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Gutierrez-Camino A, Richer C, Ouimet M, Fuchs C, Langlois S, Khater F, Caron M, Beaulieu P, St-Onge P, Bataille AR, Sinnett D. Characterisation of FLT3 alterations in childhood acute lymphoblastic leukaemia. Br J Cancer 2024; 130:317-326. [PMID: 38049555 PMCID: PMC10803556 DOI: 10.1038/s41416-023-02511-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Alterations of FLT3 are among the most common driver events in acute leukaemia with important clinical implications, since it allows patient classification into prognostic groups and the possibility of personalising therapy thanks to the availability of FLT3 inhibitors. Most of the knowledge on FLT3 implications comes from the study of acute myeloid leukaemia and so far, few studies have been performed in other leukaemias. METHODS A comprehensive genomic (DNA-seq in 267 patients) and transcriptomic (RNA-seq in 160 patients) analysis of FLT3 in 342 childhood acute lymphoblastic leukaemia (ALL) patients was performed. Mutations were functionally characterised by in vitro experiments. RESULTS Point mutations (PM) and internal tandem duplications (ITD) were detected in 4.3% and 2.7% of the patients, respectively. A new activating mutation of the TKD, G846D, conferred oncogenic properties and sorafenib resistance. Moreover, a novel alteration involving the circularisation of read-through transcripts (rt-circRNAs) was observed in 10% of the cases. Patients presenting FLT3 alterations exhibited higher levels of the receptor. In addition, patients with ZNF384- and MLL/KMT2A-rearranged ALL, as well as hyperdiploid subtype, overexpressed FLT3. DISCUSSION Our results suggest that specific ALL subgroups may also benefit from a deeper understanding of the biology of FLT3 alterations and their clinical implications.
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Affiliation(s)
- Angela Gutierrez-Camino
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Chantal Richer
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Manon Ouimet
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Claire Fuchs
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Sylvie Langlois
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Fida Khater
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Maxime Caron
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Patrick Beaulieu
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Pascal St-Onge
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Alain R Bataille
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada.
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.
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2
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Lee C, Kim HN, Kwon JA, Hwang J, Park JY, Shin OS, Yoon SY, Yoon J. Identification of a Complex Karyotype Signature with Clinical Implications in AML and MDS-EB Using Gene Expression Profiling. Cancers (Basel) 2023; 15:5289. [PMID: 37958462 PMCID: PMC10648390 DOI: 10.3390/cancers15215289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Complex karyotype (CK) is associated with a poor prognosis in both acute myeloid leukemia (AML) and myelodysplastic syndrome with excess blasts (MDS-EB). Transcriptomic analyses have improved our understanding of the disease and risk stratification of myeloid neoplasms; however, CK-specific gene expression signatures have been rarely investigated. In this study, we developed and validated a CK-specific gene expression signature. Differential gene expression analysis between the CK and non-CK groups using data from 348 patients with AML and MDS-EB from four cohorts revealed enrichment of the downregulated genes localized on chromosome 5q or 7q, suggesting that haploinsufficiency due to the deletion of these chromosomes possibly underlies CK pathogenesis. We built a robust transcriptional model for CK prediction using LASSO regression for gene subset selection and validated it using the leave-one-out cross-validation method for fitting the logistic regression model. We established a 10-gene CK signature (CKS) predictive of CK with high predictive accuracy (accuracy 94.22%; AUC 0.977). CKS was significantly associated with shorter overall survival in three independent cohorts, and was comparable to that of previously established risk stratification models for AML. Furthermore, we explored of therapeutic targets among the genes comprising CKS and identified the dysregulated expression of superoxide dismutase 1 (SOD1) gene, which is potentially amenable to SOD1 inhibitors.
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Affiliation(s)
- Cheonghwa Lee
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 08308, Republic of Korea; (C.L.); (H.N.K.); (J.A.K.); (J.H.)
| | - Ha Nui Kim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 08308, Republic of Korea; (C.L.); (H.N.K.); (J.A.K.); (J.H.)
| | - Jung Ah Kwon
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 08308, Republic of Korea; (C.L.); (H.N.K.); (J.A.K.); (J.H.)
| | - Jinha Hwang
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 08308, Republic of Korea; (C.L.); (H.N.K.); (J.A.K.); (J.H.)
| | - Ji-Ye Park
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea (O.S.S.)
| | - Ok Sarah Shin
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea (O.S.S.)
| | - Soo-Young Yoon
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 08308, Republic of Korea; (C.L.); (H.N.K.); (J.A.K.); (J.H.)
| | - Jung Yoon
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 08308, Republic of Korea; (C.L.); (H.N.K.); (J.A.K.); (J.H.)
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3
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Davis K, Sheikh T, Aggarwal N. Emerging molecular subtypes and therapies in acute lymphoblastic leukemia. Semin Diagn Pathol 2023; 40:202-215. [PMID: 37120350 DOI: 10.1053/j.semdp.2023.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/01/2023]
Abstract
Tremendous strides have been made in the molecular and cytogenetic classification of acute lymphoblastic leukemia based on gene expression profiling data, leading to an expansion of entities in the recent International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias and 2022 WHO Classification of Tumours: Haematolymphoid Tumors, 5th edition. This increased diagnostic and therapeutic complexity can be overwhelming, and this review compares nomenclature differences between the ICC and WHO 5th edition publications, compiles key features of each entity, and provides a diagnostic algorithmic approach. In covering B-lymphoblastic leukemia (B-ALL), we divided the entities into established (those present in the revised 4th edition WHO) and novel (those added to either the ICC or WHO 5th edition) groups. The established B-ALL entities include B-ALL with BCR::ABL1 fusion, BCR::ABL1-like features, KMT2A rearrangement, ETV6::RUNX1 rearrangement, high hyperdiploidy, hypodiploidy (focusing on near haploid and low hypodiploid), IGH::IL3 rearrangement, TCF3::PBX1 rearrangement, and iAMP21. The novel B-ALL entities include B-ALL with MYC rearrangement; DUX4 rearrangement; MEF2D rearrangement; ZNF384 or ZNF362 rearrangement, NUTM1 rearrangement; HLF rearrangement; UBTF::ATXN7L3/PAN3,CDX2; mutated IKZF1 N159Y; mutated PAX5 P80R; ETV6::RUNX1-like features; PAX5 alteration; mutated ZEB2 (p.H1038R)/IGH::CEBPE; ZNF384 rearranged-like; KMT2A-rearranged-like; and CRLF2 rearrangement (non-Ph-like). Classification of T-ALL is complex with some variability in how the subtypes are defined in recent literature. It was classified as early T-precursor lymphoblastic leukemia/lymphoma and T-ALL, NOS in the WHO revised 4th edition and WHO 5th edition. The ICC added an entity into early T-cell precursor ALL, BCL11B-activated, and also added provisional entities subclassified based on transcription factor families that are aberrantly activated.
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Affiliation(s)
- Katelynn Davis
- Department of Hematopathology, School of Medicine and UPMC, University of Pittsburgh, USA
| | | | - Nidhi Aggarwal
- Department of Hematopathology, School of Medicine and UPMC, University of Pittsburgh, USA.
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4
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Yasuda T, Sanada M, Tsuzuki S, Hayakawa F. Oncogenic lesions and molecular subtypes in adults with B-cell acute lymphoblastic leukemia. Cancer Sci 2022; 114:8-15. [PMID: 36106363 PMCID: PMC9807527 DOI: 10.1111/cas.15583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/12/2022] [Accepted: 09/04/2022] [Indexed: 01/07/2023] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL), a genetically heterogeneous disease, is classified into different molecular subtypes that are defined by recurrent gene rearrangements, gross chromosomal abnormalities, or specific gene mutations. Cells with these genetic alterations acquire a leukemia-initiating ability and show unique expression profiles. The distribution of B-ALL molecular subtypes is greatly dependent on age, which also affects treatment responsiveness and long-term survival, partly accounting for the inferior outcome in adolescents and young adults (AYA) and (older) adults with B-ALL. Recent advances in sequencing technology, especially RNA sequencing and the application of these technologies in large B-ALL cohorts have uncovered B-ALL molecular subtypes prevalent in AYA and adults. These new insights supply more precise estimations of prognoses and targeted therapies informed by sequencing results, as well as a deeper understanding of the genetic basis of AYA/adult B-ALL. This article provides an account of these technological advances and an overview of the recent major findings of B-ALL molecular subtypes in adults.
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Affiliation(s)
- Takahiko Yasuda
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Masashi Sanada
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Shinobu Tsuzuki
- Department of BiochemistryAichi Medical University School of MedicineNagakuteJapan
| | - Fumihiko Hayakawa
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
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5
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Zhao X, Wang P, Diedrich JD, Smart B, Reyes N, Yoshimura S, Zhang J, Yang W, Barnett K, Xu B, Li Z, Huang X, Yu J, Crews K, Yeoh AEJ, Konopleva M, Wei CL, Pui CH, Savic D, Yang JJ. Epigenetic activation of the FLT3 gene by ZNF384 fusion confers a therapeutic susceptibility in acute lymphoblastic leukemia. Nat Commun 2022; 13:5401. [PMID: 36104354 PMCID: PMC9474531 DOI: 10.1038/s41467-022-33143-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
FLT3 is an attractive therapeutic target in acute lymphoblastic leukemia (ALL) but the mechanism for its activation in this cancer is incompletely understood. Profiling global gene expression in large ALL cohorts, we identify over-expression of FLT3 in ZNF384-rearranged ALL, consistently across cases harboring different fusion partners with ZNF384. Mechanistically, we discover an intergenic enhancer element at the FLT3 locus that is exclusively activated in ZNF384-rearranged ALL, with the enhancer-promoter looping directly mediated by the fusion protein. There is also a global enrichment of active enhancers within ZNF384 binding sites across the genome in ZNF384-rearranged ALL cells. Downregulation of ZNF384 blunts FLT3 activation and decreases ALL cell sensitivity to FLT3 inhibitor gilteritinib in vitro. In patient-derived xenograft models of ZNF384-rearranged ALL, gilteritinib exhibits significant anti-leukemia efficacy as a monotherapy in vivo. Collectively, our results provide insights into FLT3 regulation in ALL and point to potential genomics-guided targeted therapy for this patient population.
