1
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Shim Y, Koo YK, Shin S, Lee ST, Lee KA, Choi JR. Comparison of Optical Genome Mapping With Conventional Diagnostic Methods for Structural Variant Detection in Hematologic Malignancies. Ann Lab Med 2024; 44:324-334. [PMID: 38433573 PMCID: PMC10961627 DOI: 10.3343/alm.2023.0339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/21/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Background Structural variants (SVs) are currently analyzed using a combination of conventional methods; however, this approach has limitations. Optical genome mapping (OGM), an emerging technology for detecting SVs using a single-molecule strategy, has the potential to replace conventional methods. We compared OGM with conventional diagnostic methods for detecting SVs in various hematologic malignancies. Methods Residual bone marrow aspirates from 27 patients with hematologic malignancies in whom SVs were observed using conventional methods (chromosomal banding analysis, FISH, an RNA fusion panel, and reverse transcription PCR) were analyzed using OGM. The concordance between the OGM and conventional method results was evaluated. Results OGM showed concordance in 63% (17/27) and partial concordance in 37% (10/27) of samples. OGM detected 76% (52/68) of the total SVs correctly (concordance rate for each type of SVs: aneuploidies, 83% [15/18]; balanced translocation, 80% [12/15] unbalanced translocation, 54% [7/13] deletions, 81% [13/16]; duplications, 100% [2/2] inversion 100% [1/1]; insertion, 100% [1/1]; marker chromosome, 0% [0/1]; isochromosome, 100% [1/1]). Sixteen discordant results were attributed to the involvement of centromeric/telomeric regions, detection sensitivity, and a low mapping rate and coverage. OGM identified additional SVs, including submicroscopic SVs and novel fusions, in five cases. Conclusions OGM shows a high level of concordance with conventional diagnostic methods for the detection of SVs and can identify novel variants, suggesting its potential utility in enabling more comprehensive SV analysis in routine diagnostics of hematologic malignancies, although further studies and improvements are required.
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Affiliation(s)
- Yeeun Shim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
- MDxK (Molecular Diagnostics Korea), Inc., Gwacheon, Korea
| | - Yu-Kyung Koo
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co., Ltd., Seongnam, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co., Ltd., Seongnam, Korea
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2
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Yamada C, Okada K, Odaira K, Tokoro M, Iwamoto E, Sanada M, Noura M, Okamoto S, Yasuda T, Tsuzuki S, Kiyoi H, Hayakawa F. RGS1 and CREB5 are direct and common transcriptional targets of ZNF384-fusion proteins. Cancer Med 2024; 13:e7471. [PMID: 39015025 PMCID: PMC11252495 DOI: 10.1002/cam4.7471] [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: 01/18/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND ZNF384-fusion (Z-fusion) genes were recently identified in B-cell acute lymphoblastic leukemia (B-ALL) and are frequent in Japanese adult patients. The frequency is about 20% in those with Philadelphia chromosome-negative B-ALL. ZNF384 is a transcription factor and Z-fusion proteins have increased transcriptional activity; however, the detailed mechanisms of leukemogenesis of Z-fusion proteins have yet to be clarified. METHODS We established three transfectants of cell lines expressing different types of Z-fusion proteins, and analyzed their gene expression profile (GEP) by RNA-seq. We also analyzed the GEP of clinical ALL samples using our previous RNA-seq data of 323 Japanese ALL patients. We selected upregulated genes in both Z-fusion gene-expressing transfectants and Z-fusion gene-positive ALL samples, and investigated the binding of Z-fusion proteins to regulatory regions of the candidate genes by ChIP-qPCR. RESULTS We selected six commonly upregulated genes. After the investigation by ChIP-qPCR, we finally identified CREB5 and RGS1 as direct and common target genes. RGS1 is an inhibitor of CXCL12-CXCR4 signaling that is required for the homing of hematopoietic progenitor cells to the bone marrow microenvironment and development of B cells. Consistent with this, Z-fusion gene transfectants showed impaired migration toward CXCL12. CONCLUSIONS We identified CREB5 and RGS1 as direct and common transcriptional targets of Z-fusion proteins. The present results provide novel insight into the aberrant transcriptional regulation by Z-fusion proteins.
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Affiliation(s)
- Chiharu Yamada
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Kentaro Okada
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Koya Odaira
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Mahiru Tokoro
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Eisuke Iwamoto
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Masashi Sanada
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Mina Noura
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Syuichi Okamoto
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Takahiko Yasuda
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Shinobu Tsuzuki
- Department of BiochemistryAichi Medical University School of MedicineNagakuteJapan
| | - Hitoshi Kiyoi
- Department of Hematology and OncologyNagoya University Graduate School of MedicineNagoyaJapan
| | - Fumihiko Hayakawa
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
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3
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Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
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Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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4
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Budak B, Tükel EY, Turanlı B, Kiraz Y. Integrated systems biology analysis of acute lymphoblastic leukemia: unveiling molecular signatures and drug repurposing opportunities. Ann Hematol 2024:10.1007/s00277-024-05821-w. [PMID: 38836918 DOI: 10.1007/s00277-024-05821-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/27/2024] [Indexed: 06/06/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematological malignancy characterized by aberrant proliferation and accumulation of lymphoid precursor cells within the bone marrow. The tyrosine kinase inhibitor (TKI), imatinib mesylate, has played a significant role in the treatment of Philadelphia chromosome-positive ALL (Ph + ALL). However, the achievement of durable and sustained therapeutic success remains a challenge due to the development of TKI resistance during the clinical course.The primary objective of this investigation is to propose a novel and efficacious treatment approach through drug repositioning, targeting ALL and its Ph + subtype by identifying and addressing differentially expressed genes (DEGs). This study involves a comprehensive analysis of transcriptome datasets pertaining to ALL and Ph + ALL in order to identify DEGs associated with the progression of these diseases to identify possible repurposable drugs that target identified hub proteins.The outcomes of this research have unveiled 698 disease-related DEGs for ALL and 100 for Ph + ALL. Furthermore, a subset of drugs, specifically glipizide for Ph + ALL, and maytansine and isoprenaline for ALL, have been identified as potential candidates for therapeutic intervention. Subsequently, cytotoxicity assessments were performed to confirm the in vitro cytotoxic effects of these selected drugs on both ALL and Ph + ALL cell lines.In conclusion, this study offers a promising avenue for the management of ALL and Ph + ALL through drug repurposed drugs. Further investigations are necessary to elucidate the mechanisms underlying cell death, and clinical trials are recommended to validate the promising results obtained through drug repositioning strategies.
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Affiliation(s)
- Betül Budak
- Department of Bioengineering, Marmara University, Istanbul, Türkiye
- Department of Genetics and Bioengineering, Istanbul Bilgi University, Istanbul, Türkiye
| | - Ezgi Yağmur Tükel
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balçova, Izmir, Türkiye
| | - Beste Turanlı
- Department of Bioengineering, Marmara University, Istanbul, Türkiye
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Türkiye
| | - Yağmur Kiraz
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balçova, Izmir, Türkiye.
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5
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Choi JK, Xiao W, Chen X, Loghavi S, Elenitoba-Johnson KS, Naresh KN, Medeiros LJ, Czader M. Fifth Edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues: Acute Lymphoblastic Leukemias, Mixed-Phenotype Acute Leukemias, Myeloid/Lymphoid Neoplasms With Eosinophilia, Dendritic/Histiocytic Neoplasms, and Genetic Tumor Syndromes. Mod Pathol 2024; 37:100466. [PMID: 38460674 DOI: 10.1016/j.modpat.2024.100466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/11/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
This manuscript represents a review of lymphoblastic leukemia/lymphoma (acute lymphoblastic leukemia/lymphoblastic lymphoma), acute leukemias of ambiguous lineage, mixed-phenotype acute leukemias, myeloid/lymphoid neoplasms with eosinophilia and defining gene rearrangements, histiocytic and dendritic neoplasms, and genetic tumor syndromes of the 5th edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues. The diagnostic, clinicopathologic, cytogenetic, and molecular genetic features are discussed. The differences in comparison to the 4th revised edition of the World Health Organization classification of hematolymphoid neoplasms are highlighted.
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Affiliation(s)
- John K Choi
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xueyan Chen
- Section of Pathology, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Sanam Loghavi
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas
| | - Kojo S Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kikkeri N Naresh
- Section of Pathology, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - L Jeffrey Medeiros
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
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6
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Hou Z, Ren Y, Zhang X, Huang D, Yan F, Sun W, Zhang W, Zhang Q, Fu X, Lang Z, Chu C, Zou B, Gao B, Jin B, Kang Z, Liu Q, Yan J. EP300-ZNF384 transactivates IL3RA to promote the progression of B-cell acute lymphoblastic leukemia. Cell Commun Signal 2024; 22:211. [PMID: 38566191 PMCID: PMC10986138 DOI: 10.1186/s12964-024-01596-9] [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: 12/12/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
The EP300-ZNF384 fusion gene is an oncogenic driver in B-cell acute lymphoblastic leukemia (B-ALL). In the present study, we demonstrated that EP300-ZNF384 substantially induces the transcription of IL3RA and the expression of IL3Rα (CD123) on B-ALL cell membranes. Interleukin 3 (IL-3) supplementation promotes the proliferation of EP300-ZNF348-positive B-ALL cells by activating STAT5. Conditional knockdown of IL3RA in EP300-ZF384-positive cells inhibited the proliferation in vitro, and induced a significant increase in overall survival of mice, which is attributed to impaired propagation ability of leukemia cells. Mechanistically, the EP300-ZNF384 fusion protein transactivates the promoter activity of IL3RA by binding to an A-rich sequence localized at -222/-234 of IL3RA. Furthermore, forced EP300-ZNF384 expression induces the expression of IL3Rα on cell membranes and the secretion of IL-3 in CD19-positive B precursor cells derived from healthy individuals. Doxorubicin displayed a selective killing of EP300-ZNF384-positive B-ALL cells in vitro and in vivo. Collectively, we identify IL3RA as a direct downstream target of EP300-ZNF384, suggesting CD123 is a potent biomarker for EP300-ZNF384-driven B-ALL. Targeting CD123 may be a novel therapeutic approach to EP300-ZNF384-positive patients, alternative or, more likely, complementary to standard chemotherapy regimen in clinical setting.
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Affiliation(s)
- Zhijie Hou
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China.
| | - Yifei Ren
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China
| | - Xuehong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Dan Huang
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China
| | - Fanzhi Yan
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China
| | - Wentao Sun
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Wenjuan Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Qingqing Zhang
- Department of Pathology, Dalian Medical University, Dalian, 116044, China
| | - Xihui Fu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Zhenghui Lang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Chenyang Chu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Boyang Zou
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Beibei Gao
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Zhijie Kang
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
| | - Quentin Liu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China.
| | - Jinsong Yan
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of hematology, Diamond Bay institute of hematology, Blood Stem Cell Transplantation Institute, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
- Department of Pediatric, Pediatric Oncology and Hematology Center, the Second Hospital of Dalian Medical University, Dalian, 116027, China.
