts the RING domain of CREBBP, discover cis activation of the MYC oncogene by duplication of the NOTCH1-MYC enhancer in B-lineage acute lymphoblastic leukemia, and explore the inter- and intra-tumor heterogeneity at EGFR in adult glioblastomas. These examples demonstrate that deep multi-omics exploration of individual cancer genomes enabled by GenomePaint can lead to biological insights for follow-up validation.
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Affiliation(s)
- Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jaimin Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marc Valentine
- Cytogenetics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Diane Flasch
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Robin Paul
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Michael C Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Chunliang Li
- Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Suzanne J Baker
- Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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371
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Borenäs M, Umapathy G, Lai WY, Lind DE, Witek B, Guan J, Mendoza-Garcia P, Masudi T, Claeys A, Chuang TP, El Wakil A, Arefin B, Fransson S, Koster J, Johansson M, Gaarder J, Van den Eynden J, Hallberg B, Palmer RH. ALK ligand ALKAL2 potentiates MYCN-driven neuroblastoma in the absence of ALK mutation. EMBO J 2021; 40:e105784. [PMID: 33411331 PMCID: PMC7849294 DOI: 10.15252/embj.2020105784] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022] Open
Abstract
High‐risk neuroblastoma (NB) is responsible for a disproportionate number of childhood deaths due to cancer. One indicator of high‐risk NB is amplification of the neural MYC (MYCN) oncogene, which is currently therapeutically intractable. Identification of anaplastic lymphoma kinase (ALK) as an NB oncogene raised the possibility of using ALK tyrosine kinase inhibitors (TKIs) in treatment of patients with activating ALK mutations. 8–10% of primary NB patients are ALK‐positive, a figure that increases in the relapsed population. ALK is activated by the ALKAL2 ligand located on chromosome 2p, along with ALK and MYCN, in the “2p‐gain” region associated with NB. Dysregulation of ALK ligand in NB has not been addressed, although one of the first oncogenes described was v‐sis that shares > 90% homology with PDGF. Therefore, we tested whether ALKAL2 ligand could potentiate NB progression in the absence of ALK mutation. We show that ALKAL2 overexpression in mice drives ALK TKI‐sensitive NB in the absence of ALK mutation, suggesting that additional NB patients, such as those exhibiting 2p‐gain, may benefit from ALK TKI‐based therapeutic intervention.
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Affiliation(s)
- Marcus Borenäs
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Dan E Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Barbara Witek
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Patricia Mendoza-Garcia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tafheem Masudi
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Arne Claeys
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent, Belgium
| | - Tzu-Po Chuang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Abeer El Wakil
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Badrul Arefin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susanne Fransson
- Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathias Johansson
- Clinical Genomics, Science for life laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Jennie Gaarder
- Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jimmy Van den Eynden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent, Belgium
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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372
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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: 101] [Impact Index Per Article: 33.7] [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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373
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The Role of Cannabinoids as Anticancer Agents in Pediatric Oncology. Cancers (Basel) 2021; 13:cancers13010157. [PMID: 33466435 PMCID: PMC7796497 DOI: 10.3390/cancers13010157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/01/2021] [Accepted: 01/02/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The endocannabinoid system (ECS) is a complex signaling pathway system involved in the regulation of multiple functions in both normal tissues and cancer. Δ9-tetrahydrocannabinol and cannabidiol are plant-derived cannabinoids that possess some efficacy against adult cancer, in part via modulation of the ECS, and may be less toxic agents compared to other treatments used in oncology. To date, there are minimal studies that have investigated these drugs in the pediatric cancer setting. Indeed, there are currently no preclinical or clinical studies examining the effects of cannabinoids in pediatric brain cancer, although there is some evidence that they can alleviate symptoms associated with childhood cancer therapy, such as vomiting and nausea. Given there is accumulating evidence that cannabis use during adolescence is associated with poor mental and cognitive health, there is a present and urgent need to investigate the safety and efficacy of cannabinoids in pediatric oncology to provide guidance to families and physicians. Abstract Cannabinoids are a group of chemicals that bind to receptors in the human body and, in turn, modulate the endocannabinoid system (ECS). They can be endogenously produced, synthetic, or derived from the plant Cannabis sativa L. Research over the past several decades has shown that the ECS is a cellular communication network essential to maintain multiple biological functions and the homeostasis of the body. Indeed, cannabinoids have been shown to influence a wide variety of biological effects, including memory, pain, reproduction, bone remodeling or immunity, to name a few. Unsurprisingly, given these broad physiological effects, alterations of the ECS have been found in different diseases, including cancer. In recent years, the medical use of cannabis has been approved in different countries for a variety of human conditions. However, the use of these compounds, specifically as anticancer agents, remains controversial. Studies have shown that cannabinoids do have anticancer activity in different tumor types such as breast cancer, melanoma, lymphoma and adult brain cancer. Specifically, phytocannabinoids Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) has been shown to induce apoptosis and inhibit proliferation of adult cancer cells, as well as modulate angiogenesis and metastasis. Despite increasing evidence that cannabinoids elicit antitumor effects in adult cancers, there is minimal data available on their effects in children or in pediatric cancers despite public and clinical demand for information. Here we describe a comprehensive and critical review of what is known about the effects of cannabinoids on pediatric cancers, highlight current gaps in knowledge and identify the critical issues that need addressing before considering these promising but controversial drugs for use in pediatric oncology.
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374
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Milanese JS, Wang E. Germline Genetics in Cancer: The New Frontier. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11667-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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375
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Jin Y, Lyu Q. Basic research in childhood cancer: Progress and future directions in China. Cancer Lett 2020; 495:156-164. [PMID: 32841714 DOI: 10.1016/j.canlet.2020.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Childhood cancer is a leading cause of death in children. Some childhood cancers have a particularly high mortality rate. Following the World Health Organization's emphasis on child health, most governments worldwide have taken measures to facilitate childhood cancer research. Thus, the scientific community is showing increasing interest in this area. Chinese government has prominence in building a system for the diagnosis and treatment of childhood cancer, thereby promoting the development of childhood cancer research. This review summarizes the research progress, challenges, and perspectives in childhood cancer, and the increasing contributions of National Natural Science Foundation of China (NSFC) in the past decade (2008-2018).