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Affiliation(s)
- Xujie Zhao
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jonathan D Diedrich
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon Smart
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Noemi Reyes
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingliao Zhang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kelly Barnett
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allen Eng Juh Yeoh
- Department of Pediatrics, National University of Singapore, Singapore, Singapore
| | - Marina Konopleva
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling. PLoS Comput Biol 2022; 18:e1010438. [PMID: 35994503 PMCID: PMC9436053 DOI: 10.1371/journal.pcbi.1010438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/01/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
The development of cancer therapies may be improved by the discovery of tumor-specific molecular dependencies. The requisite tools include genetic and chemical perturbations, each with its strengths and limitations. Chemical perturbations can be readily applied to primary cancer samples at large scale, but mechanistic understanding of hits and further pharmaceutical development is often complicated by the fact that a chemical compound has affinities to multiple proteins. To computationally infer specific molecular dependencies of individual cancers from their ex vivo drug sensitivity profiles, we developed a mathematical model that deconvolutes these data using measurements of protein-drug affinity profiles. Through integrating a drug-kinase profiling dataset and several drug response datasets, our method, DepInfeR, correctly identified known protein kinase dependencies, including the EGFR dependence of HER2+ breast cancer cell lines, the FLT3 dependence of acute myeloid leukemia (AML) with FLT3-ITD mutations and the differential dependencies on the B-cell receptor pathway in the two major subtypes of chronic lymphocytic leukemia (CLL). Furthermore, our method uncovered new subgroup-specific dependencies, including a previously unreported dependence of high-risk CLL on Checkpoint kinase 1 (CHEK1). The method also produced a detailed map of the kinase dependencies in a heterogeneous set of 117 CLL samples. The ability to deconvolute polypharmacological phenotypes into underlying causal molecular dependencies should increase the utility of high-throughput drug response assays for functional precision oncology. As survival and proliferation of cancer cells depend on molecular aberrations that can be highly specific to cancer types and individual tumors, identifying such dependence is pivotal to designing individualized tumor therapy. Chemical perturbations, through screening of bioactive compounds using primary cancer cells, provide an important tool for identifying tumor-specific dependencies. However, many chemical compounds bind multiple proteins, which complicates interpreting screening results and pinpointing the phenotype-causing target. To overcome this challenge and increase the utility of drug screening approaches for functional precision medicine, we developed a computational framework, DepInfeR, to identify tumor-specific dependencies on druggable proteins through integrating two sources of information: drug sensitivity assays and drug-protein affinity profiling. Our approach correctly identifies known kinase dependencies, which validates our approach. Furthermore, by integrating a newly generated drug screening dataset on primary tumor samples, we discovered a previously unreported survival dependence on Checkpoint kinase 1 (CHEK1) by a molecular subgroup of chronic lymphocytic leukemia samples, highlighting the clinical potential of our method.
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7
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Dickerson KM, Qu C, Gao Q, Iacobucci I, Gu Z, Yoshihara H, Backhaus EA, Chang Y, Janke LJ, Xu B, Wu G, Papachristou EK, D'Santos CS, Roberts KG, Mullighan CG. ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia. Blood Cancer Discov 2022; 3:240-263. [PMID: 35247902 DOI: 10.1158/2643-3230.bcd-21-0163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/21/2021] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
ZNF384-rearranged fusion oncoproteins (FO) define a subset of lineage ambiguous leukemias, but their mechanistic role in leukemogenesis and lineage ambiguity is poorly understood. Using viral expression in mouse and human hematopoietic stem and progenitor cells (HSPCs) and a Ep300::Znf384 knockin mouse model, we show that ZNF384 FO promote hematopoietic expansion, myeloid lineage skewing, and self-renewal. In mouse HSPCs, concomitant lesions, such as NRASG12D, were required for fully penetrant leukemia, whereas in human HSPCs expression of ZNF384 FO drove B/myeloid leukemia, with sensitivity of a ZNF384-rearranged xenograft to FLT3 inhibition in vivo. Mechanistically, ZNF384 FO occupy a subset of predominantly intragenic/enhancer regions with increased histone 3 lysine acetylation and deregulate expression of hematopoietic stem cell transcription factors. These data define a paradigm for FO-driven lineage ambiguous leukemia, in which expression in HSPCs results in deregulation of lineage-specific genes and hematopoietic skewing, progressing to full leukemia in the context of proliferative stress.
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Affiliation(s)
| | - Chunxu Qu
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Qingsong Gao
- St. Jude Children's Research Hospital, Memphis, United States
| | - Ilaria Iacobucci
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Zhaohui Gu
- City Of Hope National Medical Center, United States
| | | | - Emily A Backhaus
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Yunchao Chang
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Laura J Janke
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Beisi Xu
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Gang Wu
- St. Jude Children's Research Hospital, Memphis, United States
| | | | - Clive S D'Santos
- Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom
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8
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Lejman M, Chałupnik A, Chilimoniuk Z, Dobosz M. Genetic Biomarkers and Their Clinical Implications in B-Cell Acute Lymphoblastic Leukemia in Children. Int J Mol Sci 2022; 23:2755. [PMID: 35269896 PMCID: PMC8911213 DOI: 10.3390/ijms23052755] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a heterogeneous group of hematologic malignancies characterized by abnormal proliferation of immature lymphoid cells. It is the most commonly diagnosed childhood cancer with an almost 80% cure rate. Despite favorable survival rates in the pediatric population, a significant number of patients develop resistance to therapy, resulting in poor prognosis. ALL is a heterogeneous disease at the genetic level, but the intensive development of sequencing in the last decade has made it possible to broaden the study of genomic changes. New technologies allow us to detect molecular changes such as point mutations or to characterize epigenetic or proteomic profiles. This process made it possible to identify new subtypes of this disease characterized by constellations of genetic alterations, including chromosome changes, sequence mutations, and DNA copy number alterations. These genetic abnormalities are used as diagnostic, prognostic and predictive biomarkers that play an important role in earlier disease detection, more accurate risk stratification, and treatment. Identification of new ALL biomarkers, and thus a greater understanding of their molecular basis, will lead to better monitoring of the course of the disease. In this article, we provide an overview of the latest information on genomic alterations found in childhood ALL and discuss their impact on patients' clinical outcomes.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Aleksandra Chałupnik
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
| | - Zuzanna Chilimoniuk
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
| | - Maciej Dobosz
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
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9
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Xu H, Yu H, Jin R, Wu X, Chen H. Genetic and Epigenetic Targeting Therapy for Pediatric Acute Lymphoblastic Leukemia. Cells 2021; 10:cells10123349. [PMID: 34943855 PMCID: PMC8699354 DOI: 10.3390/cells10123349] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/06/2021] [Accepted: 11/25/2021] [Indexed: 12/31/2022] Open
Abstract
Acute lymphoblastic leukemia is the most common malignancy in children and is characterized by numerous genetic and epigenetic abnormalities. Epigenetic mechanisms, including DNA methylations and histone modifications, result in the heritable silencing of genes without a change in their coding sequence. Emerging studies are increasing our understanding of the epigenetic role of leukemogenesis and have demonstrated the potential of DNA methylations and histone modifications as a biomarker for lineage and subtypes classification, predicting relapse, and disease progression in acute lymphoblastic leukemia. Epigenetic abnormalities are relatively reversible when treated with some small molecule-based agents compared to genetic alterations. In this review, we conclude the genetic and epigenetic characteristics in ALL and discuss the future role of DNA methylation and histone modifications in predicting relapse, finally focus on the individual and precision therapy targeting epigenetic alterations.
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10
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Alpár D, Egyed B, Bödör C, Kovács GT. Single-Cell Sequencing: Biological Insight and Potential Clinical Implications in Pediatric Leukemia. Cancers (Basel) 2021; 13:5658. [PMID: 34830811 PMCID: PMC8616124 DOI: 10.3390/cancers13225658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/15/2023] Open
Abstract
Single-cell sequencing (SCS) provides high-resolution insight into the genomic, epigenomic, and transcriptomic landscape of oncohematological malignancies including pediatric leukemia, the most common type of childhood cancer. Besides broadening our biological understanding of cellular heterogeneity, sub-clonal architecture, and regulatory network of tumor cell populations, SCS can offer clinically relevant, detailed characterization of distinct compartments affected by leukemia and identify therapeutically exploitable vulnerabilities. In this review, we provide an overview of SCS studies focused on the high-resolution genomic and transcriptomic scrutiny of pediatric leukemia. Our aim is to investigate and summarize how different layers of single-cell omics approaches can expectedly support clinical decision making in the future. Although the clinical management of pediatric leukemia underwent a spectacular improvement during the past decades, resistant disease is a major cause of therapy failure. Currently, only a small proportion of childhood leukemia patients benefit from genomics-driven therapy, as 15-20% of them meet the indication criteria of on-label targeted agents, and their overall response rate falls in a relatively wide range (40-85%). The in-depth scrutiny of various cell populations influencing the development, progression, and treatment resistance of different disease subtypes can potentially uncover a wider range of driver mechanisms for innovative therapeutic interventions.
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Affiliation(s)
- Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary; (D.A.); (B.E.); (C.B.)
| | - Bálint Egyed
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary; (D.A.); (B.E.); (C.B.)