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7
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Iorgulescu JB, Medeiros LJ, Patel KP. Predictive and prognostic molecular biomarkers in lymphomas. Pathology 2024; 56:239-258. [PMID: 38216400 DOI: 10.1016/j.pathol.2023.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
Recent advances in molecular diagnostics have markedly expanded our understanding of the genetic underpinnings of lymphomas and catalysed a transformation in not just how we classify lymphomas, but also how we treat, target, and monitor affected patients. Reflecting these advances, the World Health Organization Classification, International Consensus Classification, and National Comprehensive Cancer Network guidelines were recently updated to better integrate these molecular insights into clinical practice. We summarise here the molecular biomarkers of lymphomas with an emphasis on biomarkers that have well-supported prognostic and predictive utility, as well as emerging biomarkers that show promise for clinical practice. These biomarkers include: (1) diagnostic entity-defining genetic abnormalities [e.g., B-cell acute lymphoblastic leukaemia (B-ALL) with KMT2A rearrangement]; (2) molecular alterations that guide patients' prognoses (e.g., TP53 loss frequently conferring worse prognosis); (3) mutations that serve as the targets of, and often a source of acquired resistance to, small molecular inhibitors (e.g., ABL1 tyrosine kinase inhibitors for B-ALL BCR::ABL1, hindered by ABL1 kinase domain resistance mutations); (4) the growing incorporation of molecular measurable residual disease (MRD) in the management of lymphoma patients (e.g., molecular complete response and sequencing MRD-negative criteria in multiple myeloma). Altogether, our review spans the spectrum of lymphoma types, from the genetically defined subclasses of precursor B-cell lymphomas to the highly heterogeneous categories of small and large cell mature B-cell lymphomas, Hodgkin lymphomas, plasma cell neoplasms, and T/NK-cell lymphomas, and provides an expansive summary of our current understanding of their molecular pathology.
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Affiliation(s)
- J Bryan Iorgulescu
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keyur P Patel
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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8
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Buckley J, Schmidt RJ, Ostrow D, Maglinte D, Bootwalla M, Ruble D, Govindarajan A, Ji J, Kovach AE, Orgel E, Raca G, Navid F, Mascarenhas L, Pawel B, Robison N, Gai X, Biegel JA. An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors. J Mol Diagn 2024; 26:127-139. [PMID: 38008288 DOI: 10.1016/j.jmoldx.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023] Open
Abstract
This study reports the development of an exome capture-based RNA-sequencing assay to detect recurring and novel fusions in hematologic, solid, and central nervous system tumors. The assay used Twist Comprehensive Exome capture with either fresh or formalin-fixed samples and a bioinformatic platform that provides fusion detection, prioritization, and downstream curation. A minimum of 50 million uniquely mapped reads, a consensus read alignment/fusion calling approach using four callers (Arriba, FusionCatcher, STAR-Fusion, and Dragen), and custom software were used to integrate, annotate, and rank the candidate fusion calls. In an evaluation of 50 samples, the number of calls varied substantially by caller, from a mean of 24.8 with STAR-Fusion to 259.6 with FusionCatcher; only 1.1% of calls were made by all four callers. Therefore a filtering and ranking algorithm was developed based on multiple criteria, including number of supporting reads, calling consensus, genes involved, and cross-reference against databases of known cancer-associated or likely false-positive fusions. This approach was highly effective in pinpointing known clinically relevant fusions, ranking them first in 47 of 50 samples (94%). Detection of pathogenic gene fusions in three diagnostically challenging cases highlights the importance of a genome-wide and nontargeted method for fusion detection in pediatric cancer.
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Affiliation(s)
- Jonathan Buckley
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Ryan J Schmidt
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Dejerianne Ostrow
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dennis Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Moiz Bootwalla
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - David Ruble
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Ananthanarayanan Govindarajan
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Alexandra E Kovach
- Keck School of Medicine of University of Southern California, Los Angeles, California; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Etan Orgel
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Gordana Raca
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Fariba Navid
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Leo Mascarenhas
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Bruce Pawel
- Keck School of Medicine of University of Southern California, Los Angeles, California; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Nathan Robison
- Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California.
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9
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De Sa H, Leonard J. Novel Biomarkers and Molecular Targets in ALL. Curr Hematol Malig Rep 2024; 19:18-34. [PMID: 38048037 DOI: 10.1007/s11899-023-00718-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 12/05/2023]
Abstract
PURPOSE OF REVIEW Acute lymphoblastic leukemia (ALL) is a widely heterogeneous disease in terms of genomic alterations, treatment options, and prognosis. While ALL is considered largely curable in children, adults tend to have higher risk disease subtypes and do not respond as favorably to conventional chemotherapy. Identifying genomic drivers of leukemogenesis and applying targeted therapies in an effort to improve disease outcomes is an exciting focus of current ALL research. Here, we review recent updates in ALL targeted therapy and present promising opportunities for future research. RECENT FINDINGS With the utilization of next-generation sequencing techniques, the genomic landscape of ALL has greatly expanded to encompass novel subtypes characterized by recurrent chromosomal rearrangements, gene fusions, sequence mutations, and distinct gene expression profiles. The evolution of small molecule inhibitors and immunotherapies, and the exploration of unique therapy combinations are some examples of recent advancements in the field. Targeted therapies are becoming increasingly important in the treatment landscape of ALL to improve outcomes and minimize toxicity. Significant recent advancements have been made in the detection of susceptible genomic drivers and the use of novel therapies to target them.
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Affiliation(s)
- Hong De Sa
- OHSU Center for Health and Healing, Oregon Health & Science University, 3485 S Bond Ave, Mail Code OC14HO, Portland, OR, 97239, USA
| | - Jessica Leonard
- OHSU Center for Health and Healing, Oregon Health & Science University, 3485 S Bond Ave, Mail Code OC14HO, Portland, OR, 97239, USA.
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10
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de Smith AJ, Spector LG. In Utero Origins of Acute Leukemia in Children. Biomedicines 2024; 12:236. [PMID: 38275407 PMCID: PMC10813074 DOI: 10.3390/biomedicines12010236] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Acute leukemias, mainly consisting of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML), comprise a major diagnostic group among hematologic cancers. Due to the early age at onset of ALL, particularly, it has long been suspected that acute leukemias of childhood may have an in utero origin. This supposition has motivated many investigations seeking direct proof of prenatal leukemogenesis, in particular, twin and "backtracking studies". The suspected in utero origin has also focused on gestation as a critical window of risk, resulting in a rich literature on prenatal risk factors for pediatric acute leukemias. In this narrative review, we recount the circumstantial and direct evidence for an in utero origin of childhood acute leukemias.
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Affiliation(s)
- Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Logan G. Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Xiao YP, Cheng YC, Chen C, Xue HM, Yang M, Lin C. Identification of the Shared Gene Signatures of HCK, NOG, RNF125 and Biological Mechanism in Pediatric Acute Lymphoblastic Leukaemia and Pediatric Sepsis. Mol Biotechnol 2023:10.1007/s12033-023-00979-6. [PMID: 38123749 DOI: 10.1007/s12033-023-00979-6] [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: 08/20/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023]
Abstract
The shared mechanisms between pediatric acute lymphoblastic leukaemia (ALL) and pediatric sepsis are currently unclear. This study was aimed to explore the shared key genes of pediatric ALL and pediatric sepsis. The datasets involved were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between disease and control samples in GSE13904 and GSE79533 were intersected. The least absolute shrinkage and selection operator (LASSO) and the boruta analyses were performed in GSE13904 and GSE79533 separately based on shared DEGs, and shared key genes were obtained by taking the intersection of sepsis-related key genes and ALL-related key genes. Three shared key genes (HCK, NOG, RNF125) were obtained, that have a good diagnostic value for both sepsis and ALL. The correlation between shared key genes and differentially expressed immune cells was higher in GSE13904 and conversely, the correlation of which was lower in GSE79533. Suggesting that the sharing key genes had a different impact on the immune environment in pediatric ALL and pediatric sepsis. We make the case that this study provides a new perspective to study the relationship between pediatric ALL and pediatric sepsis.
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Affiliation(s)
- Ying-Ping Xiao
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Yu-Cai Cheng
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Chun Chen
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Hong-Man Xue
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Mo Yang
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Chao Lin
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
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12
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Pieters R, Mullighan CG, Hunger SP. Advancing Diagnostics and Therapy to Reach Universal Cure in Childhood ALL. J Clin Oncol 2023; 41:5579-5591. [PMID: 37820294 PMCID: PMC10730082 DOI: 10.1200/jco.23.01286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 10/13/2023] Open
Abstract
Systemic combination chemotherapy and intrathecal chemotherapy markedly increased the survival rate of children with ALL. In the past two decades, the use of minimal (measurable) residual disease (MRD) measurements early in therapy improved risk group stratification with subsequent treatment intensifications for patients at high risk of relapse, and enabled a reduction of treatment for low-risk patients. The recent development of more sensitive MRD technologies may further affect risk stratification. Molecular genetic profiling has led to the discovery of many new subtypes and their driver genetic alterations. This increased our understanding of the biological basis of ALL, improved risk classification, and enabled implementation of precision medicine. In the past decade, immunotherapies, including bispecific antibodies, antibody-drug conjugates, and cellular therapies directed against surface proteins, led to more effective and less toxic therapies, replacing intensive chemotherapy courses and allogeneic stem-cell transplantation in patients with relapsed and refractory ALL, and are now being tested in newly diagnosed patients. It has taken 50-60 years to increase the cure rate in childhood ALL from 0% to 90% by stepwise improvements in chemotherapy. This review provides an overview of how the developments over the past 10-15 years mentioned above have significantly changed the diagnostic and treatment approach in ALL, and discusses how the integrated use of molecular and immunotherapeutic insights will very likely direct efforts to cure those children with ALL who are not cured today, and improve the quality of life for survivors who should have decades of life ahead. Future efforts must focus on making effective, yet very expensive, new technologies and therapies available to children with ALL worldwide.
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Affiliation(s)
- Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Charles G. Mullighan
- Department of Pathology and Hematological Malignancies Program, Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN
| | - Stephen P. Hunger
- Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
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13
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Antić Ž, Lentes J, Bergmann AK. Cytogenetics and genomics in pediatric acute lymphoblastic leukaemia. Best Pract Res Clin Haematol 2023; 36:101511. [PMID: 38092485 DOI: 10.1016/j.beha.2023.101511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 12/18/2023]
Abstract
The last five decades have witnessed significant improvement in diagnostics, treatment and management of children with acute lymphoblastic leukaemia (ALL). These advancements have become possible through progress in our understanding of the genetic and biological background of ALL, resulting in the introduction of risk-adapted treatment and novel therapeutic targets, e.g., tyrosine kinase inhibitors for BCR::ABL1-positive ALL. Further advances in the taxonomy of ALL and the discovery of new genetic biomarkers and therapeutic targets, as well as the introduction of targeted and immunotherapies into the frontline treatment protocols, may improve management and outcome of children with ALL. In this review we describe the current developments in the (cyto)genetic diagnostics and management of children with ALL, and provide an overview of the most important advances in the genetic classification of ALL. Furthermore, we discuss perspectives resulting from the development of new techniques, including artificial intelligence (AI).
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Affiliation(s)
- Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Jana Lentes
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany.
