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Hu Y, Oleshko S, Firmani S, Zhu Z, Cheng H, Ulmer M, Arnold M, Colomé-Tatché M, Tang J, Xhonneux S, Marsico A. Path-based reasoning for biomedical knowledge graphs with BioPathNet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599219. [PMID: 39149355 PMCID: PMC11326122 DOI: 10.1101/2024.06.17.599219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer's, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet's interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.
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Affiliation(s)
- Yue Hu
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
| | - Svitlana Oleshko
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Computation, Information and Technology, Technical University of Munich, Arcisstrasse 21, Munich, 80333, Bavaria, Germany
| | - Samuele Firmani
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
| | - Zhaocheng Zhu
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Quebec, Canada
| | - Hui Cheng
- School of Computation, Information and Technology, Technical University of Munich, Arcisstrasse 21, Munich, 80333, Bavaria, Germany
| | - Maria Ulmer
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
| | - Matthias Arnold
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- Department of Psychiatry and Behavioural Sciences, Duke University, 905 W Main St., Durham, NC 27701, North Carolina, United States
| | - Maria Colomé-Tatché
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
- Faculty of Biology, Ludwig-Maximilian University of Munich, Grosshaderner Str. 2, Planegg-Martinsried, 82152, Bavaria, Germany
| | - Jian Tang
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, CIFAR AI Chair, 661 University Ave, Toronto, ON M5G 1M1, Ontario, Canada
- Department, HEC Montréal, 3000 Chem. de la Côte-Sainte-Catherine, Montréal, QC H3T 2A7, Quebec, Canada
| | - Sophie Xhonneux
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Quebec, Canada
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
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2
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Yoshimura S, Li Z, Gocho Y, Yang W, Crews KR, Lee SHR, Roberts KG, Mullighan CG, Relling MV, Yu J, Yeoh AEJ, Loh ML, Saygin C, Litzow MR, Jeha S, Karol SE, Inaba H, Pui CH, Konopleva M, Jain N, Stock W, Paietta E, Jabbour E, Kornblau SM, Evans WE, Yang JJ. Impact of Age on Pharmacogenomics and Treatment Outcomes of B-Cell Acute Lymphoblastic Leukemia. J Clin Oncol 2024:JCO2400500. [PMID: 39102629 DOI: 10.1200/jco.24.00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/02/2024] [Accepted: 05/20/2024] [Indexed: 08/07/2024] Open
Abstract
PURPOSE Acute lymphoblastic leukemia (ALL) can occur across all age groups, with a strikingly higher cure rate in children compared with adults. However, the pharmacological basis of age-related differences in ALL treatment response remains unclear. METHODS Studying 767 children and 309 adults with newly diagnosed B-cell ALL enrolled on frontline trials at St Jude Children's Research Hospital, MD Anderson Cancer Center, the Alliance for Clinical Trials in Oncology, and the ECOG-ACRIN Cancer Research Group, we determined the ex vivo sensitivity of leukemia cells to 21 drugs. Twenty-three ALL molecular subtypes were identified using RNA sequencing. We systematically characterized the associations between drug response and ALL genomics in children, adolescents and young adults, and elderly adults. We evaluated the effect of age-related gene expression signature on ALL treatment outcomes. RESULTS Seven ALL drugs (asparaginase, prednisolone, mercaptopurine, dasatinib, nelarabine, daunorubicin, and inotuzumab ozogamicin) showed differential activity between children and adults, of which six were explained by age-related differences in leukemia molecular subtypes. Adolescents and young adults showed similar patterns of drug resistance as older adults, relative to young children. Mercaptopurine exhibited subtype-independent greater sensitivity in children. Transcriptomic profiling uncovered subclusters within CRLF2-, DUX4-, and KMT2A-rearranged ALL that were linked to age and cytotoxic drug resistance. In particular, a subset of children had adult-like ALL on the basis of leukemia gene expression patterns across subtypes, despite their chronological age. Resistant to cytotoxic drugs, children with adult-like ALL exhibited poor prognosis in pediatric ALL trials, even after adjusting for age and minimal residual diseases. CONCLUSION Our results provide pharmacogenomic insights into age-related disparities in ALL cure rates and identify leukemia prognostic features for treatment individualization across age groups.