- 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary; (D.A.); (B.E.); (C.B.)
| | - Gábor T. Kovács
- 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
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11
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Zhang XY, Dai HP, Zhang L, Liu SN, Dai Y, Wu DP, Tang XW. MRD-Negative Remission Induced in EP300-ZNF384 Positive B-ALL Patients by Tandem CD19/CD22 CAR T-Cell Therapy Bridging to Allogeneic Stem Cell Transplantation. Onco Targets Ther 2021; 14:5197-5204. [PMID: 34744437 PMCID: PMC8565984 DOI: 10.2147/ott.s324765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/08/2021] [Indexed: 11/23/2022] Open
Abstract
EP300-ZNF384-positive B cell acute lymphoblastic leukemia (B-ALL) patients are reported to have a unique immunophenotype with high expression of CD19 and CD22, weak expression of CD20 and aberrant expression of CD13 and/or CD33, sensitivity to chemotherapy and a favorable outcome. To date, the cases of only 53 patients have been reported, albeit few reports on salvage therapy when conventional chemotherapies failed. Here, we describe two relapsed and refractory adult B-ALL patients with EP300-ZNF384 who achieved second remission through tandem CD19/CD22 CAR T-cell therapy. Grade 3 and 2 cytokine release syndrome were observed in cases 1 and 2, respectively. No immune effector cell-associated neurotoxicity syndrome was detected. Both patients underwent consolidate haploidentical hematopoietic stem cell transplantation (HSCT), and each maintained measurable residual disease-negative remission for 14 and 13 months, respectively. Our study suggests that CD19/CD22 CAR T-cell therapy bridging to allogeneic HSCT may be a viable option for EP300-ZNF384-positive B-ALL.
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Affiliation(s)
- Xin-Yue Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
| | - Hai-Ping Dai
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
| | - Ling Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
| | - Si-Ning Liu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
| | - Yin Dai
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
| | - De-Pei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
| | - Xiao-Wen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, People's Republic of China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215123, People's Republic of China
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12
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Yeung DTO, Osborn MP, White DL. B-cell acute lymphoblastic leukaemia: recent discoveries in molecular pathology, their prognostic significance, and a review of the current classification. Br J Haematol 2021; 197:13-27. [PMID: 34747016 DOI: 10.1111/bjh.17879] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acute lymphoblastic leukaemia (ALL) remains a leading cause of non-traumatic death in children, and the majority of adults diagnosed will succumb to the disease. Recent advances in molecular biology and bioinformatics have enabled more detailed genomic analysis and a better understanding of the molecular biology of ALL. A number of recurrent genomic drivers have recently been described, which not only aid in diagnosis and prognostication, but also may offer opportunities for specific therapeutic targeting. The present review summarises B-ALL genomic pathology at diagnosis, including lesions detectable using traditional cytogenetic methods as well as those detected only through advanced molecular techniques.
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Affiliation(s)
- David T O Yeung
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia.,Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Michael P Osborn
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia.,Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Deborah L White
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia.,Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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13
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Two novel high-risk adult B-cell acute lymphoblastic leukemia subtypes with high expression of CDX2 and IDH1/2 mutations. Blood 2021; 139:1850-1862. [PMID: 34695176 DOI: 10.1182/blood.2021011921] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022] Open
Abstract
The genetic basis of leukemogenesis in adults with B-cell acute lymphoblastic leukemia (B-ALL) is largely unclear and its clinical outcome remains unsatisfactory. This study aimed to advance the understanding of biological characteristics, improve disease stratification, and identify molecular targets of adult B-ALL. Adolescents and young adults (AYA; 15-39 years old, n = 193) and adults (40-64 years old, n = 161) with Philadelphia chromosome-negative B-ALL were included in this study. Integrated transcriptomic and genetic analyses were used to classify the cohort into defined subtypes. Of the 323 cases included in the RNA sequencing analysis, 278 (86.1%) were classified into 18 subtypes. The ZNF384 subtype (22.6%) was the most prevalent, with two novel subtypes (CDX2-high and IDH1/2-mut) identified among cases not assigned to the established subtypes. The CDX2-high subtype (3.4%) was characterized by high expression of CDX2 and recurrent gain of chromosome 1q. The IDH1/2-mut subtype (1.9%) was defined by IDH1 R132C or IDH2 R140Q mutations with specific transcriptional and high-methylation profiles. Both subtypes showed poor prognosis and were considered inferior prognostic factors independent of clinical parameters. Comparison with a previously reported pediatric B-ALL cohort (n = 1003) showed that the frequencies of these subtypes were significantly higher in AYA/adults than in children. We delineated the genetic and transcriptomic landscape of adult B-ALL and identified two novel subtypes that predict poor disease outcomes. Our findings highlight the age-dependent distribution of subtypes, which partially accounts for the prognostic differences between adult and pediatric B-ALL.
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14
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Paietta E, Roberts KG, Wang V, Gu Z, Buck GAN, Pei D, Cheng C, Levine RL, Abdel-Wahab O, Cheng Z, Wu G, Qu C, Shi L, Pounds S, Willman CL, Harvey R, Racevskis J, Barinka J, Zhang Y, Dewald GW, Ketterling RP, Alejos D, Lazarus HM, Luger SM, Foroni L, Patel B, Fielding AK, Melnick A, Marks DI, Moorman AV, Wiernik PH, Rowe JM, Tallman MS, Goldstone AH, Mullighan CG, Litzow MR. Molecular classification improves risk assessment in adult BCR-ABL1-negative B-ALL. Blood 2021; 138:948-958. [PMID: 33895809 PMCID: PMC9069478 DOI: 10.1182/blood.2020010144] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/20/2022] Open
Abstract
Genomic classification has improved risk assignment of pediatric, but not adult B-lineage acute lymphoblastic leukemia (B-ALL). The international UKALLXII/ECOG-ACRIN E2993 (#NCT00002514) trial accrued 1229 adolescent/adult patients with BCR-ABL1- B-ALL (aged 14 to 65 years). Although 93% of patients achieved remission, 41% relapsed at a median of 13 months (range, 28 days to 12 years). Five-year overall survival (OS) was 42% (95% confidence interval, 39, 44). Transcriptome sequencing, gene expression profiling, cytogenetics, and fusion polymerase chain reaction enabled genomic subtyping of 282 patient samples, of which 264 were eligible for trial, accounting for 64.5% of E2993 patients. Among patients with outcome data, 29.5% with favorable outcomes (5-year OS 65% to 80%) were deemed standard risk (DUX4-rearranged [9.2%], ETV6-RUNX1/-like [2.3%], TCF3-PBX1 [6.9%], PAX5 P80R [4.1%], high-hyperdiploid [6.9%]); 50.2% had high-risk genotypes with 5-year OS of 0% to 27% (Ph-like [21.2%], KMT2A-AFF1 [12%], low-hypodiploid/near-haploid [14.3%], BCL2/MYC-rearranged [2.8%]); 20.3% had intermediate-risk genotypes with 5-year OS of 33% to 45% (PAX5alt [12.4%], ZNF384/-like [5.1%], MEF2D-rearranged [2.8%]). IKZF1 alterations occurred in 86% of Ph-like, and TP53 mutations in patients who were low-hypodiploid (54%) and BCL2/MYC-rearranged (33%) but were not independently associated with outcome. Of patients considered high risk based on presenting age and white blood cell count, 40% harbored subtype-defining genetic alterations associated with standard- or intermediate-risk outcomes. We identified distinct immunophenotypic features for DUX4-rearranged, PAX5 P80R, ZNF384-R/-like, and Ph-like genotypes. These data in a large adult B-ALL cohort treated with a non-risk-adapted approach on a single trial show the prognostic importance of genomic analyses, which may translate into future therapeutic benefits.
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Affiliation(s)
| | - Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Victoria Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Zhaohui Gu
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Georgina A N Buck
- Clinical Trial Service Unit, Nuttfield Department of Population Health, Oxford, United Kingdom
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Ross L Levine
- Human Oncology and Pathogenesis Program-Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program-Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zhongshan Cheng
- Centre for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN
| | - Gang Wu
- Centre for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN
| | - Chunxu Qu
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheryl L Willman
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - Richard Harvey
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - Janis Racevskis
- Department of Oncology, Montefiore Medical Center, Bronx, NY
| | - Jan Barinka
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gordon W Dewald
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - David Alejos
- Department of Oncology, Montefiore Medical Center, Bronx, NY
| | - Hillard M Lazarus
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH
| | - Selina M Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Letizia Foroni
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London, United Kingdom
| | - Bela Patel
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | | | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY
| | - David I Marks
- Bristol Haematology and Oncology Centre, Bristol, United Kingdom
| | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Newcastle University Translational and Clinical Research Institute, Newcastle-upon-Tyne, United Kingdom
| | | | - Jacob M Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Martin S Tallman
- Leukemia Service, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY
| | | | | | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
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15
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Manzano-Muñoz A, Alcon C, Menéndez P, Ramírez M, Seyfried F, Debatin KM, Meyer LH, Samitier J, Montero J. MCL-1 Inhibition Overcomes Anti-apoptotic Adaptation to Targeted Therapies in B-Cell Precursor Acute Lymphoblastic Leukemia. Front Cell Dev Biol 2021; 9:695225. [PMID: 34568318 PMCID: PMC8458912 DOI: 10.3389/fcell.2021.695225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022] Open
Abstract
Multiple targeted therapies are currently explored for pediatric and young adult B-cell precursor acute lymphoblastic leukemia (BCP-ALL) treatment. However, this new armamentarium of therapies faces an old problem: choosing the right treatment for each patient. The lack of predictive biomarkers is particularly worrying for pediatric patients since it impairs the implementation of new treatments in the clinic. In this study, we used the functional assay dynamic BH3 profiling (DBP) to evaluate two new treatments for BCP-ALL that could improve clinical outcome, especially for relapsed patients. We found that the MEK inhibitor trametinib and the multi-target tyrosine kinase inhibitor sunitinib exquisitely increased apoptotic priming in an NRAS-mutant and in a KMT2A-rearranged cell line presenting a high expression of FLT3, respectively. Following these observations, we sought to study potential adaptations to these treatments. Indeed, we identified with DBP anti-apoptotic changes in the BCL-2 family after treatment, particularly involving MCL-1 - a pro-survival strategy previously observed in adult cancers. To overcome this adaptation, we employed the BH3 mimetic S63845, a specific MCL-1 inhibitor, and evaluated its sequential addition to both kinase inhibitors to overcome resistance. We observed that the metronomic combination of both drugs with S63845 was synergistic and showed an increased efficacy compared to single agents. Similar observations were made in BCP-ALL KMT2A-rearranged PDX cells in response to sunitinib, showing an analogous DBP profile to the SEM cell line. These findings demonstrate that rational sequences of targeted agents with BH3 mimetics, now extensively explored in clinical trials, may improve treatment effectiveness by overcoming anti-apoptotic adaptations in BCP-ALL.