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Affiliation(s)
- Yaqiong Jin
- Department of Health Sciences, National Natural Science Foundation of China, Beijing, 100085, China; Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Qunyan Lyu
- Department of Health Sciences, National Natural Science Foundation of China, Beijing, 100085, China.
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376
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Noy-Lotan S, Krasnov T, Dgany O, Jeison M, Yanir AD, Gilad O, Toledano H, Barzilai-Birenboim S, Yacobovich J, Izraeli S, Tamary H, Steinberg-Shemer O. Incorporation of somatic panels for the detection of haematopoietic transformation in children and young adults with leukaemia predisposition syndromes and with acquired cytopenias. Br J Haematol 2020; 193:570-580. [PMID: 33368157 DOI: 10.1111/bjh.17285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Detection of somatic mutations may help verify the diagnosis of myelodysplastic syndrome (MDS) in patients with persistent cytopenias or with MDS-predisposition syndromes, prior to the development of overt leukemia. However, the spectrum and consequences of acquired changes in paediatric patients have not been fully evaluated, and especially not in the context of an underlying syndrome. We incorporated a targeted next-generation-sequencing panel of 54 genes for the detection of somatic mutations in paediatric and young adult patients with inherited or acquired cytopenias. Sixty-five patients were included in this study, of whom 17 (26%) had somatic mutations. We detected somatic mutations in 20% of individuals with inherited MDS-predisposition syndromes, including in patients with severe congenital neutropenia and Fanconi anaemia, and with germline mutations in SAMD9L. Thirty-eight per cent of children with acquired cytopenias and suspected MDS had somatic changes, most commonly in genes related to signal transduction and transcription. Molecularly abnormal clones often preceded cytogenetic changes. Thus, routine performance of somatic panels can establish the diagnosis of MDS and determine the optimal timing of haematopoietic stem cell transplantation, prior to the development of leukaemia. In addition, performing somatic panels in patients with inherited MDS-predisposition syndromes may reveal their unique spectrum of acquired mutations.
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Affiliation(s)
- Sharon Noy-Lotan
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Marta Jeison
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Asaf D Yanir
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Oded Gilad
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Helen Toledano
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shlomit Barzilai-Birenboim
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joanne Yacobovich
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shai Izraeli
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hannah Tamary
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel.,Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Steinberg-Shemer
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel.,Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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377
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Kaito S, Iwama A. Pathogenic Impacts of Dysregulated Polycomb Repressive Complex Function in Hematological Malignancies. Int J Mol Sci 2020; 22:ijms22010074. [PMID: 33374737 PMCID: PMC7793497 DOI: 10.3390/ijms22010074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 02/06/2023] Open
Abstract
Polycomb repressive complexes (PRCs) are epigenetic regulators that mediate repressive histone modifications. PRCs play a pivotal role in the maintenance of hematopoietic stem cells through repression of target genes involved in cell proliferation and differentiation. Next-generation sequencing technologies have revealed that various hematologic malignancies harbor mutations in PRC2 genes, such as EZH2, EED, and SUZ12, and PRC1.1 genes, such as BCOR and BCORL1. Except for the activating EZH2 mutations detected in lymphoma, most of these mutations compromise PRC function and are frequently associated with resistance to chemotherapeutic agents and poor prognosis. Recent studies have shown that mutations in PRC genes are druggable targets. Several PRC2 inhibitors, including EZH2-specific inhibitors and EZH1 and EZH2 dual inhibitors have shown therapeutic efficacy for tumors with and without activating EZH2 mutations. Moreover, EZH2 loss-of-function mutations appear to be attractive therapeutic targets for implementing the concept of synthetic lethality. Further understanding of the epigenetic dysregulation associated with PRCs in hematological malignancies should improve treatment outcomes.
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Affiliation(s)
| | - Atsushi Iwama
- Correspondence: ; Tel.: +81-3-6409-2181; Fax: +81-3-6409-2182
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378
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Cimmino F, Lasorsa VA, Vetrella S, Iolascon A, Capasso M. A Targeted Gene Panel for Circulating Tumor DNA Sequencing in Neuroblastoma. Front Oncol 2020; 10:596191. [PMID: 33381456 PMCID: PMC7769379 DOI: 10.3389/fonc.2020.596191] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Liquid biopsies do not reflect the complete mutation profile of the tumor but have the potential to identify actionable mutations when tumor biopsies are not available as well as variants with low allele frequency. Most retrospective studies conducted in small cohorts of pediatric cancers have illustrated that the technology yield substantial potential in neuroblastoma. Aim The molecular landscape of neuroblastoma harbors potentially actionable genomic alterations. We aimed to study the utility of liquid biopsy to characterize the mutational landscape of primary neuroblastoma using a custom gene panel for ctDNA targeted sequencing. Methods Targeted next-generation sequencing (NGS) was performed on ctDNA of 11 patients with primary neuroblastoma stage 4. To avoid the detection of false variants, we used UMIs (unique molecular identifiers) for the library construction, increased the sequencing depth and developed ad hoc bioinformatic analyses including the hard filtering of the variant calls. Results We identified 9/11 (81.8%) patients who carry at least one pathogenic variation. The most frequently mutated genes were KMT2C (five cases), NOTCH1/2 (four cases), CREBBP (three cases), ARID1A/B (three cases), ALK (two cases), FGFR1 (two cases), FAT4 (two cases) and CARD11 (two cases). Conclusions We developed a targeted NGS approach to identify tumor-specific alterations in ctDNA of neuroblastoma patients. Our results show the reliability of our approach to generate genomic information which can be integrated with clinical and pathological data at diagnosis.