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Affiliation(s)
- Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Yoshihiro Gocho
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Shawn H R Lee
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | | | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Jiyang Yu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN
| | - Allen E J Yeoh
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Mignon L Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Caner Saygin
- Department of Medicine Section of Hematology-Oncology, University of Chicago, Chicago, IL
| | | | - Sima Jeha
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Seth E Karol
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Hiroto Inaba
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Marina Konopleva
- Department of Oncology and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY
| | - Nitin Jain
- Division of Cancer Medicine, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wendy Stock
- Department of Medicine Section of Hematology-Oncology, University of Chicago, Chicago, IL
| | - Elisabeth Paietta
- Cancer Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Elias Jabbour
- Division of Cancer Medicine, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Steven M Kornblau
- Division of Cancer Medicine, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - William E Evans
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
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3
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Duranti E, Villa C. Insights into Dysregulated Neurological Biomarkers in Cancer. Cancers (Basel) 2024; 16:2680. [PMID: 39123408 PMCID: PMC11312413 DOI: 10.3390/cancers16152680] [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: 06/20/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
The link between neurodegenerative diseases (NDs) and cancer has generated greater interest in biomedical research, with decades of global studies investigating neurodegenerative biomarkers in cancer to better understand possible connections. Tau, amyloid-β, α-synuclein, SOD1, TDP-43, and other proteins associated with nervous system diseases have also been identified in various types of solid and malignant tumors, suggesting a potential overlap in pathological processes. In this review, we aim to provide an overview of current evidence on the role of these proteins in cancer, specifically examining their effects on cell proliferation, apoptosis, chemoresistance, and tumor progression. Additionally, we discuss the diagnostic and therapeutic implications of this interconnection, emphasizing the importance of further research to completely comprehend the clinical implications of these proteins in tumors. Finally, we explore the challenges and opportunities in targeting these proteins for the development of new targeted anticancer therapies, providing insight into how to integrate knowledge of NDs in oncology research.
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Affiliation(s)
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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4
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Schinnerl D, Riebler M, Schumich A, Haslinger S, Bramböck A, Inthal A, Nykiel M, Maurer-Granofszky M, Haas OA, Pötschger U, Köhrer S, Nebral K, Dworzak MN, Attarbaschi A, Strehl S. Risk factors in DUX4-positive childhood and adolescent B-cell acute lymphoblastic leukemia. Blood Cancer J 2024; 14:119. [PMID: 39039054 PMCID: PMC11263571 DOI: 10.1038/s41408-024-01099-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Affiliation(s)
- Dagmar Schinnerl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marion Riebler
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Angela Schumich
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Sabrina Haslinger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Alice Bramböck
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Andrea Inthal
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Marek Nykiel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Margarita Maurer-Granofszky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Oskar A Haas
- St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Stefan Köhrer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Karin Nebral
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Michael N Dworzak
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
- St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Andishe Attarbaschi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Sabine Strehl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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5
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Hodder A, Leiter SM, Kennedy J, Addy D, Ahmed M, Ajithkumar T, Allinson K, Ancliff P, Bailey S, Barnard G, Burke GAA, Burns C, Cano-Flanagan J, Chalker J, Coleman N, Cheng D, Clinch Y, Dryden C, Ghorashian S, Griffin B, Horan G, Hubank M, May P, McDerra J, Nagrecha R, Nicholson J, O'Connor D, Pavasovic V, Quaegebeur A, Rao A, Roberts T, Samarasinghe S, Stasevich I, Tadross JA, Trayers C, Trotman J, Vora A, Watkins J, Chitty LS, Bowdin S, Armstrong R, Murray MJ, Hook CE, Tarpey P, Vedi A, Bartram J, Behjati S. Benefits for children with suspected cancer from routine whole-genome sequencing. Nat Med 2024; 30:1905-1912. [PMID: 38956197 PMCID: PMC11271414 DOI: 10.1038/s41591-024-03056-w] [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: 11/20/2023] [Accepted: 05/08/2024] [Indexed: 07/04/2024]
Abstract
Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.
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Affiliation(s)
- Angus Hodder
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sarah M Leiter
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Jonathan Kennedy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Dilys Addy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Munaza Ahmed
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Phil Ancliff
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Shivani Bailey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gemma Barnard
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Charlotte Burns
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Danny Cheng
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Caryl Dryden
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sara Ghorashian
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Blanche Griffin
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
| | - Gail Horan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael Hubank
- North Thames Genomic Laboratory Hub, London, UK
- The Institute of Cancer Research, London, UK
| | - Phillippa May
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Joanna McDerra
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rajvi Nagrecha
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David O'Connor
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Vesna Pavasovic
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Annelies Quaegebeur
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anupama Rao
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Thomas Roberts
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | | | - Iryna Stasevich
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - John A Tadross
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ajay Vora
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Watkins
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Lyn S Chitty
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah Bowdin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ruth Armstrong
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Catherine E Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Patrick Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- East Genomics Laboratory Hub, Cambridge, UK.
| | - Aditi Vedi
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Jack Bartram
- Great Ormond Street Hospital NHS Foundation Trust, London, UK.