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Affiliation(s)
- Albert Manzano-Muñoz
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Clara Alcon
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Pablo Menéndez
- Stem Cell Biology, Developmental Leukemia and Immunotherapy, Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Manuel Ramírez
- Department of Pediatric Hematology and Oncology, Niño Jesús University Children’s Hospital, Madrid, Spain
| | - Felix Seyfried
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Lüder H. Meyer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Josep Samitier
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona, Barcelona, Spain
- Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Joan Montero
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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16
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Iacobucci I, Kimura S, Mullighan CG. Biologic and Therapeutic Implications of Genomic Alterations in Acute Lymphoblastic Leukemia. J Clin Med 2021; 10:3792. [PMID: 34501239 PMCID: PMC8432032 DOI: 10.3390/jcm10173792] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most successful paradigm of how risk-adapted therapy and detailed understanding of the genetic alterations driving leukemogenesis and therapeutic response may dramatically improve treatment outcomes, with cure rates now exceeding 90% in children. However, ALL still represents a leading cause of cancer-related death in the young, and the outcome for older adolescents and young adults with ALL remains poor. In the past decade, next generation sequencing has enabled critical advances in our understanding of leukemogenesis. These include the identification of risk-associated ALL subtypes (e.g., those with rearrangements of MEF2D, DUX4, NUTM1, ZNF384 and BCL11B; the PAX5 P80R and IKZF1 N159Y mutations; and genomic phenocopies such as Ph-like ALL) and the genomic basis of disease evolution. These advances have been complemented by the development of novel therapeutic approaches, including those that are of mutation-specific, such as tyrosine kinase inhibitors, and those that are mutation-agnostic, including antibody and cellular immunotherapies, and protein degradation strategies such as proteolysis-targeting chimeras. Herein, we review the genetic taxonomy of ALL with a focus on clinical implications and the implementation of genomic diagnostic approaches.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
- Comprehensive Cancer Center, Hematological Malignancies Program, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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17
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Novakova M, Zaliova M, Fiser K, Vakrmanova B, Slamova L, Musilova A, Brüggemann M, Ritgen M, Fronkova E, Kalina T, Stary J, Winkowska L, Svec P, Kolenova A, Stuchly J, Zuna J, Trka J, Hrusak O, Mejstrikova E. DUX4r, ZNF384r and PAX5-P80R mutated B-cell precursor acute lymphoblastic leukemia frequently undergo monocytic switch. Haematologica 2021; 106:2066-2075. [PMID: 32646889 PMCID: PMC8327733 DOI: 10.3324/haematol.2020.250423] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, we described B-cell precursor acute lymphoblastic leukemia (BCP-ALL) subtype with an early switch to the monocytic lineage and the loss of the B-cell immunophenotype, including CD19 expression. Thus far, the genetic background has remained unknown. Among 726 children consecutively diagnosed with BCP-ALL, 8% patients experienced a switch detectable by flow cytometry (FC). Using exome and RNA sequencing, the switch was found to positively correlate with three different genetic subtypes: PAX5-P80R mutation (five cases with switch of five), rearranged (DUX4r) (30 cases of 41) and rearranged (ZNF384r) (four cases of ten). Expression profiles or phenotypic patterns correlated with genotypes, but within each genotype no cases who subsequently switched could be indentified. If switching was not taken into account, the B-cell-oriented FC assessment underestimated the minimal residual disease level. For patients with PAX5-P80R, a discordance between FC-determined and polymerase chain reactiondetermined minimal residual disease was found on day 15, resulting from a rapid loss of the B-cell phenotype. Discordance on day 33 was observed in all the DUX4r, PAX5-P80R and ZNF384r subtypes. Importantly, despite the substantial phenotypic changes, possibly even challenging the appropriateness of BCP-ALL therapy, the monocytic switch was not associated with a higher incidence of relapse and poorer prognosis in patients undergoing standard ALL treatment.
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Affiliation(s)
- Michaela Novakova
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Marketa Zaliova
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Karel Fiser
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Barbora Vakrmanova
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Lucie Slamova
- Dpt.of Paediatric Haematology/Oncology, University Hospital Motol, Charles University, Czech Rep
| | - Alena Musilova
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Monika Brüggemann
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Ritgen
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Eva Fronkova
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Tomas Kalina
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Jan Stary
- Dpt.of Paediatric Haematology/Oncology, University Hospital Motol, Charles University, Czech Rep
| | - Lucie Winkowska
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Peter Svec
- Comenius University, National Institute of Children Diseases, Bratislava, Slovakia
| | - Alexandra Kolenova
- Comenius University, National Institute of Children Diseases, Bratislava, Slovakia
| | - Jan Stuchly
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Jan Zuna
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Jan Trka
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Ondrej Hrusak
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
| | - Ester Mejstrikova
- CLIP-Dpt.of Paediatric Haematology/Oncology, Charles University, Prague, Czech Republic
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18
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Lin N, Yan X, Cai D, Wang L. Leukemia With TCF3-ZNF384 Rearrangement as a Distinct Subtype of Disease With Distinct Treatments: Perspectives From A Case Report and Literature Review. Front Oncol 2021; 11:709036. [PMID: 34395283 PMCID: PMC8357369 DOI: 10.3389/fonc.2021.709036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background ZNF384 rearrangements are found in 5-10% of B-cell acute lymphoblastic leukemia (B-ALL) and 48% of B cell/myeloid mixed phenotype acute leukemia (B/M MPAL). ZNF384-rearranged B-ALL is prone to lineage conversion after chemotherapy. TCF3 is the second most common rearrangement partner of ZNF384 in B-ALL (27.5%) and the most common partner in B/M MPAL (53.3%). TCF3-ZNF384 fusion is related to a poor steroid response and a high frequency of relapse. It is mostly reported in children and adolescents but rarely seen in adults. Patients and Methods Here, we report a rare case of adult common B-ALL with TCF3-ZNF384 fusion in which the patient relapsed after one cycle of consolidation chemotherapy. Relapsed leukemia cells from the bone marrow were cultured for 72 hours ex vivo, and a panel of 156 kinds of cytotoxic drugs, targeted therapy drugs, combination chemotherapy drugs, etc., was used for sensitivity screening. The literature on TCF3-ZNF384 fusion was reviewed, and reported cases with TCF3-ZNF384 fusion were summarized. Clinical characteristics were compared between B-ALL and MPAL with TCF3-ZNF384 fusion. Results The relapsed lymphoblasts showed moderate sensitivity to both acute myelocytic leukemia (AML) - and acute lymphoblastic leukemia (ALL)-directed combination chemotherapy schemes, as well as to multiple targeted therapeutic drugs. The hyper-CVAD (B) scheme showed synergistic effects with multiple targeted compounds and had the highest sensitivity. The patient chose the hyper-CVAD (B) scheme combined with sorafenib and achieved complete remission (CR), then consolidated with myeloid-directed homoharringtonine+cytarabine+daunorubicin (HAD) scheme and gained molecular CR. By reviewing the literature, we found that both the genomic landscapes and gene expression profiles of ZNF384-rearranged B-ALL and MPAL are similar and that both diseases have lineage plasticity. The gene expression profile in TCF3-ZNF384-positive patients shows enrichment of hematopoietic stem cell features. No significant differences in clinical characteristics were found between TCF3-ZNF384-positive ALL and MPAL. Conclusion TCF3-ZNF384-positive leukemia may be a distinct subtype of leukemia regardless of immunophenotype. Considering the frequent lineage switches and sensitivity to both ALL- and AML-directed schemes, a uniform strategy directed at both lymphoid and myeloid lineages or at hematopoietic stem cells may be better for TCF3-ZNF384-positive leukemia. Small molecule targeted therapies may be promising treatment options and deserve further investigation.
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Affiliation(s)
- Na Lin
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaojing Yan
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Dali Cai
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Lei Wang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
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19
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13q12.2 deletions and FLT3 overexpression in acute leukemias. Blood Adv 2021; 5:2075-2078. [PMID: 33877294 DOI: 10.1182/bloodadvances.2020003643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 11/20/2022] Open
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20
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Jiang D, He Y, Mo Q, Liu E, Li X, Huang L, Zhang Q, Chen F, Li Y, Shao H. PRICKLE1, a Wnt/PCP signaling component, is overexpressed and associated with inferior prognosis in acute myeloid leukemia. J Transl Med 2021; 19:211. [PMID: 34001134 PMCID: PMC8130533 DOI: 10.1186/s12967-021-02873-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/03/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Prickle planar cell polarity protein 1 (PRICKLE1), a core component of the non-canonical Wnt/planar cell polarity (PCP) pathway, was recently reported to be upregulated and correlated with poor prognosis in solid cancers. However, the effect of PRICKLE1 on acute myeloid leukemia (AML) remains unknown. This study aims to characterize the prognostic significance of PRICKLE1 expression in patients with AML. METHODS RNA-seq was performed to compare mRNA expression profiles of AML patients and healthy controls. qRT-PCR and western blotting were used to analyze the expression of PRICKLE1 in AML patients and cell lines, and two independent datasets (TCGA-LAML and TARGET-AML) online were used to validate the expression results. The correlations between the expression of PRICKLE1 and clinical features were further analyzed. RESULTS Our data showed that PRICKLE1 expression levels were markedly high in AML patients at the time of diagnosis, decreased after complete remission and increased again at relapse. Of note, PRICKLE1 was highly expressed in drug resistant AML cells and monocytic-AML patients. High PRICKLE1 expression was found in FLT3/DNMT3A/IDH1/IDH2-mutant AML and associated with poor prognosis. Furthermore, high expression of PRICKLE1 may be correlated with migration and invasion components upregulation in AML patients. CONCLUSIONS These results indicated that high PRICKLE1 expression may be a poor prognostic biomarker and therapeutic target of AML.