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14
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Wang H, Sun H, Liang B, Zhang F, Yang F, Cui B, Ding L, Wang X, Wang R, Cai J, Tang Y, Rao J, Hu W, Zhao S, Wu W, Chen X, Wu K, Lai J, Xie Y, Li B, Tang J, Shen S, Liu Y. Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia. Nat Commun 2023; 14:6792. [PMID: 37880218 PMCID: PMC10600232 DOI: 10.1038/s41467-023-42565-z] [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: 03/03/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
For around half of the pediatric B-lineage acute lymphoblastic leukemia (B-ALL) patients, the molecular mechanism of relapse remains unclear. To fill this gap in knowledge, here we characterize the chromatin accessibility landscape in pediatric relapsed B-ALL. We observe rewired accessible chromatin regions (ACRs) associated with transcription dysregulation in leukemia cells as compared with normal B-cell progenitors. We show that over a quarter of the ACRs in B-ALL are in quiescent regions with high heterogeneity among B-ALLs. We identify subtype-specific and allele-imbalanced chromatin accessibility by integrating multi-omics data. By characterizing the differential ACRs between diagnosis and relapse in B-ALL, we identify alterations in chromatin accessibility during drug treatment. Further analysis of ACRs associated with relapse free survival leads to the identification of a subgroup of B-ALL which show early relapse. These data provide an advanced and integrative portrait of the importance of chromatin accessibility alterations in tumorigenesis and drug responses.
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Affiliation(s)
- Han Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bilin Liang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Zhang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Wang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ronghua Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaoyang Cai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Hu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Wu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxiao Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kefei Wu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junchen Lai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangyang Xie
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyan Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
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15
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Tueur G, Quessada J, De Bie J, Cuccuini W, Toujani S, Lefebvre C, Luquet I, Michaux L, Lafage-Pochitaloff M. Cytogenetics in the management of B-cell acute lymphoblastic leukemia: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103434. [PMID: 38064905 DOI: 10.1016/j.retram.2023.103434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
Cytogenetic analysis is mandatory at initial assessment of B-cell acute lymphoblastic leukemia (B-ALL) due to its diagnostic and prognostic value. Results from chromosome banding analysis and complementary FISH are taken into account in therapeutic protocols and further completed by other techniques (RT-PCR, SNP-array, MLPA, NGS, OGM). Indeed, new genomic entities have been identified by NGS, mostly RNA sequencing, such as Ph-like ALL that can benefit from targeted therapy. Here, we have attempted to establish cytogenetic guidelines by reviewing the most recent published data including the novel 5th World Health Organization and International Consensus Classifications. We also focused on newly described cytogenomic entities and indicate alternative diagnostic tools such as NGS technology, as its importance is vastly increasing in the diagnostic setting.
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Affiliation(s)
- Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Saloua Toujani
- Service de cytogénétique et biologie cellulaire, CHU de Rennes, Rennes 35033, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France.
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16
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Yin H, Wang J, Tan Y, Jiang M, Zhang H, Meng G. Transcription factor abnormalities in B-ALL leukemogenesis and treatment. Trends Cancer 2023; 9:855-870. [PMID: 37407363 DOI: 10.1016/j.trecan.2023.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023]
Abstract
The biological regulation of transcription factors (TFs) and repressor proteins is an important mechanism for maintaining cell homeostasis. In B cell acute lymphoblastic leukemia (B-ALL) TF abnormalities occur at high frequency and are often recognized as the major driving factor in carcinogenesis. We provide an in-depth review of molecular mechanisms of six major TF rearrangements in B-ALL, including DUX4-rearranged (DUX4-R), MEF2D-R, ZNF384-R, ETV6-RUNX1 and TCF3-PBX1 fusions, and KMT2A-R. In addition, the therapeutic options and prognoses for patients who harbor these TF abnormalities are discussed. This review aims to provide an up-to-date panoramic view of how TF-based oncogenic fusions might drive carcinogenesis and impact on potential therapeutic exploration of B-ALL treatments.
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Affiliation(s)
- Hongxin Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Junfei Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yangxia Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Minghao Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Hao Zhang
- Institute for Translational Brain Research, Ministry of Education (MOE) Frontiers Center for Brain Science, Fudan University, 200032 Shanghai, China.
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China.
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17
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Rezayee F, Eisfeldt J, Skaftason A, Öfverholm I, Sayyab S, Syvänen AC, Maqbool K, Lilljebjörn H, Johansson B, Olsson-Arvidsson L, Pietras CO, Staffas A, Palmqvist L, Fioretos T, Cavelier L, Fogelstrand L, Nordlund J, Wirta V, Rosenquist R, Barbany G. Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia. Front Oncol 2023; 13:1217712. [PMID: 37664045 PMCID: PMC10470829 DOI: 10.3389/fonc.2023.1217712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods. Methods For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL. Results Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions. Discussion The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.
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Affiliation(s)
- Fatemah Rezayee
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ingegerd Öfverholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Shumaila Sayyab
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann Christine Syvänen
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Khurram Maqbool
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | | | - Anna Staffas
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Pappalardo XG, Risiglione P, Zinghirino F, Ostuni A, Luciano D, Bisaccia F, De Pinto V, Guarino F, Messina A. Human VDAC pseudogenes: an emerging role for VDAC1P8 pseudogene in acute myeloid leukemia. Biol Res 2023; 56:33. [PMID: 37344914 DOI: 10.1186/s40659-023-00446-1] [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: 01/21/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Voltage-dependent anion selective channels (VDACs) are the most abundant mitochondrial outer membrane proteins, encoded in mammals by three genes, VDAC1, 2 and 3, mostly ubiquitously expressed. As 'mitochondrial gatekeepers', VDACs control organelle and cell metabolism and are involved in many diseases. Despite the presence of numerous VDAC pseudogenes in the human genome, their significance and possible role in VDAC protein expression has not yet been considered. RESULTS We investigated the relevance of processed pseudogenes of human VDAC genes, both in physiological and in pathological contexts. Using high-throughput tools and querying many genomic and transcriptomic databases, we show that some VDAC pseudogenes are transcribed in specific tissues and pathological contexts. The obtained experimental data confirm an association of the VDAC1P8 pseudogene with acute myeloid leukemia (AML). CONCLUSIONS Our in-silico comparative analysis between the VDAC1 gene and its VDAC1P8 pseudogene, together with experimental data produced in AML cellular models, indicate a specific over-expression of the VDAC1P8 pseudogene in AML, correlated with a downregulation of the parental VDAC1 gene.
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Affiliation(s)
- Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Pierpaolo Risiglione
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Federica Zinghirino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Angela Ostuni
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Daniela Luciano
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Faustino Bisaccia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
- we.MitoBiotech S.R.L, C.so Italia 172, 95125, Catania, Italy
- I.N.B.B, National Institute for Biostructures and Biosystems, Interuniversity Consortium, Catania, Italy
- Research Centre on Nutraceuticals and Health Products (CERNUT), University of Catania, 95125, Catania, Italy
| | - Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy
- we.MitoBiotech S.R.L, C.so Italia 172, 95125, Catania, Italy
- I.N.B.B, National Institute for Biostructures and Biosystems, Interuniversity Consortium, Catania, Italy
- Research Centre on Nutraceuticals and Health Products (CERNUT), University of Catania, 95125, Catania, Italy
| | - Angela Messina
- we.MitoBiotech S.R.L, C.so Italia 172, 95125, Catania, Italy.
- I.N.B.B, National Institute for Biostructures and Biosystems, Interuniversity Consortium, Catania, Italy.
- Research Centre on Nutraceuticals and Health Products (CERNUT), University of Catania, 95125, Catania, Italy.
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Santa Sofia 97, 95123, Catania, Italy.
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19
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Liu YC, Geyer JT. Pediatric Hematopathology in the Era of Advanced Molecular Diagnostics: What We Know and How We Can Apply the Updated Classifications. Pathobiology 2023; 91:30-44. [PMID: 37311434 PMCID: PMC10857803 DOI: 10.1159/000531480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023] Open
Abstract
Pediatric hematologic malignancies often show genetic features distinct from their adult counterparts, which reflect the differences in their pathogenesis. Advances in the molecular diagnostics including the widespread use of next-generation sequencing technology have revolutionized the diagnostic workup for hematologic disorders and led to the identification of new disease subgroups as well as prognostic information that impacts the clinical treatment. The increasing recognition of the importance of germline predisposition in various hematologic malignancies also shapes the disease models and management. Although germline predisposition variants can occur in patients with myelodysplastic syndrome/neoplasm (MDS) of all ages, the frequency is highest in the pediatric patient population. Therefore, evaluation for germline predisposition in the pediatric group can have significant clinical impact. This review discusses the recent advances in juvenile myelomonocytic leukemia, pediatric acute myeloid leukemia, B-lymphoblastic leukemia/lymphoma, and pediatric MDS. This review also includes a brief discussion of the updated classifications from the International Consensus Classification (ICC) and the 5th edition World Health Organization (WHO) classification regarding these disease entities.
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Affiliation(s)
- Yen-Chun Liu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Julia T. Geyer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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20
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Öfverholm I, Rezayee F, Heyman M, Harila A, Arvidsson L, Schmiegelow K, Norén-Nyström U, Barbany G. The prognostic impact of IKZF1 deletions and UKALL genetic classifiers in paediatric B-cell precursor acute lymphoblastic leukaemia treated according to NOPHO 2008 protocols. Br J Haematol 2023. [PMID: 37156607 DOI: 10.1111/bjh.18852] [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: 03/02/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
We investigated 390 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) patients treated according to NOPHO ALL 2008, regarding copy number alterations (CNA) of eight loci associated with adverse prognosis, including IKZF1. The impact on outcome was investigated for each locus individually, combined as CNA profiles and together with cytogenetic information. The presence of IKZF1 deletion or a poor-risk CNA profile was associated with poor outcome in the whole cohort. In the standard-risk group, IKZF1-deleted cases had an inferior probability of relapse-free survival (pRFS) (p ≤ 0.001) and overall survival (pOS) (p ≤ 0.001). Additionally, among B-other patients, IKZF1 deletion correlated with poor pRFS (60% vs. 90%) and pOS (65% vs. 89%). Both IKZF1 deletion and a poor-risk CNA profile were independent factors for relapse and death in multivariable analyses adjusting for known risk factors including measurable residual disease. Our data indicate that BCP-ALL patients with high-risk CNA or IKZF1 deletion have worse prognosis despite otherwise low-risk features. Conversely, patients with both a good CNA and cytogenetic profile had a superior relapse-free (p ≤ 0.001) and overall survival (p ≤ 0.001) in the cohort, across all risk groups. Taken together, our findings highlight the potential of CNA assessment to refine stratification in ALL.