- North Thames Genomic Laboratory Hub, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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6
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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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7
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Morii M, Kubota S, Iimori M, Yokomizo-Nakano T, Hamashima A, Bai J, Nishimura A, Tasaki M, Ando Y, Araki K, Sashida G. TIF1β activates leukemic transcriptional program in HSCs and promotes BCR::ABL1-induced myeloid leukemia. Leukemia 2024; 38:1275-1286. [PMID: 38734786 DOI: 10.1038/s41375-024-02276-w] [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: 05/04/2023] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
TIF1β/KAP1/TRIM28, a chromatin modulator, both represses and activates the transcription of genes in normal and malignant cells. Analyses of datasets on leukemia patients revealed that the expression level of TIF1β was increased in patients with chronic myeloid leukemia at the blast crisis and acute myeloid leukemia. We generated a BCR::ABL1 conditional knock-in (KI) mouse model, which developed aggressive myeloid leukemia, and demonstrated that the deletion of the Tif1β gene inhibited the progression of myeloid leukemia and showed longer survival than that in BCR::ABL1 KI mice, suggesting that Tif1β drove the progression of BCR::ABL1-induced leukemia. In addition, the deletion of Tif1β sensitized BCR::ABL1 KI leukemic cells to dasatinib. The deletion of Tif1β decreased the expression levels of TIF1β-target genes and chromatin accessibility peaks enriched with the Fosl1-binding motif in BCR::ABL1 KI stem cells. TIF1β directly bound to the promoters of proliferation genes, such as FOSL1, in human BCR::ABL1 cells, in which TIF1β and FOSL1 bound to adjacent regions of chromatin. Since the expression of Fosl1 was critical for the enhanced growth of BCR::ABL1 KI cells, Tif1β and Fosl1 interacted to activate the leukemic transcriptional program in and cellular function of BCR::ABL1 KI stem cells and drove the progression of myeloid leukemia.
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MESH Headings
- Animals
- Mice
- Humans
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Gene Expression Regulation, Leukemic
- Tripartite Motif-Containing Protein 28/metabolism
- Tripartite Motif-Containing Protein 28/genetics
- Transcription, Genetic
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Affiliation(s)
- Mariko Morii
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sho Kubota
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mihoko Iimori
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takako Yokomizo-Nakano
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Ai Hamashima
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jie Bai
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akiho Nishimura
- Gastrointestinal Cancer Biology, International Research Center of Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Masayoshi Tasaki
- Department of Biomedical Laboratory Sciences, Graduate School of Health Sciences, Kumamoto University, Kumamoto, Japan
| | - Yukio Ando
- Department of Amyloidosis Research, Nagasaki International University, Sasebo, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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8
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Hu Z, Jia Z, Liu J, Mao A, Han H, Gu Z. MD-ALL: an integrative platform for molecular diagnosis of B-acute lymphoblastic leukemia. Haematologica 2024; 109:1741-1754. [PMID: 37981856 PMCID: PMC11141650 DOI: 10.3324/haematol.2023.283706] [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: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
B-acute lymphoblastic leukemia (B-ALL) consists of dozens of subtypes defined by distinct gene expression profiles (GEP) and various genetic lesions. With the application of transcriptome sequencing (RNA sequencing [RNA-seq]), multiple novel subtypes have been identified, which lead to an advanced B-ALL classification and risk-stratification system. However, the complexity of analyzing RNA-seq data for B-ALL classification hinders the implementation of the new B-ALL taxonomy. Here, we introduce Molecular Diagnosis of Acute Lymphoblastic Leukemia (MD-ALL), an integrative platform featuring sensitive and accurate B-ALL classification based on GEP and sentinel genetic alterations from RNA-seq data. In this study, we systematically analyzed 2,955 B-ALL RNA-seq samples and generated a reference dataset representing all the reported B-ALL subtypes. Using multiple machine learning algorithms, we identified the feature genes and then established highly sensitive and accurate models for B-ALL classification using either bulk or single-cell RNA-seq data. Importantly, this platform integrates multiple aspects of key genetic lesions acquired from RNA-seq data, which include sequence mutations, large-scale copy number variations, and gene rearrangements, to perform comprehensive and definitive B-ALL classification. Through validation in a hold-out cohort of 974 samples, our models demonstrated superior performance for B-ALL classification compared with alternative tools. Moreover, to ensure accessibility and user-friendly navigation even for users with limited or no programming background, we developed an interactive graphical user interface for this MD-ALL platform, using the R Shiny package. In summary, MD-ALL is a user-friendly B-ALL classification platform designed to enable integrative, accurate, and comprehensive B-ALL subtype classification. MD-ALL is available from https://github.com/gu-lab20/MD-ALL.