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Affiliation(s)
| | - Vito Alessandro Lasorsa
- CEINGE Biotecnologie Avanzate, Napoli, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Simona Vetrella
- Department of Pediatric Oncology, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate, Napoli, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate, Napoli, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
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379
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Abstract
Diseases that manifest themselves in the pediatric age group frequently have a more diverse spectrum of abnormalities and a greater rarity than diseases that are primarily seen in adults. The complexity and the relatively small populations with specific diseases are factors that have hindered progress in the treatment of pediatric disorders. Personalized medical therapies that are specifically tailored for individuals with unusual or unique problems have great potential to assist in overcoming these factors that have been a bottleneck to pediatric medical success. Personalization of therapies will necessarily be data driven and will require delineation of the proteomic, genomic, epigenomic, and immune characteristics of patients in comparison to the general population. It follows that there is a need to provide researchers with accessible high-quality pediatric tissue collections to facilitate the acquisition of the molecular information needed to support personalized medicine. Because of the unusual nature of many pediatric diseases, sample pools from individual institutions are often too small to adequately power definitive studies. Thus, etiological and translational research in this area are increasingly relying on biobanking networks to provide investigators with adequate numbers of tissue samples. Several pediatric biobanking networks have been formed, which are aimed at increasing the power of research studies and desired pools of high-quality samples. However, despite the concerted efforts, these multicenter networks and collaborations have met with mixed outcomes owing to increasing complexities and heterogeneity in the biobanking arena. While there have been challenges and roadblocks, there also have been some positive outcomes that have had paradigm impacts on diagnosis, study, and treatment of specific diseases. This article highlights the need for establishing pediatric biobanks, how current efforts in pediatric biobanking are influencing the pediatric research landscape, and attempts to identify practical impediments that continue to hamper advancements for the future.
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Affiliation(s)
- Lalita Wadhwa
- Department of Congenital Heart Surgery, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
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380
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Chiu YC, Chen HIH, Gorthi A, Mostavi M, Zheng S, Huang Y, Chen Y. Deep learning of pharmacogenomics resources: moving towards precision oncology. Brief Bioinform 2020; 21:2066-2083. [PMID: 31813953 PMCID: PMC7711267 DOI: 10.1093/bib/bbz144] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
The recent accumulation of cancer genomic data provides an opportunity to understand how a tumor's genomic characteristics can affect its responses to drugs. This field, called pharmacogenomics, is a key area in the development of precision oncology. Deep learning (DL) methodology has emerged as a powerful technique to characterize and learn from rapidly accumulating pharmacogenomics data. We introduce the fundamentals and typical model architectures of DL. We review the use of DL in classification of cancers and cancer subtypes (diagnosis and treatment stratification of patients), prediction of drug response and drug synergy for individual tumors (treatment prioritization for a patient), drug repositioning and discovery and the study of mechanism/mode of action of treatments. For each topic, we summarize current genomics and pharmacogenomics data resources such as pan-cancer genomics data for cancer cell lines (CCLs) and tumors, and systematic pharmacologic screens of CCLs. By revisiting the published literature, including our in-house analyses, we demonstrate the unprecedented capability of DL enabled by rapid accumulation of data resources to decipher complex drug response patterns, thus potentially improving cancer medicine. Overall, this review provides an in-depth summary of state-of-the-art DL methods and up-to-date pharmacogenomics resources and future opportunities and challenges to realize the goal of precision oncology.
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Affiliation(s)
- Yu-Chiao Chiu
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Hung-I Harry Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Aparna Gorthi
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Milad Mostavi
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Siyuan Zheng
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yidong Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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381
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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382
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Sentís I, Gonzalez S, Genescà E, García-Hernández V, Muiños F, Gonzalez C, López-Arribillaga E, Gonzalez J, Fernandez-Ibarrondo L, Mularoni L, Espinosa L, Bellosillo B, Ribera JM, Bigas A, Gonzalez-Perez A, Lopez-Bigas N. The evolution of relapse of adult T cell acute lymphoblastic leukemia. Genome Biol 2020; 21:284. [PMID: 33225950 PMCID: PMC7682094 DOI: 10.1186/s13059-020-02192-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to study the mechanisms of relapse of adult T-ALL cases. RESULTS We profile whole-genome somatic mutations of 19 primary T-ALLs from adult patients and the corresponding relapse malignancies and analyze their evolution upon treatment in comparison with 238 pediatric and young adult ALL cases. We compare the mutational processes and driver mutations active in primary and relapse adult T-ALLs with those of pediatric patients. A precise estimation of clock-like mutations in leukemic cells shows that the emergence of the relapse clone occurs several months before the diagnosis of the primary T-ALL. Specifically, through the doubling time of the leukemic population, we find that in at least 14 out of the 19 patients, the population of relapse leukemia present at the moment of diagnosis comprises more than one but fewer than 108 blasts. Using simulations, we show that in all patients the relapse appears to be driven by genetic mutations. CONCLUSIONS The early appearance of a population of leukemic cells with genetic mechanisms of resistance across adult T-ALL cases constitutes a challenge for treatment. Improving early detection of the malignancy is thus key to prevent its relapse.
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Affiliation(s)
- Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Santiago Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Eulalia Genescà
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Violeta García-Hernández
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Celia Gonzalez
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Erika López-Arribillaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jessica Gonzalez
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | | | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- CMR[B] Center of Regenerative Medicine, Barcelona, Spain
| | - Lluís Espinosa
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, CIBERONC, Hospital del Mar, IMIM, Barcelona, Spain
| | - Josep-Maria Ribera
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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383
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Yurchenko AA, Padioleau I, Matkarimov BT, Soulier J, Sarasin A, Nikolaev S. XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature. Nat Commun 2020; 11:5834. [PMID: 33203900 PMCID: PMC7672101 DOI: 10.1038/s41467-020-19633-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022] Open
Abstract
Recent studies demonstrated a dramatically increased risk of leukemia in patients with a rare genetic disorder, Xeroderma Pigmentosum group C (XP-C), characterized by constitutive deficiency of global genome nucleotide excision repair (GG-NER). The genetic mechanisms of non-skin cancers in XP-C patients remain unexplored. In this study, we analyze a unique collection of internal XP-C tumor genomes including 6 leukemias and 2 sarcomas. We observe a specific mutational pattern and an average of 25-fold increase of mutation rates in XP-C versus sporadic leukemia which we presume leads to its elevated incidence and early appearance. We describe a strong mutational asymmetry with respect to transcription and the direction of replication in XP-C tumors suggesting association of mutagenesis with bulky purine DNA lesions of probably endogenous origin. These findings suggest existence of a balance between formation and repair of bulky DNA lesions by GG-NER in human body cells which is disrupted in XP-C patients. Xeroderma Pigmentosum group C (XP-C) is a rare genetic disorder characterised by deficient DNA repair leading to skin and internal cancer, but the latter is not well understood molecularly. Here the authors sequence genomes of non-skin cancers from XP-C patients to unravel its mutational patterns.