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Affiliation(s)
- Ingegerd Öfverholm
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Fatemah Rezayee
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mats Heyman
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Arja Harila
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Linda Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
- Faculty of Medicine, Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Gisela Barbany
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
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21
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Goodlad JR, Xiao W, Amador C, Cook JR, Happ L, Thakkar D, Dave S, Dogan A, Duffield A, Nejati R, Ott G, Wasik M, Czader M. Phenotypic and genotypic infidelity in B-lineage neoplasms, including transdifferentiation following targeted therapy: Report from the 2021 SH/EAHP Workshop. Am J Clin Pathol 2023:7135991. [PMID: 37085149 DOI: 10.1093/ajcp/aqad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/13/2023] [Indexed: 04/23/2023] Open
Abstract
OBJECTIVES Session 2 of the 2021 Society for Hematopathology and European Association for Haematopathology Workshop collected examples of lineage infidelity and transdifferentiation in B-lineage neoplasms, including after targeted therapy. METHODS Twenty cases were submitted. Whole-exome sequencing and genome-wide RNA expression analysis were available on a limited subsample. RESULTS A diagnosis of B-cell acute lymphoblastic leukemia (B-ALL) was rendered on at least 1 biopsy from 13 patients. There was 1 case of acute myeloid leukemia (AML); the remaining 6 cases were mature B-cell neoplasms. Targeted therapy was administered in 7 cases of B-ALL and 4 cases of mature B-cell neoplasms. Six cases of B-ALL underwent lineage switch to AML or mixed-phenotype acute leukemia at relapse, 5 of which had rearranged KMT2A. Changes in maturational state without lineage switch were observed in 2 cases. Examples of de novo aberrant T-cell antigen expression (n = 2) were seen among the mature B-cell lymphoma cohort, and their presence correlated with alterations in tumor cell gene expression patterns. CONCLUSIONS This cohort of cases enabled us to illustrate, discuss, and review current concepts of lineage switch and aberrant antigen expression in a variety of B-cell neoplasms and draw attention to the role targeted therapies may have in predisposing neoplasms to transdifferentiation as well as other, less expected changes in maturational status.
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Affiliation(s)
- John R Goodlad
- Department of Pathology, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Catalina Amador
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, US
| | - James R Cook
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, US
| | | | | | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University School of Medicine, Durham, NC, US
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Amy Duffield
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, US
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22
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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: 3] [Impact Index Per Article: 3.0] [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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23
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Vieler LM, Nilius-Eliliwi V, Schroers R, Vangala DB, Nguyen HP, Gerding WM. Optical Genome Mapping Reveals and Characterizes Recurrent Aberrations and New Fusion Genes in Adult ALL. Genes (Basel) 2023; 14:genes14030686. [PMID: 36980958 PMCID: PMC10048194 DOI: 10.3390/genes14030686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/14/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
(1) Background: In acute lymphoblastic leukemia (ALL) the genetic characterization remains challenging. Due to the genetic heterogeneity of mutations in adult patients, only a small proportion of aberrations can be analyzed with standard routine diagnostics. Optical genome mapping (OGM) has recently opened up new possibilities for the characterization of structural variants on a genome-wide level, thus enabling simultaneous analysis for a broad spectrum of genetic aberrations. (2) Methods: 11 adult ALL patients were examined using OGM. (3) Results: Genetic results obtained by karyotyping and FISH were confirmed by OGM for all patients. Karyotype was redefined, and additional genetic information was obtained in 82% (9/11) of samples by OGM, previously not diagnosed by standard of care. Besides gross-structural chromosome rearrangements, e.g., ring chromosome 9 and putative isodicentric chromosome 8q, deletions in CDKN2A/2B were detected in 7/11 patients, defining an approx. 20 kb minimum region of overlap, including an alternative exon 1 of the CDKN2A gene. The results further confirm recurrent ALL aberrations (e.g., PAX5, ETV6, VPREB1, IKZF1). (4) Conclusions: Genome-wide OGM analysis enables a broad genetic characterization in adult ALL patients in one single workup compared to standard clinical testing, facilitating a detailed genetic diagnosis, risk-stratification, and target-directed treatment strategies.
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Affiliation(s)
- Lisa-Marie Vieler
- Department of Human Genetics, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Verena Nilius-Eliliwi
- Center for Hemato-Oncological Diseases, University Hospital Knappschaftskrankenhaus Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Roland Schroers
- Center for Hemato-Oncological Diseases, University Hospital Knappschaftskrankenhaus Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Deepak Ben Vangala
- Center for Hemato-Oncological Diseases, University Hospital Knappschaftskrankenhaus Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
- Correspondence:
| | - Wanda Maria Gerding
- Department of Human Genetics, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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24
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Schwab C, Cranston RE, Ryan SL, Butler E, Winterman E, Hawking Z, Bashton M, Enshaei A, Russell LJ, Kingsbury Z, Peden JF, Barretta E, Murray J, Gibson J, Hinchliffe AC, Bain R, Vora A, Bentley DR, Ross MT, Moorman AV, Harrison CJ. Integrative genomic analysis of childhood acute lymphoblastic leukaemia lacking a genetic biomarker in the UKALL2003 clinical trial. Leukemia 2023; 37:529-538. [PMID: 36550215 PMCID: PMC9991913 DOI: 10.1038/s41375-022-01799-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Incorporating genetics into risk-stratification for treatment of childhood B-progenitor acute lymphoblastic leukaemia (B-ALL) has contributed significantly to improved survival. In about 30% B-ALL (B-other-ALL) without well-established chromosomal changes, new genetic subtypes have recently emerged, yet their true prognostic relevance largely remains unclear. We integrated next generation sequencing (NGS): whole genome sequencing (WGS) (n = 157) and bespoke targeted NGS (t-NGS) (n = 175) (overlap n = 36), with existing genetic annotation in a representative cohort of 351 B-other-ALL patients from the childhood ALL trail, UKALL2003. PAX5alt was most frequently observed (n = 91), whereas PAX5 P80R mutations (n = 11) defined a distinct PAX5 subtype. DUX4-r subtype (n = 80) was defined by DUX4 rearrangements and/or ERG deletions. These patients had a low relapse rate and excellent survival. ETV6::RUNX1-like subtype (n = 21) was characterised by multiple abnormalities of ETV6 and IKZF1, with no reported relapses or deaths, indicating their excellent prognosis in this trial. An inferior outcome for patients with ABL-class fusions (n = 25) was confirmed. Integration of NGS into genomic profiling of B-other-ALL within a single childhood ALL trial, UKALL2003, has shown the added clinical value of NGS-based approaches, through improved accuracy in detection and classification into the range of risk stratifying genetic subtypes, while validating their prognostic significance.
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Affiliation(s)
- Claire Schwab
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Ruth E Cranston
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Sarra L Ryan
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Ellie Butler
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Emily Winterman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Zoe Hawking
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Matthew Bashton
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Amir Enshaei
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Lisa J Russell
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - John F Peden
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Emilio Barretta
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - James Murray
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Jude Gibson
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Andrew C Hinchliffe
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Robert Bain
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK.
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25
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Ryan SL, Peden JF, Kingsbury Z, Schwab CJ, James T, Polonen P, Mijuskovic M, Becq J, Yim R, Cranston RE, Hedges DJ, Roberts KG, Mullighan CG, Vora A, Russell LJ, Bain R, Moorman AV, Bentley DR, Harrison CJ, Ross MT. Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia. Leukemia 2023; 37:518-528. [PMID: 36658389 PMCID: PMC9991920 DOI: 10.1038/s41375-022-01806-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/20/2023]
Abstract
Childhood B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by recurrent genetic abnormalities that drive risk-directed treatment strategies. Using current techniques, accurate detection of such aberrations can be challenging, due to the rapidly expanding list of key genetic abnormalities. Whole genome sequencing (WGS) has the potential to improve genetic testing, but requires comprehensive validation. We performed WGS on 210 childhood B-ALL samples annotated with clinical and genetic data. We devised a molecular classification system to subtype these patients based on identification of key genetic changes in tumour-normal and tumour-only analyses. This approach detected 294 subtype-defining genetic abnormalities in 96% (202/210) patients. Novel genetic variants, including fusions involving genes in the MAP kinase pathway, were identified. WGS results were concordant with standard-of-care methods and whole transcriptome sequencing (WTS). We expanded the catalogue of genetic profiles that reliably classify PAX5alt and ETV6::RUNX1-like subtypes. Our novel bioinformatic pipeline improved detection of DUX4 rearrangements (DUX4-r): a good-risk B-ALL subtype with high survival rates. Overall, we have validated that WGS provides a standalone, reliable genetic test to detect all subtype-defining genetic abnormalities in B-ALL, accurately classifying patients for the risk-directed treatment stratification, while simultaneously performing as a research tool to identify novel disease biomarkers.
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Affiliation(s)
- Sarra L Ryan
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - John F Peden
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Claire J Schwab
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Terena James
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Petri Polonen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Jenn Becq
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Richard Yim
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Ruth E Cranston
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Dale J Hedges
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, UK
| | - Lisa J Russell
- Biosciences Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Robert Bain
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Anthony V Moorman
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Christine J Harrison
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK.
| | - Mark T Ross
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK.
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26
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Wang Y, Li J, Xue TL, Tian S, Yue ZX, Liu SG, Gao C. Clinical, biological, and outcome features of P2RY8-CRLF2 and CRLF2 over-expression in pediatric B-cell precursor acute lymphoblastic leukemia according to the CCLG-ALL 2008 and 2018 protocol. Eur J Haematol 2023; 110:669-679. [PMID: 36814093 DOI: 10.1111/ejh.13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
OBJECTIVES CRLF2 alterations are associated with B-cell precursor acute lymphoblastic leukemia (BCP-ALL). This study aimed to explore the clinical, biological, and outcome features of pediatric BCP-ALL with CRLF2 abnormalities. METHODS This study enrolled 630 childhood BCP-ALLs treated on CCLG-ALL 2008 or 2018 protocol. P2RY8-CRLF2 was determined by Sanger sequencing and CRLF2 expression was evaluated by qRT-PCR. The correlation between clinical, biological features and outcomes with P2RY8-CRLF2 or CRLF2 over-expression were analyzed. RESULTS P2RY8-CRLF2 and CRLF2 over-expression were found in 3.33% and 5.71% respectively. P2RY8-CRLF2 was associated with male, higher frequency of CD7 expression, high WBC and MRD before consolidation. CRLF2 over-expression showed ETV6-RUNX1- , higher frequency of CD22, CD34, CD66c, CD86 expression, hyperdiploidy and high MRD at early treatment. The lower overall survival (OS) was found in patients with P2RY8-CRLF2 and confined only in IR group. Furthermore, adverse event-free survival and OS of P2RY8-CRLF2 were discovered comparing to those without known fusions or treated on CCLG-ALL 2008 protocol. However, P2RY8-CRLF2 was not confirmed as independent prognostic factors and no prognostic impact of CRLF2 over-expression was found. CONCLUSIONS These findings indicate P2RY8-CRLF2 identifies a subset of patients with specific features and adverse outcomes that could be improved by risk-directed treatment.