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Affiliation(s)
- Zunsong Hu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhilian Jia
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Jiangyue Liu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA, USA; Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA
| | - Allen Mao
- Research Informatics, City of Hope National Medical Center, Duarte, CA
| | - Helen Han
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA.
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9
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Yu CH, Su YH, Jou ST, Lu MY, Lin CY, Lin KH, Chang HH, Chou SW, Huang YH, Lin DT, Lin SW, Chen HY, Chang YH, Yang YL. Terminal deoxynucleotidyl transferase expression in different subtypes of childhood B-cell acute lymphoblastic leukemia. Pathol Res Pract 2024; 256:155287. [PMID: 38579576 DOI: 10.1016/j.prp.2024.155287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/07/2024]
Abstract
The lack of expression of terminal deoxynucleotidyl transferase (TdT) is frequently associated with KMT2A-rearranged subtype of pediatric acute lymphoblastic leukemia (ALL). However, this association has not been investigated extensively in the Asian population. A retrospective analysis of TdT expression in pediatric B-cell ALL (B-ALL) was performed in patients treated using the Taiwan Pediatric Oncology Group (TPOG) ALL 2002 and 2013 protocols. Among the 331 patients with B-ALL, 12 patients showed TdT negativity at initial diagnosis. Among these, eight patients showed KMT2A rearrangement (66.7%). Other patients showing negative TdT expression had ETV6::RUNX1, MEF2D-rearranged, and other B-ALL subtypes. However, in the context of KMT2A-rearranged B-ALL (n = 20), only eight patients showed TdT negativity. The 5-year event-free survival and overall survival of patients with and without TdT expression were 83.8% versus 46.8% (P <0.001) and 86.3% versus 55.4% (P = 0.004), respectively. Moreover, several aberrant markers, such as CD2, CD56, CD7, and CD117, were rarely expressed in the B-ALL samples, and if expressed, they were enriched in specific genetic subtypes. The results of this study indicate that immunophenotypic features are correlated with specific genetic subtypes of childhood B-ALL.
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Affiliation(s)
- Chih-Hsiang Yu
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan; Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | | | - Shiann-Tarng Jou
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Yao Lu
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Lin
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan
| | - Kai-Hsin Lin
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsiu-Hao Chang
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Wei Chou
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Dong-Tsamn Lin
- Childhood Cancer Foundation, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science Academia Sinica, Taipei, Taiwan
| | - Ya-Hsuan Chang
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Miaoli, Taiwan.
| | - Yung-Li Yang
- Department of Pediatrics, National Taiwan University 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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10
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Steinemann D, Dawidowska M, Russell LJ, Harrison CJ, Göhring G. Genetic alterations in lymphoblastic leukaemia / lymphoma - a practical guide to WHO HAEM5. MED GENET-BERLIN 2024; 36:39-45. [PMID: 38835965 PMCID: PMC11006319 DOI: 10.1515/medgen-2024-2007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
We present a practical guide for analyzing the genetic aspects of lymphoblastic leukaemia/lymphoma according to the 5th edition of the World Health Organization (WHO) classification of haematolymphoid neoplasms (WHO-HAEM5) issued in 2024. The WHO-HAEM5 acknowledges the increasing importance of genetics in the diagnosis of lymphoid neoplasia. Classification is based on the established genetic subtypes according to cell lineage, with precursor cell neoplasms followed by mature malignancies. This guide describes those genetic abnormalities in acute precursor B- and T-cell neoplasms required for risk stratification, and for treatment, providing diagnostic algorithms under the headings of 'essential' and 'desirable' diagnostic criteria.