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Affiliation(s)
- Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Ismael Padioleau
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Bakhyt T Matkarimov
- National Laboratory Astana, Nazarbayev University, 010000, Astana, Kazakhstan
| | - Jean Soulier
- University of Paris, INSERM U944 and CNRS UMR7212, Institut de Recherche Saint-Louis, F-75010, Paris, France
| | - Alain Sarasin
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sergey Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France.
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384
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Rosales-Rodríguez B, Núñez-Enríquez JC, Mejía-Aranguré JM, Rosas-Vargas H. Prognostic Impact of Somatic Copy Number Alterations in Childhood B-Lineage Acute Lymphoblastic Leukemia. Curr Oncol Rep 2020; 23:2. [PMID: 33190177 DOI: 10.1007/s11912-020-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW The high prevalence of relapse in pediatric B-lineage acute lymphoblastic leukemia (B-ALL) despite the improvements achieved using current risk stratification schemes, demands more accurate methods for outcome prediction. Here, we provide a concise overview about the key advances that have expanded our knowledge regarding the somatic defects across B-ALL genomes, particularly focusing on copy number alterations (CNAs) and their prognostic impact. RECENT FINDINGS The identification of commonly altered genes in B-ALL has inspired the development of risk classifiers based on copy number states such as the IKZF1plus and the United Kingdom (UK) ALL-CNA classifiers to improve outcome prediction in B-ALL. CNA-risk classifiers have emerged as effective tools to predict disease relapse; though, their clinical applications are yet to be transferred to routine practice.
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Affiliation(s)
- Beatriz Rosales-Rodríguez
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, 06720, Ciudad de México, Mexico.,Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, 06720, Ciudad de México, Mexico
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, 06720, Ciudad de México, Mexico. .,Coordinación de Investigación en Salud, IMSS, Torre Academia Nacional de Medicina, 06720, Ciudad de México, Mexico.
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, 06720, Ciudad de México, Mexico.
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385
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Michmerhuizen NL, Klco JM, Mullighan CG. Mechanistic insights and potential therapeutic approaches for NUP98-rearranged hematologic malignancies. Blood 2020; 136:2275-2289. [PMID: 32766874 PMCID: PMC7702474 DOI: 10.1182/blood.2020007093] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleoporin 98 (NUP98) fusion oncoproteins are observed in a spectrum of hematologic malignancies, particularly pediatric leukemias with poor patient outcomes. Although wild-type full-length NUP98 is a member of the nuclear pore complex, the chromosomal translocations leading to NUP98 gene fusions involve the intrinsically disordered and N-terminal region of NUP98 with over 30 partner genes. Fusion partners include several genes bearing homeodomains or having known roles in transcriptional or epigenetic regulation. Based on data in both experimental models and patient samples, NUP98 fusion oncoprotein-driven leukemogenesis is mediated by changes in chromatin structure and gene expression. Multiple cofactors associate with NUP98 fusion oncoproteins to mediate transcriptional changes possibly via phase separation, in a manner likely dependent on the fusion partner. NUP98 gene fusions co-occur with a set of additional mutations, including FLT3-internal tandem duplication and other events contributing to increased proliferation. To improve the currently dire outcomes for patients with NUP98-rearranged malignancies, therapeutic strategies have been considered that target transcriptional and epigenetic machinery, cooperating alterations, and signaling or cell-cycle pathways. With the development of more faithful experimental systems and continued study, we anticipate great strides in our understanding of the molecular mechanisms and therapeutic vulnerabilities at play in NUP98-rearranged models. Taken together, these studies should lead to improved clinical outcomes for NUP98-rearranged leukemia.
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Affiliation(s)
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
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386
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Lee E, Lee JW, Lee B, Park K, Shim J, Yoo KH, Koo HH, Sung KW, Park WY. Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastoma. BMC Med Genomics 2020; 13:171. [PMID: 33172452 PMCID: PMC7653769 DOI: 10.1186/s12920-020-00819-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/30/2020] [Indexed: 02/08/2023] Open
Abstract
Background MYCN amplification is the most important genomic feature in neuroblastoma (NB). However, limited studies have been conducted on the MYCN non-amplified NB including low- and intermediate-risk NB. Here, the genomic characteristics of MYCN non-amplified NB were studied to allow for the identification of biomarkers for molecular stratification. Methods Fifty-eight whole exome sequencing (WES) and forty-eight whole transcriptome sequencing (WTS) samples of MYCN non-amplified NB were analysed. Forty-one patients harboured WES and WTS pairs. Results In the MYCN non-amplified NB WES data, maximum recurrent mutations were found in MUC4 (26%), followed by RBMXL3 (19%), ALB (17%), and MUC16 and SEPD8 (14% each). Two gene fusions, CCDC32-CBX3 (10%) and SAMD5-SASH1 (6%), were recurrent in WTS analysis, and these fusions were detected mostly in non-high-risk patients with ganglioneuroblastoma histology. Analysis of risk-group-specific biomarkers showed that several genes and gene sets were differentially expressed between the risk groups, and some immune-related pathways tended to be activated in the high-risk group. Mutational signatures 6 and 18, which represent DNA mismatch repair associated mutations, were commonly detected in 60% of the patients. In the tumour mutation burden (TMB) analysis, four patients showed high TMB (> 3 mutations/Mb), and had mutations in genes related to either MMR or homologous recombination. Excluding four outlier samples with TMB > 3 Mb, high-risk patients had significantly higher levels of TMB compared with the non-high-risk patients. Conclusions This study provides novel insights into the genomic background of MYCN non-amplified NB. Activation of immune-related pathways in the high-risk group and the results of TMB and mutational signature analyses collectively suggest the need for further investigation to discover potential immunotherapeutic strategies for NB.
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Affiliation(s)
- Eunjin Lee
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Boram Lee
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Joonho Shim
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea. .,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea. .,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.