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Affiliation(s)
- Ying Wang
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
| | - Jun Li
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
| | - Tian-Lin Xue
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
| | - Shuo Tian
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
| | - Zhi-Xia Yue
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
| | - Shu-Guang Liu
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
| | - Chao Gao
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Beijing, People's Republic of China
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27
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Zhu Y, Wang Z, Li Y, Peng H, Liu J, Zhang J, Xiao X. The Role of CREBBP/EP300 and Its Therapeutic Implications in Hematological Malignancies. Cancers (Basel) 2023; 15:cancers15041219. [PMID: 36831561 PMCID: PMC9953837 DOI: 10.3390/cancers15041219] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Disordered histone acetylation has emerged as a key mechanism in promoting hematological malignancies. CREB-binding protein (CREBBP) and E1A-binding protein P300 (EP300) are two key acetyltransferases and transcriptional cofactors that regulate gene expression by regulating the acetylation levels of histone proteins and non-histone proteins. CREBBP/EP300 dysregulation and CREBBP/EP300-containing complexes are critical for the initiation, progression, and chemoresistance of hematological malignancies. CREBBP/EP300 also participate in tumor immune responses by regulating the differentiation and function of multiple immune cells. Currently, CREBBP/EP300 are attractive targets for drug development and are increasingly used as favorable tools in preclinical studies of hematological malignancies. In this review, we summarize the role of CREBBP/EP300 in normal hematopoiesis and highlight the pathogenic mechanisms of CREBBP/EP300 in hematological malignancies. Moreover, the research basis and potential future therapeutic implications of related inhibitors were also discussed from several aspects. This review represents an in-depth insight into the physiological and pathological significance of CREBBP/EP300 in hematology.
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Affiliation(s)
- Yu Zhu
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Zi Wang
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Yanan Li
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Jing Liu
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
| | - Ji Zhang
- The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang 421001, China
- Correspondence: (J.Z.); (X.X.); Tel.: +86-734-8279050 (J.Z.); +86-731-84805449 (X.X.)
| | - Xiaojuan Xiao
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
- Correspondence: (J.Z.); (X.X.); Tel.: +86-734-8279050 (J.Z.); +86-731-84805449 (X.X.)
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28
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Chiaretti S, Taherinasab A, Della Starza I, Canichella M, Ansuinelli M, De Propris MS, Messina M, Spinelli O, Santoro A, De Novi LA, Cardinali D, Schipani M, Arena V, Bassan R, Guarini A, Foà R. ZNF384 rearrangement is the most frequent genetic lesion in adult PH-negative and Ph-like-negative B-other acute lymphoblastic leukemia. Biological and clinical findings. Leuk Lymphoma 2023; 64:483-486. [PMID: 36533589 DOI: 10.1080/10428194.2022.2148217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Akram Taherinasab
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy.,Fondazione GIMEMA Onlus, Rome, Italy
| | - Martina Canichella
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Michela Ansuinelli
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Maria Stefania De Propris
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Orietta Spinelli
- Haematology and Bone Marrow Transplant Unit, ASST-Papa Giovanni XXIII, Bergamo
| | - Alessandra Santoro
- Department of Hemato Oncology, AOR "VillaSofia-Cervello", Palermo, Italy
| | - Lucia Anna De Novi
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Deborah Cardinali
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Mattia Schipani
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | | | - Renato Bassan
- Division of Hematology, Ospedale dell'Angelo, Mestre, Venezia, Italy
| | - Anna Guarini
- Department of Molecular Medicine, "Sapienza" University of Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy
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29
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Nagel S. The Role of IRX Homeobox Genes in Hematopoietic Progenitors and Leukemia. Genes (Basel) 2023; 14:genes14020297. [PMID: 36833225 PMCID: PMC9957183 DOI: 10.3390/genes14020297] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
IRX genes are members of the TALE homeobox gene class and encode six related transcription factors (IRX1-IRX6) controlling development and cell differentiation of several tissues in humans. Classification of TALE homeobox gene expression patterns for the hematopoietic compartment, termed TALE-code, has revealed exclusive IRX1 activity in pro-B-cells and megakaryocyte erythroid progenitors (MEPs), highlighting its specific contribution to developmental processes at these early stages of hematopoietic lineage differentiation. Moreover, aberrant expression of IRX homeobox genes IRX1, IRX2, IRX3 and IRX5 has been detected in hematopoietic malignancies, including B-cell precursor acute lymphoblastic leukemia (BCP-ALL), T-cell ALL, and some subtypes of acute myeloid leukemia (AML). Expression analyses of patient samples and experimental studies using cell lines and mouse models have revealed oncogenic functions in cell differentiation arrest and upstream and downstream genes, thus, revealing normal and aberrant regulatory networks. These studies have shown how IRX genes play key roles in the development of both normal blood and immune cells, and hematopoietic malignancies. Understanding their biology serves to illuminate developmental gene regulation in the hematopoietic compartment, and may improve diagnostic classification of leukemias in the clinic and reveal new therapeutic targets and strategies.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Cultures, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
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30
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Graiqevci-Uka V, Behluli E, Spahiu L, Liehr T, Temaj G. Targeted Treatment and Immunotherapy in High-risk and Relapsed/ Refractory Pediatric Acute Lymphoblastic Leukemia. Curr Pediatr Rev 2023; 19:150-156. [PMID: 36056858 PMCID: PMC10009894 DOI: 10.2174/1573396318666220901165247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/18/2022] [Accepted: 08/01/2022] [Indexed: 02/08/2023]
Abstract
Acute lymphoblastic leukemia is the most frequent pediatric malignancy in children, comprising 30% of all pediatric malignancies; adult ALL comprises 5% of all ALL cases, which have a 186.6 per 1 million incidence. In pediatric ALL (pALL), on which this review focuses, approximately 1 in 285 children are diagnosed with cancer before the age of 20, and approximately 1 in 530 young adults between the ages of 20 and 39 years old is a childhood cancer survivor. The survival probability in pALL is now very high, approximately 80-90%. Thus, the most important is to improve supportive care and treatment based on relapse risk, optimally being based on the genetic feature of malignant cells. Improvements made by now are mainly the classifying of subgroups based on genetic characteristics such as aneuploidy or translocation and aligning them with treatment response. Relevant genetic changes in ALL pathogenesis are transcription regulators of lymphoid development (PAX5, IKZF1, EBF1, and LEF1) and/or coactivators (TBL1XR1 and ERG), lymphoid signaling (BTLA, and CD200 TOX), and tumor suppressor genes (CDKN2A, CDKN2B, RB1, and TP53). This review aims to summarize treatment strategies inhibiting tyrosine kinases, influencing different signaling pathways, BCL inhibitors, and anti-CD therapy (anti-cluster differentiation therapy) in pALL. CAR T-cell therapy (chimeric antigen receptors T-cell therapy) is under research and requires further development.
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Affiliation(s)
| | - Emir Behluli
- Department of Pediatrics, University Clinical Center, Prishtina, Kosovo
| | - Lidvana Spahiu
- Department of Pediatrics, University Clinical Center, Prishtina, Kosovo
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
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31
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Duffield AS, Mullighan CG, Borowitz MJ. International Consensus Classification of acute lymphoblastic leukemia/lymphoma. Virchows Arch 2023; 482:11-26. [PMID: 36422706 PMCID: PMC10646822 DOI: 10.1007/s00428-022-03448-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022]
Abstract
The updated International Consensus Classification (ICC) of B-acute lymphoblastic leukemia (B-ALL) and T-acute lymphoblastic leukemia (T-ALL) includes both revisions to subtypes previously outlined in the 2016 WHO classification and several newly described entities. The ICC classification incorporates recent clinical, cytogenetic, and molecular data, with a particular emphasis on whole transcriptome analysis and gene expression (GEX) clustering studies. B-ALL classification is modified to further subclassify BCR::ABL1-positive B-ALL and hypodiploid B-ALL. Additionally, nine new categories of B-ALL are defined, including seven that contain distinguishing gene rearrangements, as well as two new categories that are characterized by a specific single gene mutation. Four provisional entities are also included in the updated B-ALL classification, although definitive identification of these subtypes requires GEX studies. T-ALL classification is also updated to incorporate BCL11B-activating rearrangements into early T-precursor (ETP) ALL taxonomy. Additionally, eight new provisional entities are added to the T-ALL subclassification. The clinical implications of the new entities are discussed, as are practical approaches to the use of different technologies in diagnosis. The enhanced specificity of the new classification will allow for improved risk stratification and optimized treatment plans for patients with ALL.
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Affiliation(s)
- Amy S. Duffield
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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32
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Meng QX, Wang KN, Li JH, Zhang H, Chen ZH, Zhou XJ, Cao XC, Wang P, Yu Y. ZNF384–ZEB1 feedback loop regulates breast cancer metastasis. Mol Med 2022; 28:111. [PMID: 36100877 PMCID: PMC9469556 DOI: 10.1186/s10020-022-00541-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background Breast cancer has become the most frequently diagnosed cancer worldwide. Increasing evidence indicated that zinc finger proteins (ZNFs), the largest family of transcription factors, contribute to cancer development and progression. Although ZNF384 is overexpressed in several types of human cancer, the role of ZNF384 in breast cancer remains unknown. Therefore, our research focused on ZNF384 regulation of the malignant phenotype of breast cancer and the underlying molecular mechanisms. Methods CCK-8 and colony formation assays were used to evaluate cell proliferation. Transwell and scratch assays were used to evaluate the cell migration and invasion. Chromatin immunoprecipitation (ChIP)-qPCR and luciferase reporter assays were used to confirm the target relationship between ZNF384 and zinc finger E-box binding homeobox 1 (ZEB1). Xenografts were used to monitor the targets in vivo effects. Results We noted that ZNF384 was significantly overexpressed in breast cancer and highlighted the oncogenic mechanism of ZNF384. ZNF384 transactivated ZEB1 expression and induced an epithelial and mesenchymal-like phenotype, resulting in breast cancer metastasis. Furthermore, ZNF384 may be a target of miR-485-5p, and ZEB1 can up-regulate ZNF384 expression by repressing miR-485-5p expression. Together, we unveiled a feedback loop of ZNF384–ZEB1 in breast cancer metastasis. Conclusions The findings suggest that ZNF384 can serve as a prognostic factor and a therapeutic target for breast cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00541-1.
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33
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Sudutan T, Erbilgin Y, Hatirnaz Ng O, Karaman S, Karakas Z, Kucukcankurt F, Celkan T, Timur C, Ozdemir GN, Hacısalihoglu S, Gelen SA, Sayitoğlu M. Zinc finger protein 384 ( ZNF384) impact on childhood mixed phenotype acute leukemia and B-cell precursor acute lymphoblastic leukemia. Leuk Lymphoma 2022; 63:2931-2939. [PMID: 35921545 DOI: 10.1080/10428194.2022.2095630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a heterogeneous malignancy and consists of several genetic abnormalities. Some of these abnormalities are used in clinics for risk calculation and treatment decisions. Patients with ZNF384 rearrangements had a distinct expression profile regardless of their diagnosis, BCP-ALL or mixed phenotype acute leukemia (MPAL) and defined as a new subtype of ALL. In this study, we screened 42 MPAL and 91 BCP-ALL patients for the most common ZNF384 fusions; ZNF384::TCF3, ZNF384::EP300 and ZNF384::TAF15 by using PCR. We identified ZNF384 fusions in 9.5% of MPAL and 7.6% of BCP-ALL. A novel breakpoint was identified in ZNF384::TCF3 fusion in one BCP-ALL patient. T-myeloid MPAL patients showed significantly lower ZNF384 expression compared to lymphoid groups. Patients with ZNF384r had intermediate survival rates based on other subtypes. Prognostic and patient-specific treatment evaluation of ZNF384 fusions in both ALL and MPAL might help to improve risk characterization of patients.