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Affiliation(s)
- Duanfeng Jiang
- Department of Hematology, The 3rd Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanjuan He
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiuyu Mo
- Department of Hematology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Enyi Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Li
- Department of Hematology, The 3rd Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lihua Huang
- Center for Medical Experiments, The 3rd Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Zhang
- Department of Hematology, The 3rd Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fangping Chen
- Department of Hematology, The 3rd Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Li
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Haigang Shao
- Department of Hematology, The 3rd Xiangya Hospital, Central South University, Changsha, Hunan, China.
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21
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Janet NB, Kulkarni U, Arun AK, Bensega B, Devasia AJ, Korula A, Abraham A, George B, Mathews V, Balasubramanian P. Systematic application of fluorescence in situ hybridization and immunophenotype profile for the identification of ZNF384 gene rearrangements in B cell acute lymphoblastic leukemia. Int J Lab Hematol 2021; 43:658-663. [PMID: 33988307 DOI: 10.1111/ijlh.13580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/28/2022]
Abstract
INTRODUCTION ZNF384 gene fusions resulting from translocations with several partner genes have been described in B cell acute lymphoblastic leukemia (B-ALL) with a characteristic immunophenotype (aberrant CD13 and or CD33 with dim CD10). The prognosis of patients with this rearrangement appears to depend on the fusion partner. ZNF384 rearrangements have been identified by high through put technologies such as RNA sequencing in most of the studies published. We tested the feasibility of using the characteristic immunophenotype as a tool to screen for patients with ZNF384 translocations which can be subsequently confirmed by cytogenetic / molecular methodologies. METHODS ZNF384 rearrangements in B-ALL patients at diagnosis with CD10 <80% and were negative for the BCR-ABL1 fusion (n = 109) were identified by fluorescence in situ hybridization followed by confirmation by reverse transcriptase-polymerase chain reaction and Sanger sequencing. The end of induction measurable residual disease evaluated by flow cytometry for these patients was obtained from patient records. RESULTS ZNF384 translocations were identified in 14 patients and were cytogenetically cryptic in 13. EP300-ZNF384 was the most common fusion partner (n = 12), while TAF15-ZNF384 and TCF3-ZNF384 were identified in 1 patient each. End of induction MRD by flow cytometry was positive in 5 of 8 patients with the EP300-ZNF384 fusion treated at our center. CONCLUSION Our findings show a practical approach for the identification of ZNF384 gene rearrangements by widely available technologies and indicate that the response to therapy may be heterogeneous even in this subset, which has been reported as having a favorable prognosis.
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Affiliation(s)
- Nancy Beryl Janet
- Department of Haematology, Christian Medical College, Vellore, India
| | - Uday Kulkarni
- Department of Haematology, Christian Medical College, Vellore, India
| | | | - Bexy Bensega
- Department of Haematology, Christian Medical College, Vellore, India
| | - Anup J Devasia
- Department of Haematology, Christian Medical College, Vellore, India
| | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, India
| | - Aby Abraham
- Department of Haematology, Christian Medical College, Vellore, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, India
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
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22
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Docking TR, Parker JDK, Jädersten M, Duns G, Chang L, Jiang J, Pilsworth JA, Swanson LA, Chan SK, Chiu R, Nip KM, Mar S, Mo A, Wang X, Martinez-Høyer S, Stubbins RJ, Mungall KL, Mungall AJ, Moore RA, Jones SJM, Birol İ, Marra MA, Hogge D, Karsan A. A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. Nat Commun 2021; 12:2474. [PMID: 33931648 PMCID: PMC8087683 DOI: 10.1038/s41467-021-22625-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/17/2021] [Indexed: 02/08/2023] Open
Abstract
As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of ribonucleic acid sequencing (RNA-Seq) to whole genome and exome sequencing reveals that a standalone RNA-Seq assay offers the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information. Expression data from 154 AML patients are used to develop a novel AML prognostic score, which is strongly associated with patient outcomes across 620 patients from three independent cohorts, and 42 patients from a prospective cohort. When combined with molecular risk guidelines, the risk score allows for the re-stratification of 22.1 to 25.3% of AML patients from three independent cohorts into correct risk groups. Within the adverse-risk subgroup, we identify a subset of patients characterized by dysregulated integrin signaling and RUNX1 or TP53 mutation. We show that these patients may benefit from therapy with inhibitors of focal adhesion kinase, encoded by PTK2, demonstrating additional utility of transcriptome-based testing for therapy selection in myeloid malignancy.
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Affiliation(s)
- T Roderick Docking
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jeremy D K Parker
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Martin Jädersten
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Gerben Duns
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Linda Chang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jihong Jiang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jessica A Pilsworth
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Lucas A Swanson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Simon K Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Samantha Mar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Angela Mo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Xuan Wang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Ryan J Stubbins
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - İnanç Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Donna Hogge
- Leukemia Bone Marrow Transplant Program of BC, Vancouver General Hospital, Vancouver, BC, Canada
| | - Aly Karsan
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, BC, Canada. .,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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23
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Wheeler DA, Takebe N, Hinoue T, Hoadley KA, Cardenas MF, Hamilton AM, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, Castro de Moura M, Esteller M, Shen H, Zenklusen JC, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, Ivy SP, Staudt LM. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell 2021; 39:38-53.e7. [PMID: 33217343 PMCID: PMC8478080 DOI: 10.1016/j.ccell.2020.10.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/23/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022]
Abstract
A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories-DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis-with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy.
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Affiliation(s)
- David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Maria F Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alina M Hamilton
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Ninad Dewal
- Foundation Medicine Inc, Cambridge, MA 02141, USA
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08007 Barcelona, Catalonia, Spain
| | - Hui Shen
- Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Roy Tarnuzzer
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lisa M McShane
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - James V Tricoli
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul M Williams
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Irina Lubensky
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Elise C Kohn
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard F Little
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jeffrey White
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shakun Malik
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lyndsay Harris
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carol Weil
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chris Karlovich
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Brian Rodgers
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lalitha Shankar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paula Jacobs
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracy Nolan
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | - Elijah F Edmondson
- Pathology and Histology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Barbara A Conley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - S Percy Ivy
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.
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24
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Abstract
The last decade has witnessed great advances in our understanding of the genetic and biological basis of childhood acute lymphoblastic leukemia (ALL), the development of experimental models to probe mechanisms and evaluate new therapies, and the development of more efficacious treatment stratification. Genomic analyses have revolutionized our understanding of the molecular taxonomy of ALL, and these advances have led the push to implement genome and transcriptome characterization in the clinical management of ALL to facilitate more accurate risk-stratification and, in some cases, targeted therapy. Although mutation- or pathway-directed targeted therapy (e.g., using tyrosine kinase inhibitors to treat Philadelphia chromosome [Ph]-positive and Phlike B-cell-ALL) is currently available for only a minority of children with ALL, many of the newly identified molecular alterations have led to the exploration of approaches targeting deregulated cell pathways. The efficacy of cellular or humoral immunotherapy has been demonstrated with the success of chimeric antigen receptor T-cell therapy and the bispecific engager blinatumomab in treating advanced disease. This review describes key advances in our understanding of the biology of ALL and optimal approaches to risk-stratification and therapy, and it suggests key areas for basic and clinical research.
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Affiliation(s)
- Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN.
| | - Charles G Mullighan
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN; Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN.
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25
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Vela-Ojeda J, Cardenas PV, Garcia-Ruiz Esparza MA, Montiel Cervantes LA, Chavez JG, Caballero AH, Majluf-Cruz A, Vega-López A, Reyes-Maldonado E. FLT3-ITD and CD135 Over-Expression are Frequent Findings of Poor Survival in Adult Patients with Acute Leukemias. Arch Med Res 2020; 52:217-223. [PMID: 33109387 DOI: 10.1016/j.arcmed.2020.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/06/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Fms-like tyrosine kinase 3 (FLT3) expression and mutation have been considered a poor prognostic factor in acute myeloid leukemia (AML). FLT3-ITD mutation is present in 30% of adult patients with AML and 2-5% in childhood acute lymphoblastic leukemia (ALL). The impact of these mutations on the prognosis of ALL patients, has not yet been established. Moreover, a limited number of publications regarding the level of expression of the FLT3 receptor (CD135) in both leukemias exist. This study aimed to analyze the clinical outcomes associated to the presence of FLT3-ITD mutation and the expression of CD135. METHODS 82 adult patients with newly diagnosed acute leukemia (39 with AML and 43 with ALL) were included. Flow cytometry and RT-PCR were done to analyze the expression of CD135 and the presence of FLT3 ITD mutation, respectively. RESULTS FLT3-ITD was present in 14 (36%) of AML and 15 (35%) of ALL patients. Disease free survival (DFS) and overall survival (OS) were lower in ALL patients having a CD135 expression >3000 cells/μL. There was a trend for poor OS in AML patients expressing FLT3 ITD. OS was worse in AML patients with high expression of CD135. CONCLUSION A higher (35%) frequency of FLT3-ITD was found in adult ALL patients. The presence of FLT3-ITD was associated with a trend of poor OS in AML cases, and overexpression of CD135 was correlated with poor DFS in ALL cases and poor OS in both acute leukemias.