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387
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Levinson A, Lee AG, Martell HJ, Breese MR, Zaloudek C, Van Ziffle J, Laguna B, Leung SG, Chen MD, Chen LM, Pfeil J, Ladwig NR, Shah AT, Behroozfard I, Rao AA, Salama SR, Sweet-Cordero EA, Stieglitz E. Complete Response to PD-1 Inhibition in an Adolescent With Relapsed Clear Cell Adenocarcinoma of the Cervix Predicted by Neoepitope Burden and APOBEC Signature. JCO Precis Oncol 2020; 4:2000132. [PMID: 33283136 PMCID: PMC7713560 DOI: 10.1200/po.20.00132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Anya Levinson
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Alex G Lee
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Henry J Martell
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Marcus R Breese
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Charles Zaloudek
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA.,Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Benjamin Laguna
- Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA
| | - Stanley G Leung
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - M Dwight Chen
- Department of Obstetrics and Gynecology, Sutter Health, San Francisco, CA
| | - Lee-May Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
| | - Jacob Pfeil
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Nicholas R Ladwig
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Avanthi Tayi Shah
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Inge Behroozfard
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Arjun Arkal Rao
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - E Alejandro Sweet-Cordero
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
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388
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Abstract
Informative and realistic mouse models of high-risk neuroblastoma are central to understanding mechanisms of tumour initiation, progression, and metastasis. They also play vital roles in validating tumour drivers and drug targets, as platforms for assessment of new therapies and in the generation of drug sensitivity data that can inform treatment decisions for individual patients. This review will describe genetically engineered mouse models of specific subsets of high-risk neuroblastoma, the development of patient-derived xenograft models that more broadly represent the diversity and heterogeneity of the disease, and models of primary and metastatic disease. We discuss the research applications, advantages, and limitations of each model type, the importance of model repositories and data standards for supporting reproducible, high-quality research, and potential future directions for neuroblastoma mouse models.
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Affiliation(s)
- Alvin Kamili
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Caroline Atkinson
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Toby N Trahair
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia. .,School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
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389
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Benezech S, Saintigny P, Attignon V, Pissaloux D, Paindavoine S, Faure-Conter C, Corradini N, Marec-Berard P, Bergeron C, Cassier P, Eberst L, Dufresne A, Wang Q, Agrapart V, De La Fouchardière A, Perol D, Garin G, Corset V, Ben Abdesselem L, Chabaud S, Tredan O, Blay JY, Frappaz D. Tumor Molecular Profiling: Pediatric Results of the ProfiLER Study. JCO Precis Oncol 2020; 4:785-795. [PMID: 35050753 DOI: 10.1200/po.20.00023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The Program to Establish the Genetic and Immunologic Profile of Patient's Tumor for All Types of Advanced Cancer study (ClinicalTrials.gov identifier: NCT01774409) analyzed the genome of refractory cancers to identify a potential molecular-based recommended therapy (MBRT). The objectives of the pediatric substudy were to describe the incidence of genomic mutations, the MBRT, and the treatments undertaken with a molecular-targeted agent in a pediatric cohort. METHODS The tumor genome was analyzed within a 69-gene next-generation sequencing panel and an array comparative genomic hybridization assay. The results were evaluated by a multidisciplinary molecular board, and the targeted therapies were provided in the setting of a clinical trial or through compassionate use programs, when indicated. RESULTS Between November 2013 and June 2017, 50 patients younger than 19 years who were treated for a high-risk or relapsing tumor were included. Sarcomas (n = 24; 47%), CNS tumors (n = 14; 29%), and neuroblastomas (n = 5; 10%) were the most frequent tumor subtypes. Seven patients (14%) were excluded because no DNA could be recovered. Among the 43 remaining patients, 10 exhibited at least one targetable genomic alteration. Ultimately, four patients (8%) were treated with the recommended targeted therapy. CONCLUSION The results of this study confirm treatment with a targeted therapy for pediatric patients with cancer is still limited at present, as also is reported for adults.
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Affiliation(s)
- Sarah Benezech
- Institut d'Hématologie et Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
| | - Pierre Saintigny
- Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, France
| | - Valery Attignon
- Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Daniel Pissaloux
- Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
| | | | - Cécile Faure-Conter
- Institut d'Hématologie et Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
| | - Nadège Corradini
- Institut d'Hématologie et Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
| | - Perrine Marec-Berard
- Institut d'Hématologie et Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
| | - Christophe Bergeron
- Institut d'Hématologie et Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
| | | | | | | | - Qing Wang
- Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Vincent Agrapart
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | | | - David Perol
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Gwenaëlle Garin
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Véronique Corset
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Leila Ben Abdesselem
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Sylvie Chabaud
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Olivier Tredan
- Department of Medical Oncology, Centre Léon Bérard, France.,University Claude Bernard Lyon 1, CNRS 5286, INSERM U1052, Cancer Research Center of Lyon, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, France.,University Claude Bernard Lyon 1, CNRS 5286, INSERM U1052, Cancer Research Center of Lyon, France
| | - Didier Frappaz
- Institut d'Hématologie et Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
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390
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Wong M, Mayoh C, Lau LMS, Khuong-Quang DA, Pinese M, Kumar A, Barahona P, Wilkie EE, Sullivan P, Bowen-James R, Syed M, Martincorena I, Abascal F, Sherstyuk A, Bolanos NA, Baber J, Priestley P, Dolman MEM, Fleuren EDG, Gauthier ME, Mould EVA, Gayevskiy V, Gifford AJ, Grebert-Wade D, Strong PA, Manouvrier E, Warby M, Thomas DM, Kirk J, Tucker K, O'Brien T, Alvaro F, McCowage GB, Dalla-Pozza L, Gottardo NG, Tapp H, Wood P, Khaw SL, Hansford JR, Moore AS, Norris MD, Trahair TN, Lock RB, Tyrrell V, Haber M, Marshall GM, Ziegler DS, Ekert PG, Cowley MJ. Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer. Nat Med 2020; 26:1742-1753. [PMID: 33020650 DOI: 10.1038/s41591-020-1072-4] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/20/2020] [Indexed: 02/08/2023]
Abstract
The Zero Childhood Cancer Program is a precision medicine program to benefit children with poor-outcome, rare, relapsed or refractory cancer. Using tumor and germline whole genome sequencing (WGS) and RNA sequencing (RNAseq) across 252 tumors from high-risk pediatric patients with cancer, we identified 968 reportable molecular aberrations (39.9% in WGS and RNAseq, 35.1% in WGS only and 25.0% in RNAseq only). Of these patients, 93.7% had at least one germline or somatic aberration, 71.4% had therapeutic targets and 5.2% had a change in diagnosis. WGS identified pathogenic cancer-predisposing variants in 16.2% of patients. In 76 central nervous system tumors, methylome analysis confirmed diagnosis in 71.1% of patients and contributed to a change of diagnosis in two patients (2.6%). To date, 43 patients have received a recommended therapy, 38 of whom could be evaluated, with 31% showing objective evidence of clinical benefit. Comprehensive molecular profiling resolved the molecular basis of virtually all high-risk cancers, leading to clinical benefit in some patients.