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Affiliation(s)
- Tugce Sudutan
- Genetics Department, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.,Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Yucel Erbilgin
- Genetics Department, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Ozden Hatirnaz Ng
- Genetics Department, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.,Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Serap Karaman
- Pediatric Hematology Department, Istanbul University Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Zeynep Karakas
- Pediatric Hematology Department, Istanbul University Istanbul Faculty of Medicine, Istanbul, Turkey
| | | | - Tiraje Celkan
- Faculty of Medicine, Pediatric Hematology Oncology Department, Istinye University, Istanbul, Turkey
| | - Cetin Timur
- Pediatric Hematology Department, Yeditepe University Hospital, Istanbul, Turkey
| | - Gul Nihal Ozdemir
- Faculty of Medicine, Pediatric Hematology Oncology Department, Istinye University, Istanbul, Turkey.,Faculty of Medicine, Division of Pediatric Hematology, Kocaeli University, Istanbul, Turkey
| | - Sadan Hacısalihoglu
- Faculty of Medicine, Division of Pediatric Hematology, Kocaeli University, Istanbul, Turkey
| | - Sema Aylan Gelen
- Pediatric Hematology Division, Istanbul Kanuni Sultan Suleyman Education and Research Hospital, Istanbul, Turkey
| | - Müge Sayitoğlu
- Genetics Department, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
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34
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Fei F, Zhang M, Tarighat SS, Joo EJ, Yang L, Heisterkamp N. Galectin-1 and Galectin-3 in B-Cell Precursor Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms232214359. [PMID: 36430839 PMCID: PMC9694201 DOI: 10.3390/ijms232214359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Acute lymphoblastic leukemias arising from the malignant transformation of B-cell precursors (BCP-ALLs) are protected against chemotherapy by both intrinsic factors as well as by interactions with bone marrow stromal cells. Galectin-1 and Galectin-3 are lectins with overlapping specificity for binding polyLacNAc glycans. Both are expressed by bone marrow stromal cells and by hematopoietic cells but show different patterns of expression, with Galectin-3 dynamically regulated by extrinsic factors such as chemotherapy. In a comparison of Galectin-1 x Galectin-3 double null mutant to wild-type murine BCP-ALL cells, we found reduced migration, inhibition of proliferation, and increased sensitivity to drug treatment in the double knockout cells. Plant-derived carbohydrates GM-CT-01 and GR-MD-02 were used to inhibit extracellular Galectin-1/-3 binding to BCP-ALL cells in co-culture with stromal cells. Treatment with these compounds attenuated migration of the BCP-ALL cells to stromal cells and sensitized human BCP-ALL cells to vincristine and the targeted tyrosine kinase inhibitor nilotinib. Because N-glycan sialylation catalyzed by the enzyme ST6Gal1 can regulate Galectin cell-surface binding, we also compared the ability of BCP-ALL wild-type and ST6Gal1 knockdown cells to resist vincristine treatment when they were co-cultured with Galectin-1 or Galectin-3 knockout stromal cells. Consistent with previous results, stromal Galectin-3 was important for maintaining BCP-ALL fitness during chemotherapy exposure. In contrast, stromal Galectin-1 did not significantly contribute to drug resistance, and there was no clear effect of ST6Gal1-catalysed N-glycan sialylation. Taken together, our results indicate a complicated joint contribution of Galectin-1 and Galectin-3 to BCP-ALL survival, with different roles for endogenous and stromal produced Galectins. These data indicate it will be important to efficiently block both extracellular and intracellular Galectin-1 and Galectin-3 with the goal of reducing BCP-ALL persistence in the protective bone marrow niche during chemotherapy.
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Affiliation(s)
- Fei Fei
- Section of Molecular Carcinogenesis, Department of Pediatrics, Division of Hematology/Oncology and Bone Marrow Transplantation, The Saban Research Institute of Children’s Hospital, Los Angeles, CA 90027, USA
| | - Mingfeng Zhang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
| | - Somayeh S. Tarighat
- Section of Molecular Carcinogenesis, Department of Pediatrics, Division of Hematology/Oncology and Bone Marrow Transplantation, The Saban Research Institute of Children’s Hospital, Los Angeles, CA 90027, USA
| | - Eun Ji Joo
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
| | - Nora Heisterkamp
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
- Correspondence: ; Tel.: +1-626-218-7503
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Yu CH, Wu G, Chang CC, Jou ST, Lu MY, Lin KH, Chen SH, Wu KH, Huang FL, Cheng CN, Chang HH, Hedges D, Wang JL, Yen HJ, Li MJ, Chou SW, Hung CT, Lin ZS, Lin CY, Chen HY, Ni YL, Hsu YC, Lin DT, Lin SW, Yang JJ, Pui CH, Yu SL, Yang YL. Sequential Approach to Improve the Molecular Classification of Childhood Acute Lymphoblastic Leukemia. J Mol Diagn 2022; 24:1195-1206. [PMID: 35963521 PMCID: PMC9667711 DOI: 10.1016/j.jmoldx.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 08/03/2022] [Indexed: 10/15/2022] Open
Abstract
Identification of specific leukemia subtypes is a key to successful risk-directed therapy in childhood acute lymphoblastic leukemia (ALL). Although RNA sequencing (RNA-seq) is the best approach to identify virtually all specific leukemia subtypes, the routine use of this method is too costly for patients in resource-limited countries. This study enrolled 295 patients with pediatric ALL from 2010 to 2020. Routine screening could identify major cytogenetic alterations in approximately 69% of B-cell ALL (B-ALL) cases by RT-PCR, DNA index, and multiplex ligation-dependent probe amplification. STIL-TAL1 was present in 33% of T-cell ALL (T-ALL) cases. The remaining samples were submitted for RNA-seq. More than 96% of B-ALL cases and 74% of T-ALL cases could be identified based on the current molecular classification using this sequential approach. Patients with Philadelphia chromosome-like ALL constituted only 2.4% of the entire cohort, a rate even lower than those with ZNF384-rearranged (4.8%), DUX4-rearranged (6%), and Philadelphia chromosome-positive (4.4%) ALL. Patients with ETV6-RUNX1, high hyperdiploidy, PAX5 alteration, and DUX4 rearrangement had favorable prognosis, whereas those with hypodiploid and KMT2A and MEF2D rearrangement ALL had unfavorable outcomes. With the use of multiplex ligation-dependent probe amplification, DNA index, and RT-PCR in B-ALL and RT-PCR in T-ALL followed by RNA-seq, childhood ALL can be better classified to improve clinical assessments.
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Affiliation(s)
- Chih-Hsiang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chia-Ching Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shiann-Tarng Jou
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Yao Lu
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kai-Hsin Lin
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Shu-Huey Chen
- Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital and School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Fang-Liang Huang
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chao-Neng Cheng
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Hsiu-Hao Chang
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Dale Hedges
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinn-Li Wang
- Division of Hematology Oncology, Department of Pediatrics, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsiu-Ju Yen
- Department of Pediatrics, Taipei Veterans General Hospital and National Yang-Ming Chiao-Tung University School of Medicine, Taipei, Taiwan
| | - Meng-Ju Li
- Department of Pediatrics, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Shu-Wei Chou
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Chen-Ting Hung
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ze-Shiang Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Lin
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan
| | - Yu-Ling Ni
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Chen Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Dong-Tsamn Lin
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jun J Yang
- Department of Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Yung-Li Yang
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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36
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Yoo JW, Ahn A, Lee JM, Jo S, Kim S, Lee JW, Cho B, Kim Y, Kim M, Chung NG. Spectrum of Genetic Mutations in Korean Pediatric Acute Lymphoblastic Leukemia. J Clin Med 2022; 11:jcm11216298. [PMID: 36362526 PMCID: PMC9658397 DOI: 10.3390/jcm11216298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
The wide application of next-generation sequencing (NGS) technologies has led to the discovery of multiple genetic alterations in pediatric acute lymphoblastic leukemia (ALL). In this work, we aimed to investigate the mutational spectrum in pediatric ALL. We employed a St. Mary’s customized NGS panel comprising 67 leukemia-related genes. Samples were collected from 139 pediatric ALL patients. Eighty-five patients (61.2%) harbored at least one mutation. In B-cell ALL, the RAS pathway is the most involved pathway, and the three most frequently mutated genes were NRAS (22.4%), KRAS (19.6%), and PTPN11 (8.4%). NRAS and PTPN11 were significantly associated with a high hyperdiploidy karyotype (p = 0.018 and p < 0.001, respectively). In T-cell ALL, the three most frequently mutated genes were NOTCH1 (37.5%), FBXW7 (16.6%), and PTEN (6.2%). Several pairs of co-occurring mutations were found: NRAS with SETD, NRAS with PTPN11 in B-cell ALL (p = 0.024 and p = 0.020, respectively), and NOTCH1 with FBXW7 in T-cell ALL (p < 0.001). The most frequent newly emerged mutation in relapsed ALL was NT5C2. We procured comprehensive genetic information regarding Korean pediatric ALL using NGS technology. Our findings strengthen the current knowledge of recurrent somatic mutations in pediatric ALL.
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Affiliation(s)
- Jae Won Yoo
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Ari Ahn
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jong-Mi Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Suejung Jo
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seongkoo Kim
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jae Wook Lee
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Bin Cho
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: (M.K.); (N.-G.C.); Tel.: +82-2-2258-1645 (M.K.); +82-2-2258-6188 (N.-G.C.)
| | - Nack-Gyun Chung
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: (M.K.); (N.-G.C.); Tel.: +82-2-2258-1645 (M.K.); +82-2-2258-6188 (N.-G.C.)
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Rehn J, Mayoh C, Heatley SL, McClure BJ, Eadie LN, Schutz C, Yeung DT, Cowley MJ, Breen J, White DL. RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). PLoS Genet 2022; 18:e1010300. [PMID: 36251721 PMCID: PMC9612819 DOI: 10.1371/journal.pgen.1010300] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/27/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia (ALL) have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early. However, integrating RNA-seq in a clinical setting requires rapid detection and accurate reporting of clinically relevant alterations. Here we present RaScALL, an implementation of the k-mer based variant detection tool km, capable of identifying more than 100 prognostically significant lesions observed in ALL, including gene fusions, single nucleotide variants and focal gene deletions. We compared genomic alterations detected by RaScALL and those reported by alignment-based de novo variant detection tools in a study cohort of 180 Australian patient samples. Results were validated using 100 patient samples from a published North American cohort. RaScALL demonstrated a high degree of accuracy for reporting subtype defining genomic alterations. Gene fusions, including difficult to detect fusions involving EPOR and DUX4, were accurately identified in 98% of reported cases in the study cohort (n = 164) and 95% of samples (n = 63) in the validation cohort. Pathogenic sequence variants were correctly identified in 75% of tested samples, including all cases involving subtype defining variants PAX5 p.P80R (n = 12) and IKZF1 p.N159Y (n = 4). Intragenic IKZF1 deletions resulting in aberrant transcript isoforms were also detectable with 98% accuracy. Importantly, the median analysis time for detection of all targeted alterations averaged 22 minutes per sample, significantly shorter than standard alignment-based approaches. The application of RaScALL enables rapid identification and reporting of previously identified genomic alterations of known clinical relevance.