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Affiliation(s)
- Jorge Vela-Ojeda
- Departamento de Hematología, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México; Unidad de Investigación de Medicina Traslacional en Enfermedades Hemato-Oncologicas, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México; Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Ciudad de México, México.
| | - Pamela Vazquez Cardenas
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Ciudad de México, México
| | - Miriam A Garcia-Ruiz Esparza
- Departamento de Hematología, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Laura Arcelia Montiel Cervantes
- Departamento de Hematología, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México; Unidad de Investigación de Medicina Traslacional en Enfermedades Hemato-Oncologicas, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México; Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Ciudad de México, México
| | - Jaime Garcia Chavez
- Departamento de Hematología, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Alvaro Hernandez Caballero
- Departamento de Hematología, Unidad Médica de Alta Especialidad, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Abraham Majluf-Cruz
- Unidad de Investigación Medica en Trombosis, Hemostasia y Aterogenesis, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Armando Vega-López
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Ciudad de México, México
| | - Elba Reyes-Maldonado
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Ciudad de México, México
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26
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Al-Ghabkari A, Perinpanayagam MA, Narendran A. Inhibition of PI3K/mTOR Pathways with GDC-0980 in Pediatric Leukemia: Impact on Abnormal FLT-3 Activity and Cooperation with Intracellular Signaling Targets. Curr Cancer Drug Targets 2020; 19:828-837. [PMID: 30914027 DOI: 10.2174/1568009619666190326120833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/01/2019] [Accepted: 03/18/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND GDC-0980 is a selective small molecule inhibitor of class I PI3K and mTOR pathway with a potent anti-proliferative activity. OBJECTIVE We set out to evaluate the efficacy of GDC-0980, in pre-clinical studies, against pediatric leukemia cells. METHODS The anti-neoplastic activity of GDC-0980 was evaluated in vitro using five different pediatric leukemia cells. RESULTS Our data show that GDC-0980 significantly inhibited the proliferation of leukemia cell lines, KOPN8 (IC50, 532 nM), SEM (IC50,720 nM), MOLM-13 (IC50,346 nM), MV4;11 (IC50,199 nM), and TIB-202 (IC50, 848 nM), compared to normal control cells (1.23 µM). This antiproliferative activity was associated with activation of cellular apoptotic mechanism characterized by a decrease in Bcl-2 protein phosphorylation and enhanced PARP cleavage. Western blot analyses of GDC-0980 treated cells also showed decreased phosphorylation levels of mTOR, Akt and S6, but not ERK1/2. Notably, FLT3 phosphorylation was decreased in Molm-13 and MV4;11 cells following the application of GDC-0980. We further examined cellular viability of GDC-0980-treated primary leukemia cells isolated from pediatric leukemia patients. This study revealed a potential therapeutic effect of GDC-0980 on two ALL patients (IC50's, 1.23 and 0.625 µM, respectively). Drug combination analyses of GDC-0980 demonstrated a synergistic activity with the MEK inhibitor Cobimetinib (MV4-11; 11, CI, 0.25, SEM, CI, 0.32, and TIB-202, CI, 0.55) and the targeted FLT3 inhibitor, Crenolanib (MV4-11; 11, CI, 0.25, SEM, CI, 0.7, and TIB-202, CI, 0.42). CONCLUSION These findings provide initial proof-of-concept data and rationale for further investigation of GDC-0980 in selected subgroups of pediatric leukemia patients.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, Canada
| | - Maneka A Perinpanayagam
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, Canada
| | - Aru Narendran
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, Canada
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27
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Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia. Cancer Genet 2020; 243:52-72. [PMID: 32302940 DOI: 10.1016/j.cancergen.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
Clinical management and risk stratification of B-lymphoblastic leukemia/ lymphoma (B-ALL/LBL) depend largely on identification of chromosomal abnormalities obtained using conventional cytogenetics and Fluorescence In Situ Hybridization (FISH) testing. In the last few decades, testing algorithms have been implemented to support an optimal risk-oriented therapy, leading to a large improvement in overall survival. In addition, large scale genomic studies have identified multiple aberrations of prognostic significance that are not routinely tested by existing modalities. However, as chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are increasingly used in clinical management of hematologic malignancies, these abnormalities may be more readily detected. In this article, we have compiled a comprehensive, evidence-based review of the current B-ALL literature, focusing on known and published subtypes described to date. More specifically, we describe the role of various testing modalities in the diagnosis, prognosis, and therapeutic relevance. In addition, we propose a testing algorithm aimed at assisting laboratories in the most effective detection of the underlying genomic abnormalities.
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28
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Abstract
Next-generation sequencing (NGS) has become the primary technology for discovering gene fusions. Decreasing NGS costs have resulted in a growing quantity of patients with whole transcriptome sequencing (RNA-seq) and whole genome sequencing (WGS) data. We developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read alignment. INTEGRATE has become widely adopted by the larger cancer research community to discover biologically and clinically relevant gene fusions. Here we explain the rationale driving the development of the INTEGRATE tool and describe the detailed practical procedures for applying INTEGRATE to discover gene fusions using NGS data. INTEGRATE can be applied to both combined data and RNA-seq only data.
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Affiliation(s)
- Jin Zhang
- Department of Radiation Oncology, Siteman Cancer Center, Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Maher
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, McDonell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Biomedical Engineering, University School of Medicine, St. Louis, MO, USA.
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29
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Abstract
Despite high cure rates in children, acute lymphoblastic leukemia (ALL) remains a leading cause of cancer death in the young, and the likelihood of treatment failure increases with age. With the exception of tyrosine kinase inhibitors, there have been few advances in repurposing or developing new therapeutic approaches tailored to vulnerabilities of ALL subtypes or individual cases. Large-scale genome profiling studies conducted over the last decade promise to improve ALL outcomes by refining risk stratification and modulation of therapeutic intensity, and by identifying new targets and pathways for immunotherapy. Many of these approaches have been validated in preclinical models and now merit testing in clinical trials. This review discusses the advances in our understanding of the genomic taxonomy and ontogeny of B-progenitor ALL, with an emphasis on those discoveries of clinical importance.
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30
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Khalid A, Aslam S, Ahmed M, Hasnain S, Aslam A. Risk assessment of FLT3 and PAX5 variants in B-acute lymphoblastic leukemia: a case-control study in a Pakistani cohort. PeerJ 2019; 7:e7195. [PMID: 31565544 PMCID: PMC6743442 DOI: 10.7717/peerj.7195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/28/2019] [Indexed: 11/20/2022] Open
Abstract
AIMS B-cell acute lymphoblastic leukemia (B-ALL) is amongst the most prevalent cancers of children in Pakistan. Genetic variations in FLT3 are associated with auto-phosphorylation of kinase domain that leads to increased proliferation of blast cells. Paired box family of transcription factor (PAX5) plays a critical role in commitment and differentiation of B-cells. Variations in PAX5 are associated with the risk of B-ALL. We aimed to analyze the association of FLT3 and PAX5 polymorphisms with B cell leukemia in Pakistani cohort. METHODS We collected 155 B-ALL subject and 155 control blood samples. For analysis, genotyping was done by tetra ARMS-PCR. SPSS was used to check the association of demographic factors of SNPs present in the population with the risk of B-ALL. RESULTS Risk allele frequency A at locus 13q12.2 (rs35958982, FLT3) was conspicuous and showed positive association (OR = 2.30, CI [1.20–4.50], P = 0.005) but genotype frequency (OR = 3.67, CI [0.75–18.10], P = 0.088) failed to show any association with the disease. At locus 9p13.2 (rs3780135, PAX5), the risk allele frequency was significantly higher in B-ALL subjects than ancestral allele frequency (OR = 2.17, CI [1.37–3.43], P = 0.000). Genotype frequency analysis of rs3780135 polymorphism exhibited the protective effect (OR = 0.55, CI [0.72–1.83], P = 0.029). At locus 13q12.2 (rs12430881, FLT3), the minor allele frequency G (OR = 1.15, CI [1.37–3.43], P = 0.043) and genotype frequency (OR = 2.52, P = 0.006) reached significance as showed p < 0.05. CONCLUSION In the present study, a strong risk of B-cell acute lymphoblastic leukemia was associated with rs35958982 and rs12430881 polymorphisms. However, rs3780135 polymorphism showed the protective effect. Additionally, other demographic factors like family history, smoking and consanguinity were also found to be important in risk assessment. We anticipate that the information from genetic variations in this study can aid in therapeutic approach in the future.
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Affiliation(s)
- Ammara Khalid
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Sara Aslam
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Mehboob Ahmed
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Shahida Hasnain
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Aimen Aslam
- Department of Statistics and Actuarial Science, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
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Hundal J, Kiwala S, Feng YY, Liu CJ, Govindan R, Chapman WC, Uppaluri R, Swamidass SJ, Griffith OL, Mardis ER, Griffith M. Accounting for proximal variants improves neoantigen prediction. Nat Genet 2019; 51:175-179. [PMID: 30510237 PMCID: PMC6309579 DOI: 10.1038/s41588-018-0283-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/19/2018] [Indexed: 12/30/2022]
Abstract
Recent efforts to design personalized cancer immunotherapies use predicted neoantigens, but most neoantigen prediction strategies do not consider proximal (nearby) variants that alter the peptide sequence and may influence neoantigen binding. We evaluated somatic variants from 430 tumors to understand how proximal somatic and germline alterations change the neoantigenic peptide sequence and also affect neoantigen binding predictions. On average, 241 missense somatic variants were analyzed per sample. Of these somatic variants, 5% had one or more in-phase missense proximal variants. Without incorporating proximal variant correction for major histocompatibility complex class I neoantigen peptides, the overall false discovery rate (incorrect neoantigens predicted) and the false negative rate (strong-binding neoantigens missed) across peptides of lengths 8-11 were estimated as 0.069 (6.9%) and 0.026 (2.6%), respectively.