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Affiliation(s)
- Marie Wong
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Loretta M S Lau
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Amit Kumar
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Paulette Barahona
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Emilie E Wilkie
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Rachel Bowen-James
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Mustafa Syed
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | | | | | - Alexandra Sherstyuk
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Noemi A Bolanos
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Jonathan Baber
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - Peter Priestley
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - M Emmy M Dolman
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Marie-Emilie Gauthier
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Emily V A Mould
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Dylan Grebert-Wade
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Patrick A Strong
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Elodie Manouvrier
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Meera Warby
- Cancer Centre for Children, The Children's Hospital Westmead, Westmead, NSW, Australia
| | - David M Thomas
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Katherine Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW, Australia
- Prince of Wales Hospital Clinical School, University of New South Wales, Randwick, NSW, Australia
| | - Tracey O'Brien
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Frank Alvaro
- John Hunter Children's Hospital, New Lambton Heights, NSW, Australia
| | - Geoffry B McCowage
- Cancer Centre for Children, The Children's Hospital Westmead, Westmead, NSW, Australia
| | - Luciano Dalla-Pozza
- Cancer Centre for Children, The Children's Hospital Westmead, Westmead, NSW, Australia
| | - Nicholas G Gottardo
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children's Hospital, Nedlands, WA, Australia
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
| | - Heather Tapp
- Women's and Children's Hospital, Adelaide, SA, Australia
| | - Paul Wood
- Monash Children's Hospital, Melbourne, VIC, Australia
| | - Seong-Lin Khaw
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
| | - Andrew S Moore
- Oncology Service, Oncology Service, Queensland Children's Hospital, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Toby N Trahair
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Vanessa Tyrrell
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
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391
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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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392
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Transcriptome Analysis Identifies Novel Prognostic Genes in Osteosarcoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:8081973. [PMID: 33082842 PMCID: PMC7559853 DOI: 10.1155/2020/8081973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
Osteosarcoma (OS), a malignant primary bone tumor often seen in young adults, is highly aggressive. The improvements in high-throughput technologies have accelerated the identification of various prognostic biomarkers for cancer survival prediction. However, only few studies focus on the prediction of prognosis in OS patients using gene expression data due to small sample size and the lack of public datasets. In the present study, the RNA-seq data of 82 OS samples, along with their clinical information, were collected from the TARGET database. To identify the prognostic genes for the OS survival prediction, we selected the top 50 genes of contribution as the initial candidate genes of the prognostic risk model, which were ranked by random forest model, and found that the prognostic model with five predictors including CD180, MYC, PROSER2, DNAI1, and FATE1 was the optimal multivariable Cox regression model. Moreover, based on a multivariable Cox regression model, we also developed a scoring method and stratified the OS patients into groups of different risks. The stratification for OS patients in the validation set further demonstrated that our model has a robust performance. In addition, we also investigated the biological function of differentially expressed genes between two risk groups and found that those genes were mainly involved with biological pathways and processes regarding immunity. In summary, the identification of novel prognostic biomarkers in OS would greatly assist the prediction of OS survival and development of molecularly targeted therapies, which in turn benefit patients' survival.
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393
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Brady SW, Liu Y, Ma X, Gout AM, Hagiwara K, Zhou X, Wang J, Macias M, Chen X, Easton J, Mulder HL, Rusch M, Wang L, Nakitandwe J, Lei S, Davis EM, Naranjo A, Cheng C, Maris JM, Downing JR, Cheung NKV, Hogarty MD, Dyer MA, Zhang J. Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations. Nat Commun 2020; 11:5183. [PMID: 33056981 PMCID: PMC7560655 DOI: 10.1038/s41467-020-18987-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma is a pediatric malignancy with heterogeneous clinical outcomes. To better understand neuroblastoma pathogenesis, here we analyze whole-genome, whole-exome and/or transcriptome data from 702 neuroblastoma samples. Forty percent of samples harbor at least one recurrent driver gene alteration and most aberrations, including MYCN, ATRX, and TERT alterations, differ in frequency by age. MYCN alterations occur at median 2.3 years of age, TERT at 3.8 years, and ATRX at 5.6 years. COSMIC mutational signature 18, previously associated with reactive oxygen species, is the most common cause of driver point mutations in neuroblastoma, including most ALK and Ras-activating variants. Signature 18 appears early and is continuous throughout disease evolution. Signature 18 is enriched in neuroblastomas with MYCN amplification, 17q gain, and increased expression of mitochondrial ribosome and electron transport-associated genes. Recurrent FGFR1 variants in six patients, and ALK N-terminal structural alterations in five samples, identify additional patients potentially amenable to precision therapy.