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Affiliation(s)
- Jacqueline Rehn
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Chelsea Mayoh
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Susan L Heatley
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
| | - Barbara J McClure
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura N Eadie
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Caitlin Schutz
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - David T Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia
| | - Mark J Cowley
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - James Breen
- Black Ochre Data Labs, Telethon Kids Institute, Adelaide, South Australia, Australia
- Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Deborah L White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
- Australian Genomics Health Alliance (AGHA), Parkville, Victoria, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Zhang L, Habeebu SSM, Li W. Prognostic and Predictive Biomarkers in Precursor B-cell Acute Lymphoblastic Leukemia. Leukemia 2022. [DOI: 10.36255/exon-publications-leukemia-biomarkers-lymphoblastic-leukemia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Warren CJ, Santiago ML, Pyeon D. APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis? Annu Rev Virol 2022; 9:375-395. [PMID: 35671565 PMCID: PMC9637027 DOI: 10.1146/annurev-virology-092920-030354] [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] [Indexed: 11/09/2022]
Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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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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41
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Arber DA, Orazi A, Hasserjian RP, Borowitz MJ, Calvo KR, Kvasnicka HM, Wang SA, Bagg A, Barbui T, Branford S, Bueso-Ramos CE, Cortes JE, Dal Cin P, DiNardo CD, Dombret H, Duncavage EJ, Ebert BL, Estey EH, Facchetti F, Foucar K, Gangat N, Gianelli U, Godley LA, Gökbuget N, Gotlib J, Hellström-Lindberg E, Hobbs GS, Hoffman R, Jabbour EJ, Kiladjian JJ, Larson RA, Le Beau MM, Loh MLC, Löwenberg B, Macintyre E, Malcovati L, Mullighan CG, Niemeyer C, Odenike OM, Ogawa S, Orfao A, Papaemmanuil E, Passamonti F, Porkka K, Pui CH, Radich JP, Reiter A, Rozman M, Rudelius M, Savona MR, Schiffer CA, Schmitt-Graeff A, Shimamura A, Sierra J, Stock WA, Stone RM, Tallman MS, Thiele J, Tien HF, Tzankov A, Vannucchi AM, Vyas P, Wei AH, Weinberg OK, Wierzbowska A, Cazzola M, Döhner H, Tefferi A. International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data. Blood 2022; 140:1200-1228. [PMID: 35767897 PMCID: PMC9479031 DOI: 10.1182/blood.2022015850] [Citation(s) in RCA: 900] [Impact Index Per Article: 450.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/16/2022] [Indexed: 02/02/2023] Open
Abstract
The classification of myeloid neoplasms and acute leukemias was last updated in 2016 within a collaboration between the World Health Organization (WHO), the Society for Hematopathology, and the European Association for Haematopathology. This collaboration was primarily based on input from a clinical advisory committees (CACs) composed of pathologists, hematologists, oncologists, geneticists, and bioinformaticians from around the world. The recent advances in our understanding of the biology of hematologic malignancies, the experience with the use of the 2016 WHO classification in clinical practice, and the results of clinical trials have indicated the need for further revising and updating the classification. As a continuation of this CAC-based process, the authors, a group with expertise in the clinical, pathologic, and genetic aspects of these disorders, developed the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias. Using a multiparameter approach, the main objective of the consensus process was the definition of real disease entities, including the introduction of new entities and refined criteria for existing diagnostic categories, based on accumulated data. The ICC is aimed at facilitating diagnosis and prognostication of these neoplasms, improving treatment of affected patients, and allowing the design of innovative clinical trials.
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Affiliation(s)
| | - Attilio Orazi
- Texas Tech University Health Sciences Center El Paso, El Paso, TX
| | | | | | | | | | - Sa A Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adam Bagg
- University of Pennsylvania, Philadelphia, PA
| | - Tiziano Barbui
- Clinical Research Foundation, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | | | | | | | | | | | - Hervé Dombret
- Université Paris Cité, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, Paris, France
| | | | | | | | | | | | | | | | | | | | - Jason Gotlib
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Jean-Jacques Kiladjian
- Université Paris Cité, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kimmo Porkka
- Helsinki University Central Hospital Comprehensive Cancer Center, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Akiko Shimamura
- Dana-Farber Cancer Institute, Boston, MA
- Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Jorge Sierra
- Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | | | | | - Hwei-Fang Tien
- National Taiwan University Hospital, Taipei City, Taiwan
| | | | | | - Paresh Vyas
- University of Oxford, Oxford, United Kingdom
| | - Andrew H Wei
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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42
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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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Creasey T, Barretta E, Ryan SL, Butler E, Kirkwood AA, Leongamornlert D, Papaemmanuil E, Patrick P, Clifton-Hadley L, Patel B, Menne T, McMillan AK, Harrison CJ, Rowntree CJ, Morley N, Marks DI, Fielding AK, Moorman AV. Genetic and genomic analysis of acute lymphoblastic leukemia in older adults reveals a distinct profile of abnormalities: analysis of 210 patients from the UKALL14 and UKALL60+ clinical trials. Haematologica 2022; 107:2051-2063. [PMID: 34788984 PMCID: PMC9425332 DOI: 10.3324/haematol.2021.279177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/09/2021] [Indexed: 11/09/2022] Open
Abstract
Despite being predominantly a childhood disease, the incidence of acute lymphoblastic leukemia (ALL) has a second peak in adults aged 60 years and over. These older adults fare extremely poorly with existing treatment strategies and very few studies have undertaken a comprehensive genetic and genomic characterization to improve prognosis in this age group. We performed cytogenetic, single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) analyses on samples from 210 patients aged ≥60 years from the UKALL14 and UKALL60+ clinical trials. BCR-ABL1-positive disease was present in 26% (55/210) of patients, followed by low hypodiploidy/near triploidy in 13% (28/210). Cytogenetically cryptic rearrangements in CRLF2, ZNF384 and MEF2D were detected in 5%, 1% and <1% of patients, respectively. Copy number abnormalities were common and deletions in ALL driver genes were seen in 77% of cases. IKZF1 deletion was present in 51% (40/78) of samples tested and the IKZF1plus profile was identified in over a third (28/77) of cases of B-cell precursor ALL. The genetic good-risk abnormalities high hyperdiploidy (n=2), ETV6-RUNX1 (no cases) and ERG deletion (no cases) were exceptionally rare in this cohort. RAS pathway mutations were seen in 17% (4/23) of screened samples. KDM6A abnormalities, including biallelic deletions, were discovered in 5% (4/78) of SNP arrays and 9% (2/23) of NGS samples, and represent novel, potentially therapeutically actionable lesions using EZH2 inhibitors. Outcome remained poor with 5-year event-free and overall survival rates of 17% and 24%, respectively, across the cohort, indicating a need for novel therapeutic strategies.
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Affiliation(s)
- Thomas Creasey
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne.
| | - Emilio Barretta
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Sarra L Ryan
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Ellie Butler
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Amy A Kirkwood
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute University College London
| | | | | | - Pip Patrick
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute University College London
| | - Laura Clifton-Hadley
- Cancer Research UK and UCL Cancer Trials Centre, UCL Cancer Institute University College London
| | - Bela Patel
- Department of Haematology, Queen Mary University of London, London
| | - Tobias Menne
- Department of Haematology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne
| | - Andrew K McMillan
- Department of Haematology, Nottingham University Hospital NHS Trust, Nottingham
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Clare J Rowntree
- Department of Haematology, Cardiff And Vale University Health Board, Cardiff
| | - Nick Morley
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield
| | - David I Marks
- Department of Haematology, University Hospitals Bristol NHS Foundation Trust, Bristol
| | | | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne.
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44
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Wu Z, Zhang F, Liu C, Shen S, Chu J, Yang L, Xie Z, Liu Y, Liu K, Wang N. Whole transcriptome sequencing reveals a TCF4-ZNF384 fusion in acute lymphoblastic leukemia. Front Oncol 2022; 12:900054. [PMID: 36052266 PMCID: PMC9425772 DOI: 10.3389/fonc.2022.900054] [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: 03/19/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Previous studies have shown that, the clinical features and prognosis of ZNF384-rearranged pediatric acute lymphoblastic leukemia (ALL) depend on its translocation partners. We report two cases of TCF4-ZNF384 fusion, one 6-year-old girl and one 10-year-old boy, both diagnosed by whole-transcriptome sequencing, and TCF4 is the newest fusion partner of ZNF384. As illustrated in this first report of TCF4-ZNF384 fusion in ALL patients, the identification of patients with ZNF384 rearrangement in ALL patients is critical to elucidate outcomes associated with a specific rearrangement and to develop appropriate treatment strategies. In addition, the development of other methods to detect ZNF384 specific translocation partners and leukemia specific targeting agents is of great significance to further improve the prognosis of ALL with ZNF384-rearrangement.
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Affiliation(s)
- Zhengyu Wu
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fang Zhang
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengzhu Liu
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shuhong Shen
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinhua Chu
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Linhai Yang
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhiwei Xie
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yu Liu
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kangkang Liu
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ningling Wang
- Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Ningling Wang,
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Peyam S, Bhatia P, Singh M, Sharma P, Sreedharanunni S, Sachdeva MS, Naseem S, Bansal D, Varma N, Thakur R, Trehan A. Clinico-hematological and Outcome Profile of Pediatric B-other-ALL and BCR::ABL1-like pre-B-ALL: An Integrated Genomic Study From North India. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2022; 22:e667-e679. [PMID: 35484080 DOI: 10.1016/j.clml.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
PURPOSE BCR::ABL1-like pre-B-ALL comprises a myriad of genetic lesions making molecular diagnosis challenging and expensive. Its frequency and outcome are less studied in resource-constraint settings. METHODS 154 pre-B-ALL cases (0-12 years) were enrolled as group 1 (37 cases of B-other-ALL) and group 2 (117 patients with recurrent translocations/ hyperdiploidy). Group 1 was evaluated for BCR::ABL1-like genetic lesions and copy-number abnormalities (CNAs) as per our published PACE approach supplemented with targeted RNA sequencing. RESULTS BCR::ABL1-like frequency was 5.2% (8 of 154) and 22% (8 of 37) with the PACE approach alone in the whole and B-other-ALL cohort, respectively. The addition of targeted RNA-sequencing had led to the frequency increasing to 9% (14 of 154) and 38% (14 of 37) in the whole and B-other-ALL cohort, respectively. P2RY8::CRLF2, IGH::CRLF2, and RCSD1::ABL1 were noted in 8 (57.1%), 4 (28.6%), and 2 (14.3%) patients, respectively. CNAs were noted in 56.7% (21 of 37) of patients. The BCR::ABL1-like group had a significantly higher initial WBC count of ≥ 50,000/mm3 (71.4%; P < .001) than group 2. The 4-year OS, EFS, RFS of group 1 was not statistically different from group 2, though RFS was borderline poor (84.2%, 51.7%, 56.9% Vs. 82.6%, 62.9%, 78% [P - .42, P - .53, P - .059]). The 4-year EFS and RFS for BCR::ABL1-like cases was 70.7% and 76.6%, respectively. CONCLUSIONS The sensitivity of detecting BCR::ABL1-like lesions had increased significantly from 22% using the PACE approach alone to 38% in B-other-ALLs with the integrated approach. Although outcomes were not statistically different, a higher percentage of relapses were noted in the B-other-ALL group.