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Affiliation(s)
- Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang-Yang Feng
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Connor J Liu
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ramaswamy Govindan
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - William C Chapman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ravindra Uppaluri
- Department of Surgery/Otolaryngology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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32
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A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data. Nat Genet 2018; 50:1735-1743. [PMID: 30397337 DOI: 10.1038/s41588-018-0257-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022]
Abstract
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somatic variant calls is required as a final step after automated processing. However, manual variant refinement is time-consuming, costly, poorly standardized, and non-reproducible. Here, we systematized and standardized somatic variant refinement using a machine learning approach. The final model incorporates 41,000 variants from 440 sequencing cases. This model accurately recapitulated manual refinement labels for three independent testing sets (13,579 variants) and accurately predicted somatic variants confirmed by orthogonal validation sequencing data (212,158 variants). The model improves on manual somatic refinement by reducing bias on calls otherwise subject to high inter-reviewer variability.
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33
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Wrzeszczynski KO, Felice V, Abhyankar A, Kozon L, Geiger H, Manaa D, London F, Robinson D, Fang X, Lin D, Lamendola-Essel MF, Khaira D, Dikoglu E, Emde AK, Robine N, Shah M, Arora K, Basturk O, Bhanot U, Kentsis A, Mansukhani MM, Bhagat G, Jobanputra V. Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer. J Mol Diagn 2018; 20:822-835. [PMID: 30138725 PMCID: PMC6198246 DOI: 10.1016/j.jmoldx.2018.06.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/24/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded for establishing performance validation applicable to whole-genome and transcriptome sequencing. Whole-genome sequencing laboratory protocols were validated for the Illumina HiSeq X Ten platform and RNA sequencing for Illumina HiSeq2500 platform for fresh or frozen and formalin-fixed, paraffin-embedded tumor samples. Various bioinformatics tools were also tested, and CIs for sensitivity and specificity thresholds in calling clinically significant somatic aberrations were determined. The validation was performed on a set of 125 tumor normal pairs. RNA sequencing was performed to call fusions and to confirm the DNA variants or exonic alterations. Here, we present our results and WGTS standards for variant allele frequency, reproducibility, analytical sensitivity, and present limit of detection analysis for single nucleotide variant calling, copy number identification, and structural variants. We show that The New York Genome Center WGTS clinical assay can provide a comprehensive patient variant discovery approach suitable for directed oncologic therapeutic applications.
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Affiliation(s)
| | | | | | | | | | - Dina Manaa
- New York Genome Center, New York, New York
| | | | | | | | - David Lin
- New York Genome Center, New York, New York
| | | | | | | | | | | | | | | | - Olca Basturk
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh Bhanot
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alex Kentsis
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pediatrics, Weill Cornell Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Govind Bhagat
- Columbia University Medical Center, Columbia University, New York, New York
| | - Vaidehi Jobanputra
- New York Genome Center, New York, New York; Columbia University Medical Center, Columbia University, New York, New York.
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34
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Alexander TB, Gu Z, Iacobucci I, Dickerson K, Choi JK, Xu B, Payne-Turner D, Yoshihara H, Loh ML, Horan J, Buldini B, Basso G, Elitzur S, de Haas V, Zwaan CM, Yeoh A, Reinhardt D, Tomizawa D, Kiyokawa N, Lammens T, De Moerloose B, Catchpoole D, Hori H, Moorman A, Moore AS, Hrusak O, Meshinchi S, Orgel E, Devidas M, Borowitz M, Wood B, Heerema NA, Carrol A, Yang YL, Smith MA, Davidsen TM, Hermida LC, Gesuwan P, Marra MA, Ma Y, Mungall AJ, Moore RA, Jones SJM, Valentine M, Janke LJ, Rubnitz JE, Pui CH, Ding L, Liu Y, Zhang J, Nichols KE, Downing JR, Cao X, Shi L, Pounds S, Newman S, Pei D, Guidry Auvil JM, Gerhard DS, Hunger SP, Inaba H, Mullighan CG. The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature 2018; 562:373-379. [PMID: 30209392 PMCID: PMC6195459 DOI: 10.1038/s41586-018-0436-0] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
Abstract
Mixed phenotype acute leukaemia (MPAL) is a high-risk subtype of leukaemia with myeloid and lymphoid features, limited genetic characterization, and a lack of consensus regarding appropriate therapy. Here we show that the two principal subtypes of MPAL, T/myeloid (T/M) and B/myeloid (B/M), are genetically distinct. Rearrangement of ZNF384 is common in B/M MPAL, and biallelic WT1 alterations are common in T/M MPAL, which shares genomic features with early T-cell precursor acute lymphoblastic leukaemia. We show that the intratumoral immunophenotypic heterogeneity characteristic of MPAL is independent of somatic genetic variation, that founding lesions arise in primitive haematopoietic progenitors, and that individual phenotypic subpopulations can reconstitute the immunophenotypic diversity in vivo. These findings indicate that the cell of origin and founding lesions, rather than an accumulation of distinct genomic alterations, prime tumour cells for lineage promiscuity. Moreover, these findings position MPAL in the spectrum of immature leukaemias and provide a genetically informed framework for future clinical trials of potential treatments for MPAL.
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Affiliation(s)
- Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC, USA
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John K Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - John Horan
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Department of Pediatrics, Atlanta, GA, USA
| | - Barbara Buldini
- Department of Women and Child Health, Hemato-Oncology Division, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Department of Women and Child Health, Hemato-Oncology Division, University of Padova, Padova, Italy
| | - Sarah Elitzur
- Pediatric Hematology-Oncology, Schneider Children's Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | - C Michel Zwaan
- Prinses Maxima Centre, Utrecht, The Netherlands
- Department of Pediatric Oncology, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Allen Yeoh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Daniel Catchpoole
- The Tumour Bank CCRU, The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Hiroki Hori
- Department of Pediatrics, Mie University, Tsu, Japan
| | - Anthony Moorman
- Wolfson Childhood Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Andrew S Moore
- The University of Queensland Diamantina Institute & Children's Health, Brisbane, Queensland, Australia
| | - Ondrej Hrusak
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
- Children's Oncology Group, Arcadia, CA, USA
| | - Etan Orgel
- Children's Center for Cancer and Blood Disease, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | - Brent Wood
- University of Washington, Seattle, WA, USA
| | - Nyla A Heerema
- The Ohio State University School of Medicine, Columbus, OH, USA
| | - Andrew Carrol
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yung-Li Yang
- Department of Laboratory Medicine and Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Tanja M Davidsen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Wartman LD. The future of cancer treatment using precision oncogenomics. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002824. [PMID: 29610395 PMCID: PMC5880270 DOI: 10.1101/mcs.a002824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Clinicians should soon have the opportunity to use precision oncogenomics to tailor the optimal cancer treatment to a specific patient. Precision oncogenomics will incorporate different sequencing platforms depending on the goal of the sequencing result. For example, the sequencing strategy used in immuno-oncology for the design of a tumor-specific vaccine may be different than that used by oncologists following a patient for clearance of mutations from circulating tumor DNA in the peripheral blood. I will provide a broad overview of several of the ways that precision oncogenomics is likely to influence the field of oncology over the next several years building off the experience at the Genomics Tumor Board at Washington University in St. Louis and a case of small-cell neuroendocrine carcinoma of the endometrium as examples.
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Affiliation(s)
- Lukas D Wartman
- Washington University School of Medicine, St. Louis, Missouri 63110, USA
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36
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Pan Z, Yang M, Huang K, Büsche G, Glage S, Ganser A, Li Z. Flow cytometric characterization of acute leukemia reveals a distinctive "blast gate" of murine T-lymphoblastic leukemia/lymphoma. Oncotarget 2018; 9:2320-2328. [PMID: 29416774 PMCID: PMC5788642 DOI: 10.18632/oncotarget.23410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/05/2017] [Indexed: 11/28/2022] Open
Abstract
Immunophenotypic analysis using multiparameter flow cytometry is an indispensable tool for diagnosis and management of acute leukemia. Mouse models have been widely used for medical research for more than 100 years and are indispensable for leukemia research. However, immunophenotypic analysis of murine leukemia was not always performed in published studies, and blast gating for isolation of blasts was shown only in very few studies. No systemic characterization of all types of murine acute leukemia in large cohorts by flow cytometry has been reported. In this study, we used flow cytometry to comprehensively characterize murine acute leukemia in a large cohort of mice. We found that murine T-lymphoblastic leukemia/lymphoma (T-ALL) exhibits a distinctive “blast gate” (CD45bright) with CD45/side scatter gating that differs from the “blast gate” (CD45dim) of human T-ALL. By contrast, murine B-lymphoblastic leukemia and acute myeloid leukemia show the same blast region (CD45dim) as human leukemia. Using blast cell gating, we for first time detected T-ALL development in FLT3-ITD knock-in mice (incidence: 23%). These leukemic cells were selectively killed by the FLT3 inhibitors crenolanib and midostaurin in vitro. These data suggest that FLT3-ITD plays a potential role in the pathogenesis of T-ALL and that FLT3-ITD inhibition is a therapeutic option in the management of patients with T-ALL. Our gating strategy for immunophenotypic analysis can be used for leukemogenesis and preclinical gene therapy studies in mice and may improve the quality of such analyses.
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Affiliation(s)
- Zengkai Pan
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Min Yang
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Kezhi Huang
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany.,Department of Hematology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Guntram Büsche
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Silke Glage
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Zhixiong Li
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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37
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Zhang J, Gao T, Maher CA. INTEGRATE-Vis: a tool for comprehensive gene fusion visualization. Sci Rep 2017; 7:17808. [PMID: 29259323 PMCID: PMC5736641 DOI: 10.1038/s41598-017-18257-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/08/2017] [Indexed: 01/19/2023] Open
Abstract
Despite the increasing quantity of tools for accurately predicting gene fusion candidates from sequencing data, we are still faced with the critical challenge of visualizing the corresponding gene fusion products to infer their biological consequence (i.e. novel protein and increased gene expression). This is currently accomplished by manually inspecting and inferring the biological consequence of top scoring gene fusion candidates. This labor-intensive process could be made easier by automating the annotation of gene fusion products and generating easily interpretable visualizations. We developed a gene fusion visualization tool, called INTEGRATE-Vis, that generates comprehensive, highly customizable, publication-quality graphics focused on annotating each gene fusion at the transcript- and protein-level and assessing expression within an individual sample or across a patient cohort. INTEGRATE-Vis is the first comprehensive gene fusion visualization tool to help a user infer the potential consequence of a gene fusion event. It has potential utility in both research and clinical settings. INTEGRATE-Vis is available at https://github.com/ChrisMaherLab/INTEGRATE-Vis.