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Affiliation(s)
- Samuel W Brady
- 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
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alexander M Gout
- 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
| | - 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
| | - Michael Macias
- 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
| | - 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
| | - Michael Rusch
- 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
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shaohua Lei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Eric M Davis
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Arlene Naranjo
- Department of Biostatistics, University of Florida, Children's Oncology Group Statistics & Data Center, Gainesville, FL, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D Hogarty
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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394
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Gap between pediatric and adult approvals of molecular targeted drugs. Sci Rep 2020; 10:17145. [PMID: 33051474 PMCID: PMC7555892 DOI: 10.1038/s41598-020-73028-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/04/2020] [Indexed: 12/24/2022] Open
Abstract
To clarify the approval status of molecular targeted antineoplastic drugs in the United States (U.S.), the European Union (E.U.), and Japan (JP), we checked the status of pediatric indications according to the package insert of each drug. A total of 103 drugs were approved for adult patients in at least one of the three regions whereas only 19 drugs were approved for pediatric patients. Sixty-six of 103 drugs (64.1%) had adult indications in the U.S., the E.U., and JP, whereas only three drugs had pediatric indications in all three regions. Abnormalities in six genes (NRAS, ABL1, JAK2, KIT, ALK and BRAF) were common in childhood cancers as well as adult cancers, for which at least one approved drug could be a potentially actionable drug. Although there were 16 candidate drugs that had adult indications for these abnormalities, only three drugs (18.8%) had pediatric indications. We confirmed that there were few molecular targeted antineoplastic drugs with pediatric indications in the U.S., the E.U., and JP compared with the number of approved drugs for adults. Drugs targeting genomic abnormalities which were common in both adult and pediatric cancers were considered to be good candidates for expansion of their indication for pediatric patients.
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395
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Wu Y, Zhu H, Wu H. PTEN in Regulating Hematopoiesis and Leukemogenesis. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036244. [PMID: 31712222 DOI: 10.1101/cshperspect.a036244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PTEN is one of the most frequently mutated tumor suppressor genes in human cancers. By counteracting the PI3K/AKT/mTOR pathway, PTEN plays an essential role in regulating hematopoietic stem cells (HSCs) self-renewal, migration, lineage commitment, and differentiation. PTEN also plays important roles in suppressing leukemogenesis, especially T-cell acute lymphoblastic leukemia (T-ALL). Herein, we will review the function of PTEN in regulating hematopoiesis and leukemogenesis and discuss potential therapeutic approaches against leukemia with PTEN mutations.
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Affiliation(s)
- Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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396
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Fang C, Rao S, Crispino JD, Ntziachristos P. Determinants and role of chromatin organization in acute leukemia. Leukemia 2020; 34:2561-2575. [PMID: 32690881 PMCID: PMC7999176 DOI: 10.1038/s41375-020-0981-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
DNA is compacted into higher order structures that have major implications in gene regulation. These structures allow for long-range interactions of DNA elements, such as the association of promoters with their cognate enhancers. In recent years, mutations in genes that control these structures, including the cohesin-complex and the insulator-binding protein CTCF, have been found in a spectrum of hematologic disorders, and especially in acute leukemias. Cohesin and CTCF are critical for mediating looping and establishing boundaries within chromatin. Cells that harbor mutations in these genes display aberrant chromatin architecture and resulting differences in gene expression that contribute to leukemia initiation and progression. Here, we provide detailed discussion of the nature of 3D interactions and the way that they are disrupted in acute leukemia. Continued research in this area will provide new insights into the mechanisms of leukemogenesis and may shed light on novel treatment strategies.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sridhar Rao
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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397
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Martínez-Jiménez F, Muiños F, Sentís I, Deu-Pons J, Reyes-Salazar I, Arnedo-Pac C, Mularoni L, Pich O, Bonet J, Kranas H, Gonzalez-Perez A, Lopez-Bigas N. A compendium of mutational cancer driver genes. Nat Rev Cancer 2020; 20:555-572. [PMID: 32778778 DOI: 10.1038/s41568-020-0290-x] [Citation(s) in RCA: 503] [Impact Index Per Article: 125.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
A fundamental goal in cancer research is to understand the mechanisms of cell transformation. This is key to developing more efficient cancer detection methods and therapeutic approaches. One milestone towards this objective is the identification of all the genes with mutations capable of driving tumours. Since the 1970s, the list of cancer genes has been growing steadily. Because cancer driver genes are under positive selection in tumorigenesis, their observed patterns of somatic mutations across tumours in a cohort deviate from those expected from neutral mutagenesis. These deviations, which constitute signals of positive selection, may be detected by carefully designed bioinformatics methods, which have become the state of the art in the identification of driver genes. A systematic approach combining several of these signals could lead to a compendium of mutational cancer genes. In this Review, we present the Integrative OncoGenomics (IntOGen) pipeline, an implementation of such an approach to obtain the compendium of mutational cancer drivers. Its application to somatic mutations of more than 28,000 tumours of 66 cancer types reveals 568 cancer genes and points towards their mechanisms of tumorigenesis. The application of this approach to the ever-growing datasets of somatic tumour mutations will support the continuous refinement of our knowledge of the genetic basis of cancer.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Deu-Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Iker Reyes-Salazar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jose Bonet
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hanna Kranas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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398
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Graham MS, Mellinghoff IK. Histone-Mutant Glioma: Molecular Mechanisms, Preclinical Models, and Implications for Therapy. Int J Mol Sci 2020; 21:E7193. [PMID: 33003625 PMCID: PMC7582376 DOI: 10.3390/ijms21197193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
Pediatric high-grade glioma (pHGG) is the leading cause of cancer death in children. Despite histologic similarities, it has recently become apparent that this disease is molecularly distinct from its adult counterpart. Specific hallmark oncogenic histone mutations within pediatric malignant gliomas divide these tumors into subgroups with different neuroanatomic and chronologic predilections. In this review, we will summarize the characteristic molecular alterations of pediatric high-grade gliomas, with a focus on how preclinical models of these alterations have furthered our understanding of their oncogenicity as well as their potential impact on developing targeted therapies for this devastating disease.