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Affiliation(s)
- Srinivasan Peyam
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prateek Bhatia
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Minu Singh
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Sharma
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sreejesh Sreedharanunni
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manupdesh S Sachdeva
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shano Naseem
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepak Bansal
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Varma
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rozy Thakur
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amita Trehan
- Department of Pediatrics, Pediatric Hematology-Oncology Division, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Arthur C, Rezayee F, Mogensen N, Saft L, Rosenquist R, Nordenskjöld M, Harila-Saari A, Tham E, Barbany G. Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study. Front Oncol 2022; 12:899325. [PMID: 35865473 PMCID: PMC9296121 DOI: 10.3389/fonc.2022.899325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 01/24/2023] Open
Abstract
Risk-adapted treatment in acute lymphoblastic leukemia (ALL) relies on genetic information and measurable residual disease (MRD) monitoring. In this proof of concept study, DNA from diagnostic bone marrow (BM) of six children with ALL, without stratifying genetics or central nervous system (CNS) involvement, underwent whole-genome sequencing (WGS) to identify structural variants (SVs) in the leukemic blasts. Unique sequences generated by SVs were targeted with patient-specific droplet digital PCR (ddPCR) assays. Genomic DNA (gDNA) from BM and cell-free DNA (cfDNA) from plasma and cerebrospinal fluid (CSF) were analyzed longitudinally. WGS with 30× coverage enabled target identification in all cases. Limit of quantifiability (LoQ) and limit of detection (LoD) for the ddPCR assays (n = 15) were up to 10-5 and 10-6, respectively. All targets were readily detectable in a multiplexed ddPCR with minimal DNA input (1 ng of gDNA) at a 10-1 dilution, and targets for half of the patients were also detectable at a 10-2 dilution. The level of MRD in BM at end of induction and end of consolidation block 1 was in a comparable range between ddPCR and clinical routine methods for samples with detectable residual disease, although our approach consistently detected higher MRD values for patients with B-cell precursor ALL. Additionally, several samples with undetectable MRD by flow cytometry were MRD-positive by ddPCR. In plasma, the level of leukemic targets decreased in cfDNA over time following the MRD level detected in BM. cfDNA was successfully extracted from all diagnostic CSF samples (n = 6), and leukemic targets were detected in half of these. The results suggest that our approach to design molecular assays, together with ddPCR quantification, is a technically feasible option for accurate MRD quantification and that cfDNA may contribute valuable information regarding MRD and low-grade CNS involvement.
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Affiliation(s)
- Cecilia Arthur
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden,*Correspondence: Cecilia Arthur,
| | - Fatemah Rezayee
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nina Mogensen
- Department of Pediatric Oncology, Karolinska University Hospital, Stockholm, Sweden,Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Leonie Saft
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Arja Harila-Saari
- Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Emma Tham
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gisela Barbany
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms. Leukemia 2022; 36:1720-1748. [PMID: 35732829 PMCID: PMC9214472 DOI: 10.1038/s41375-022-01620-2] [Citation(s) in RCA: 1097] [Impact Index Per Article: 548.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/17/2022] [Accepted: 05/26/2022] [Indexed: 02/05/2023]
Abstract
We herein present an overview of the upcoming 5th edition of the World Health Organization Classification of Haematolymphoid Tumours focussing on lymphoid neoplasms. Myeloid and histiocytic neoplasms will be presented in a separate accompanying article. Besides listing the entities of the classification, we highlight and explain changes from the revised 4th edition. These include reorganization of entities by a hierarchical system as is adopted throughout the 5th edition of the WHO classification of tumours of all organ systems, modification of nomenclature for some entities, revision of diagnostic criteria or subtypes, deletion of certain entities, and introduction of new entities, as well as inclusion of tumour-like lesions, mesenchymal lesions specific to lymph node and spleen, and germline predisposition syndromes associated with the lymphoid neoplasms.
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Wang YZ, Qin YZ, Chang Y, Yuan XY, Chen WM, He LL, Hao L, Shi WH, Jiang Q, Jiang H, Huang XJ, Liu YR. Immunophenotypic characteristics of ZNF384 rearrangement compared with BCR-ABL1, KMT2A rearrangement, and other adult B-cell precursor acute lymphoblastic leukemia. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2022; 102:360-369. [PMID: 35735203 DOI: 10.1002/cyto.b.22086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/22/2022] [Accepted: 06/08/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND ZNF384 rearrangement has been recently identified as a new subtype of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However, comprehensive studies clarifying immunophenotypic features and discriminating them from non-ZNF384 in adult BCP-ALL remain scarce to date. METHODS Flow cytometric assessments were retrospectively performed in 43 patients with ZNF384 rearrangement, 45 with BCR-ABL1, 29 with KMT2A rearrangement and 44 with other BCP-ALL in the analysis cohort. RESULTS CD33- and CD13-positive frequencies were significantly higher in patients with ZNF384 rearrangement than in those with non-ZNF384; however, no significant difference was observed in CD10- and CD123-positive frequencies. Analysis of antigen-positive cell proportion and median fluorescence intensity (MFI) further indicated that patients with ZNF384 rearrangement had significantly lower CD10 and higher CD33, CD13, and CD123 proportion and MFI. However, compared with KMT2A rearrangement, the CD10 expression in patients with ZNF384 rearrangement was higher, with the median percentage and MFI of 36.16 (3.63-94.79)% versus 4.53 (0.03-21.00)%, and 4.50 (0.86-32.26) versus 2.06 (0.87-4.04), respectively (p < 0.0001). Furthermore, compared with BCR-ABL1 and other BCP-ALL, ZNF384 rearrangement had significantly higher CD33 and CD13 proportion and MFI (p < 0.0001 and p < 0.05, respectively). In addition, higher CD123 proportion and MFI in ZNF384 rearrangement than those in the other three groups were reported for the first time (p < 0.01). A flow cytometry scoring system, including CD10%, CD33MFI, CD13%, and CD123MFI, was proposed and verified to predict ZNF384 rearrangement with high sensitivity and specificity, that is, 76.74% and 91.53% in the analysis and 87.50% and 91.30% in the validation cohort. CONCLUSIONS The multiparameter immunophenotypic scoring system could suggest ZNF384 rearrangement.
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Affiliation(s)
- Ya-Zhe Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Yan Chang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Xiao-Ying Yuan
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Ling-Ling He
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Le Hao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Wei-Hua Shi
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Qian Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Hao Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Xiao-Jun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Yan-Rong Liu
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
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Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. Blood 2022; 139:3519-3531. [PMID: 35192684 PMCID: PMC9203703 DOI: 10.1182/blood.2022015444] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/12/2022] [Indexed: 01/14/2023] Open
Abstract
Transcriptome sequencing has identified multiple subtypes of B-progenitor acute lymphoblastic leukemia (B-ALL) of prognostic significance, but a minority of cases lack a known genetic driver. Here, we used integrated whole-genome (WGS) and -transcriptome sequencing (RNA-seq), enhancer mapping, and chromatin topology analysis to identify previously unrecognized genomic drivers in B-ALL. Newly diagnosed (n = 3221) and relapsed (n = 177) B-ALL cases with tumor RNA-seq were studied. WGS was performed to detect mutations, structural variants, and copy number alterations. Integrated analysis of histone 3 lysine 27 acetylation and chromatin looping was performed using HiChIP. We identified a subset of 17 newly diagnosed and 5 relapsed B-ALL cases with a distinct gene expression profile and 2 universal and unique genomic alterations resulting from aberrant recombination-activating gene activation: a focal deletion downstream of PAN3 at 13q12.2 resulting in CDX2 deregulation by the PAN3 enhancer and a focal deletion of exons 18-21 of UBTF at 17q21.31 resulting in a chimeric fusion, UBTF::ATXN7L3. A subset of cases also had rearrangement and increased expression of the PAX5 gene, which is otherwise uncommon in B-ALL. Patients were more commonly female and young adult with median age 35 (range,12-70 years). The immunophenotype was characterized by CD10 negativity and immunoglobulin M positivity. Among 16 patients with known clinical response, 9 (56.3%) had high-risk features including relapse (n = 4) or minimal residual disease >1% at the end of remission induction (n = 5). CDX2-deregulated, UBTF::ATXN7L3 rearranged (CDX2/UBTF) B-ALL is a high-risk subtype of leukemia in young adults for which novel therapeutic approaches are required.
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50
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Xiang C, Wu J, Yu L. Construction of three-gene-based prognostic signature and analysis of immune cells infiltration in children and young adults with B-acute lymphoblastic leukemia. Mol Genet Genomic Med 2022; 10:e1964. [PMID: 35603962 PMCID: PMC9266608 DOI: 10.1002/mgg3.1964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/02/2022] [Accepted: 04/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background Although B‐acute lymphoblastic leukemia (B‐ALL) patients' survival has been improved dramatically, some cases still relapse. This study aimed to explore the prognosis‐related novel differentially expressed genes (DEGs) for predicting the overall survival (OS) of children and young adults (CAYAs) with B‐ALL and analyze the immune‐related factors contributing to poor prognosis. Methods GSE48558 and GSE79533 from Gene Expression Omnibus (GEO) and clinical sample information and mRNA‐seq from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database were retrieved. Prognosis‐related key genes were enrolled to build a Cox proportional model using multivariate Cox regression. Five‐year OS of patients, clinical characteristic relevance and clinical independence were assessed based on the model. The mRNA levels of prognosis‐related genes were validated in our samples and the difference of immune cells composition between high‐risk and low‐risk patients were compared. Results One hundred and twelve DEGs between normal B cells and B‐ALL cells were identified based on GSE datasets. They were mainly participated in protein binding and HIF‐1 signaling pathway. One hundred and eighty‐nine clinical samples were enrolled in the study, both Kaplan–Meier (KM) analysis and univariate Cox regression analysis showed that CYBB, BCL2A1, IFI30, and EFNB1 were associated with prognosis, CYBB, BCL2A1, and EFNB1 were used to construct prognostic risk model. Moreover, compared to clinical indicators, the three‐gene signature was an independent prognostic factor for CAYAs with B‐ALL. Finally, the mRNA levels of CYBB, BCL2A1, and EFNB1 were significantly lower in B‐ALL group as compared to controls. The high‐risk group had a significantly higher percentage of infiltrated immune cells. Conclusion We constructed a novel three‐gene signature with independent prognostic factor for predicting 5‐year OS of CAYAs with B‐ALL. Additionally, we discovered the difference of immune cells composition between high‐risk and low‐risk groups. This study may help to customize individual treatment and improve prognosis of CAYAs with B‐ALL.
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Affiliation(s)
- Chunli Xiang
- Department of Hematology, Huai'an First People's Hospital Affiliated to Nanjing Medical University, Huai'an, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
| | - Jie Wu
- Department of Emergency Medicine, The Fifth People's Hospital of Huai'an, Huai'an, China
| | - Liang Yu
- Department of Hematology, Huai'an First People's Hospital Affiliated to Nanjing Medical University, Huai'an, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing, China
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