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Affiliation(s)
- Jin Zhang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Teng Gao
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, 63110, USA.,Department of Computer Science and Engineering, Washington University, St. Louis, Missouri, 63105, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, 63110, USA. .,Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, 63110, USA. .,Department of Biomedical Engineering, Washington University, St. Louis, Missouri, 63105, USA.
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38
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Cheng J, Qu L, Wang J, Cheng L, Wang Y. High expression of FLT3 is a risk factor in leukemia. Mol Med Rep 2017; 17:2885-2892. [PMID: 29257272 PMCID: PMC5783504 DOI: 10.3892/mmr.2017.8232] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/23/2017] [Indexed: 01/23/2023] Open
Abstract
Several studies have shown that internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3) can result in the failure of leukemia treatment and contribute to a poor prognosis. However, the role of the overexpression of FLT3 in leukemia remains to be fully elucidated. By mining public database, the present study first identified that the expression of FLT3 in leukemia was markedly higher, compared with that in other types of tumor and cell lines, indicating that FLT3 is important in leukemia. In leukemia, FLT3 was found to be significantly upregulated in acute myeloid leukemia and acute lymphoblastic leukemia, and a high expression of FLT3 contributed to reduced survival rates. By analyzing Gene Expression Omnibus and The Cancer Genome Atlas data, it was found that genetic alterations and modification of DNA methylation increased the expression of FLT3 in leukemia. FLT3-ITD and FLT3 tyrosine kinase domain point mutations increased the expression of FLT3 in four independent datasets. In addition, the status of FLT3 gene methylation was negatively correlated with the expression of FLT3, and haploinsufficiency of DNA methyltransferase 1 increased the expression of Flt3 in mouse leukemia cells. By analyzing the enrichment of differentially-expressed genes in chemical and genetic perturbation datasets, it was found that genes, which were upregulated in the FLT3 high expression group had myeloid lymphoid leukemia- and nucleophosmin 1-like signatures, indicating that the overexpression of FLT3 may use the same mechanism to promote leukemia. Collectively, the results of the present study showed that the overexpression of FLT3 is a potential risk factor in leukemia.
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Affiliation(s)
- Jie Cheng
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215025, P.R. China
| | - Lijun Qu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215025, P.R. China
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215025, P.R. China
| | - Lemei Cheng
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215025, P.R. China
| | - Yi Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215025, P.R. China
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Núñez-Enríquez JC, Bárcenas-López DA, Hidalgo-Miranda A, Jiménez-Hernández E, Bekker-Méndez VC, Flores-Lujano J, Solis-Labastida KA, Martínez-Morales GB, Sánchez-Muñoz F, Espinoza-Hernández LE, Velázquez-Aviña MM, Merino-Pasaye LE, García Velázquez AJ, Pérez-Saldívar ML, Mojica-Espinoza R, Ramírez-Bello J, Jiménez-Morales S, Mejía-Aranguré JM. Gene Expression Profiling of Acute Lymphoblastic Leukemia in Children with Very Early Relapse. Arch Med Res 2017; 47:644-655. [PMID: 28476192 DOI: 10.1016/j.arcmed.2016.12.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/24/2016] [Indexed: 10/19/2022]
Abstract
BACKGROUND AND AIMS Acute lymphoblastic leukemia (ALL) is the most common childhood cancer worldwide. Mexican patients have high mortality rates, low frequency of good prognosis biomarkers (i.e., ETV6-RUNX1) and a high proportion is classified at the time of diagnosis with a high risk to relapse according to clinical features. In addition, very early relapses are more frequently observed than in other populations. The aim of the study was to identify new potential biomarkers associated with very early relapse in Mexican ALL children through transcriptome analysis. METHODS Microarray gene expression profiling on bone marrow samples of 54 pediatric ALL patients, collected at time of diagnosis and/or at relapse, was performed. Eleven patients presented relapse within the first 18 months after diagnosis. Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) was used to perform gene expression analysis. Annotation and functional enrichment analyses were carried out using Gene Ontology, KEGG pathway analysis and Ingenuity Pathway Analysis tools. RESULTS BLVRB, ZCCHC7, PAX5, EBF1, TMOD1 and BLNK were differentially expressed (fold-change >2.0 and p value <0.01) between relapsed and non-relapsed patients. Functional analysis of abnormally expressed genes revealed their important role in cellular processes related to the development of hematological diseases, cancer, cell death and survival and in cell-to-cell signaling interaction. CONCLUSIONS Our data support previous findings showing the relevance of PAX5, EBF1 and ZCCHC7 as potential biomarkers to identify a subgroup of ALL children in high risk to relapse.
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Affiliation(s)
- Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional (CMN) "La Raza", IMSS, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", "La Raza", IMSS, Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Karina Anastacia Solis-Labastida
- Servicio de Hematología Pediátrica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Gabriela Bibiana Martínez-Morales
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología "Ignacio Chávez" (INCICh), Mexico City, Mexico
| | - Laura Eugenia Espinoza-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional (CMN) "La Raza", IMSS, Mexico City, Mexico
| | | | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional (CMN) "20 de Noviembre", Instituto de Seguridad Social al Servicio de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Raúl Mojica-Espinoza
- Unidad de Genotipificación y Análisis de Expresión, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Julián Ramírez-Bello
- Unidad de Investigación de Enfermedades Metabólicas y Endócrinas, Hospital Juárez de México, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Pediatría, Centro Médico Nacional (CMN) "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico; Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico.
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- Mexican Inter-Institutional Group for the Identification of the Causes of Childhood Leukaemia, Instituto Mexicano del Seguro Social, Instituto de Seguridad Social al Servicio de los Trabajadores del Estado, Secretaría de Salud, Secretaría de Salud del Gobierno del Distrito Federal, Mexico City, México
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Kosarek N, Ho ES. IDICAP: A Novel Tool for Integrating Drug Intervention Based on Cancer Panel. J Pers Med 2016; 6:jpm6040019. [PMID: 27801815 PMCID: PMC5198058 DOI: 10.3390/jpm6040019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/05/2016] [Accepted: 10/18/2016] [Indexed: 01/20/2023] Open
Abstract
Cancer is a heterogeneous disease afflicting millions of people of all ages and their families worldwide. Tremendous resources have been and continue to be devoted to the development of cancer treatments that target the unique mutation profiles of patients, namely targeted cancer therapy. However, the sheer volume of drugs coupled with cancer heterogeneity becomes a challenge for physicians to prescribe effective therapies targeting patients’ unique genetic mutations. Developing a web service that allows clinicians as well as patients to identify effective drug therapies, both approved and experimental, would be helpful for both parties. We have developed an innovative web service, IDICAP, which stands for Integrated Drug Intervention for CAncer Panel. It uses genes that have been linked to a cancer type to search for drug and clinical trial information from ClinicalTrials.gov and DrugBank. IDICAP selects and integrates information pertaining to clinical trials, disease conditions, drugs under trial, locations of trials, drugs that are known to target the queried gene, and any known single nucleotide polymorphism (SNP) effects. We tested IDICAP by gene panels that contribute to breast cancer, ovarian cancer, and cancer in general. Clinical trials and drugs listed by our tool showed improved precision compared to the results from ClinicalTrials.gov and Drug Gene Interaction Database (DGIdb). Furthermore, IDICAP provides patients and doctors with a list of clinical facilities in their proximity, a characteristic that lends credence to the Precision Medicine Initiative launched by the White House in the United States in 2015. URL:http://idicap.lafayette.edu:8000
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Affiliation(s)
- Noelle Kosarek
- Department of Biology, Lafayette College, Easton, PA 18042, USA.
- Current address: Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA.
| | - Eric S Ho
- Department of Biology, Lafayette College, Easton, PA 18042, USA.
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Zänker KS, Borresen-Dale AL, Huber HP. Personalized Cancer Care: Risk Prediction, Early Diagnosis, Progression, and Therapy. Biomed Hub 2016; 1:1-9. [PMID: 31988890 PMCID: PMC6945940 DOI: 10.1159/000453253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
At the annual prestigious International Symposium of the Fritz-Bender Foundation, Munich, 18-20 May, 2016, researchers, clinicians, and students discussed the state of the art and future perspectives of genomic medicine in cancer. Genomic medicine (also known as precision medicine/oncology) should help clinicians to provide a more precise diagnosis and therapy in oncology for individual patients. The meeting focused on next-generation sequencing methods, analytical computational analysis of big data, and data mining on the way to translational and evidence-based medicine. The meeting covered the social and ethical impact of genomic medicine as well as news and views on antibody targeting of intracellular proteins, on the architecture of intracellular proteins and their impact on carcinogenesis, and on the adaptation of tumor therapy in due consideration of tumor evolution. Subheadings like "Genetic Profiling of Patients and Risk Prediction," "Molecular Profiling of Tumors and Metastases," "Tumor-Host Microenvironment Interaction and Metabolism," and "Targeted Therapy" were subsumed under the main heading of "Personalized Cancer Care."
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Affiliation(s)
- Kurt S. Zänker
- Institute of Immunology and Experimental Oncology, Center for Biomedical Education and Research, University Witten/Herdecke, Witten, Germany
| | - Anne-Lise Borresen-Dale
- Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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