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Affiliation(s)
- Maya S. Graham
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Ingo K. Mellinghoff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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399
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Pearson AD, Stegmaier K, Bourdeaut F, Reaman G, Heenen D, Meyers ML, Armstrong SA, Brown P, De Carvalho D, Jabado N, Marshall L, Rivera M, Smith M, Adamson PC, Barone A, Baumann C, Blackman S, Buenger V, Donoghue M, Duncan AD, Fox E, Gadbaw B, Hattersley M, Ho P, Jacobs I, Kelly MJ, Kieran M, Lesa G, Ligas F, Ludwinski D, McDonough J, Nikolova Z, Norga K, Senderowicz A, Taube T, Weiner S, Karres D, Vassal G. Paediatric Strategy Forum for medicinal product development of epigenetic modifiers for children: ACCELERATE in collaboration with the European Medicines Agency with participation of the Food and Drug Administration. Eur J Cancer 2020; 139:135-148. [PMID: 32992153 DOI: 10.1016/j.ejca.2020.08.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022]
Abstract
The fifth multistakeholder Paediatric Strategy Forum focussed on epigenetic modifier therapies for children and adolescents with cancer. As most mutations in paediatric malignancies influence chromatin-associated proteins or transcription and paediatric cancers are driven by developmental gene expression programs, targeting epigenetic mechanisms is predicted to be a very important therapeutic approach in paediatric cancer. The Research to Accelerate Cures and Equity (RACE) for Children Act FDARA amendments to section 505B of the FD&C Act was implemented in August 2020, and as there are many epigenetic targets on the FDA Paediatric Molecular Targets List, clinical evaluation of epigenetic modifiers in paediatric cancers should be considered early in drug development. Companies are also required to submit to the EMA paediatric investigation plans aiming to ensure that the necessary data to support the authorisation of a medicine for children in EU are of high quality and ethically researched. The specific aims of the forum were i) to identify epigenetic targets or mechanisms of action associated with epigenetic modification relevant to paediatric cancers and ii) to define the landscape for paediatric drug development of epigenetic modifier therapies. DNA methyltransferase inhibitors/hypomethylating agents and histone deacetylase inhibitors were largely excluded from discussion as the aim was to discuss those targets for which therapeutic agents are currently in early paediatric and adult development. Epigenetics is an evolving field and could be highly relevant to many paediatric cancers; the biology is multifaceted and new targets are frequently emerging. Targeting epigenetic mechanisms in paediatric malignancy has in most circumstances yet to reach or extend beyond clinical proof of concept, as many targets do not yet have available investigational drugs developed. Eight classes of medicinal products were discussed and prioritised based on the existing level of science to support early evaluation in children: inhibitors of menin, DOT1L, EZH2, EED, BET, PRMT5 and LSD1 and a retinoic acid receptor alpha agonist. Menin inhibitors should be moved rapidly into paediatric development, in view of their biological rationale, strong preclinical activity and ability to fulfil an unmet clinical need. A combination approach is critical for successful utilisation of any epigenetic modifiers (e.g. EZH2 and EED) and exploration of the optimum combination(s) should be supported by preclinical research and, where possible, molecular biomarker validation in advance of clinical translation. A follow-up multistakeholder meeting focussing on BET inhibitors will be held to define how to prioritise the multiple compounds in clinical development that could be evaluated in children with cancer. As epigenetic modifiers are relatively early in development in paediatrics, there is a clear opportunity to shape the landscape of therapies targeting the epigenome in order that efficient and optimum plans for their evaluation in children and adolescents are developed in a timely manner.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lynley Marshall
- Royal Marsden NHS Foundation Trust/Institute of Cancer Research, UK
| | | | | | - Peter C Adamson
- Sanofi US, Emeritus Professor of Paediatrics and Pharmacology, Perelman School of Medicine, University of Pennsylvania, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Giovanni Lesa
- Paediatric Medicines Office, Scientific Evidence Generation Department, Human Medicines Division, European Medicines Agency (EMA), Amsterdam, Netherlands
| | - Franca Ligas
- Paediatric Medicines Office, Scientific Evidence Generation Department, Human Medicines Division, European Medicines Agency (EMA), Amsterdam, Netherlands
| | | | | | | | - Koen Norga
- Antwerp University Hospital, Paediatric Committee of the European Medicines Agency, Federal Agency for Medicines and Health Products, Belgium
| | | | | | | | - Dominik Karres
- Paediatric Medicines Office, Scientific Evidence Generation Department, Human Medicines Division, European Medicines Agency (EMA), Amsterdam, Netherlands
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400
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Tan W, Xie X, Huang Z, Chen L, Tang W, Zhu R, Ye X, Zhang X, Pan L, Gao J, Tang H, Zheng W. Construction of an immune-related genes nomogram for the preoperative prediction of axillary lymph node metastasis in triple-negative breast cancer. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 48:288-297. [PMID: 31858816 DOI: 10.1080/21691401.2019.1703731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immune system disorder is associated with metastasis of triple-negative breast cancers (TNBCs). A robust, individualized immune-related genes (IRGs)-based classifier was aimed to develop and validate in our study to precisely estimate the axillary lymph node (ALN) status preoperatively in patients with early-stage TNBC. We first analyzed RNA sequencing profiles in TNBC patients from The Cancer Genome Atlas database by using bioinformatics approaches, and screened 23 differentially expressed IRGs. A 9-gene panel was generated with an area under the curve (AUC) of 0.77 [95% confidence interval (95% CI), 0.68-0.87]. We detected the 9 ALN-status-related IRGs in the training set (n = 133) and developed a reduced and optimized five-IRGs signature, which effectively distinguished TNBC patients with ALN metastasis (AUC, 0.80; 95% CI, 0.65-0.86), and was superior to preoperative ultrasound-based ALN status (AUC, 0.73; 95% CI, 0.53-0.93). Predictive efficiency (AUC, 0.77; 95% CI 0.61-0.93) of this five-IRGs signature was validated in the validation set (n = 81). Furthermore, IRGs nomogram incorporated IRGs signature with US-based ALN status showed higher ALN status prediction efficacy than US-based ALN status and five-IRGs signature alone in both training and validation sets. IRGs nomogram may aid in identifying patients who can be exempted from axillary surgery.Novelty and impact: An immune-related genes (IRGs) nomogram was first developed and externally validated in our study, which incorporated the IRGs signature with ultrasound (US)-based axillary lymph nodes (ALN) status. IRGs nomogram is superior to IRGs signature alone for preoperative estimation of ALN metastasis in patients with triple-negative breast cancer (TNBC). It is a favourable biomarker for preoperatively predicting ALN metastasis risk and may aid in clinical decision-making in early-stage TNBCs.
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Affiliation(s)
- Weige Tan
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xinhua Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Zhongying Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Lun Chen
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Tang
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Renjie Zhu
- East Hospital Affiliated to Tongji University, Shanghai, China
| | - Xigang Ye
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoshen Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lingxiao Pan
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jin Gao
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wenbo Zheng
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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