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Affiliation(s)
- Doris Steinemann
- Hannover Medical School Department of Human Genetics Hannover Germany
| | - Małgorzata Dawidowska
- Institute of Human Genetics Department of Molecular and Clinical Genetics Poznan Poland
| | - Lisa J Russell
- Newcastle University Centre for Cancer Biosciences Institute Newcastle upon Tyne UK
| | - Christine J Harrison
- Newcastle University Centre for Cancer Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle upon Tyne UK
| | - Gudrun Göhring
- Amedes genetics MVZ wagnerstibbe für Laboratoriumsmedizin, Hämostaseologie, Humangenetik und Mikrobiologie Hannover Germany
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11
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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [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: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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12
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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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13
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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14
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Cruz-Miranda GM, Olarte-Carrillo I, Bárcenas-López DA, Martínez-Tovar A, Ramírez-Bello J, Ramos-Peñafiel CO, García-Laguna AI, Cerón-Maldonado R, May-Hau D, Jiménez-Morales S. Transcriptome Analysis in Mexican Adults with Acute Lymphoblastic Leukemia. Int J Mol Sci 2024; 25:1750. [PMID: 38339034 PMCID: PMC10855968 DOI: 10.3390/ijms25031750] [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: 11/23/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) represents around 25% of adult acute leukemias. Despite the increasing improvement in the survival rate of ALL patients during the last decade, the heterogeneous clinical and molecular features of this malignancy still represent a major challenge for treatment and achieving better outcomes. To identify aberrantly expressed genes in bone marrow (BM) samples from adults with ALL, transcriptomic analysis was performed using Affymetrix Human Transcriptome Array 2.0 (HTA 2.0). Differentially expressed genes (DEGs) (±2-fold change, p-value < 0.05, and FDR < 0.05) were detected using the Transcriptome Analysis Console. Gene Ontology (GO), Database for Annotation, Visualization, and Integrated Discovery (DAVID), and Ingenuity Pathway Analysis (IPA) were employed to identify gene function and define the enriched pathways of DEGs. The protein-protein interactions (PPIs) of DEGs were constructed. A total of 871 genes were differentially expressed, and DNTT, MYB, EBF1, SOX4, and ERG were the top five up-regulated genes. Meanwhile, the top five down-regulated genes were PTGS2, PPBP, ADGRE3, LUCAT1, and VCAN. An association between ERG, CDK6, and SOX4 expression levels and the probability of relapse and death was observed. Regulation of the immune system, immune response, cellular response to stimulus, as well as apoptosis signaling, inflammation mediated by chemokines and cytokines, and T cell activation were among the most altered biological processes and pathways, respectively. Transcriptome analysis of ALL in adults reveals a group of genes consistently associated with hematological malignancies and underscores their relevance in the development of ALL in adults.
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Affiliation(s)
- Gabriela Marisol Cruz-Miranda
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Irma Olarte-Carrillo
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Diego Alberto Bárcenas-López
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Adolfo Martínez-Tovar
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Julian Ramírez-Bello
- Subdirección de Investigación Clínica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico
| | | | - Anel Irais García-Laguna
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Rafael Cerón-Maldonado
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (G.M.C.-M.)
- Laboratorio de Biología Molecular, Servicio de Hematología, Hospital General de México Dr. Eduardo Liceaga, Mexico City 06720, Mexico; (I.O.-C.); (A.M.-T.)
| | - Didier May-Hau
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación en Medicina de Precisión Núcleo A, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
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15
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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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16
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Paolino J, Tsai HK, Harris MH, Pikman Y. IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia. Biomedicines 2024; 12:89. [PMID: 38255194 PMCID: PMC10813044 DOI: 10.3390/biomedicines12010089] [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: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
IKZF1 encodes the transcription factor IKAROS, a zinc finger DNA-binding protein with a key role in lymphoid lineage development. IKAROS plays a critical role in the development of lineage-restricted mature lymphocytes. Deletions within IKZF1 in B-cell acute lymphoblastic leukemia (B-ALL) lead to a loss of normal IKAROS function, conferring leukemic stem cell properties, including self-renewal and subsequent uncontrolled growth. IKZF1 deletions are associated with treatment resistance and inferior outcomes. Early identification of IKZF1 deletions in B-ALL may inform the intensification of therapy and other potential treatment strategies to improve outcomes in this high-risk leukemia.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Harrison K. Tsai
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
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17
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Hormann FM, Mooij EJ, van de Mheen M, Beverloo HB, den Boer ML, Boer JM. The impact of an additional copy of chromosome 21 in B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2024; 63:e23217. [PMID: 38087879 DOI: 10.1002/gcc.23217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/04/2024] Open
Abstract
A common finding in pediatric B-cell precursor acute lymphoblastic leukemia (BCPALL) is that chromosome 21 is never lost and an extra chromosome 21 is often gained. This implies an important role for chromosome 21 in the pathobiology of BCPALL, emphasized by the increased risk of BCPALL in children with Down syndrome. However, model systems of chromosome 21 gain are lacking. We therefore developed a BCPALL cell line (Nalm-6, DUX4-rearranged) with an additional chromosome 21 by means of microcell-mediated chromosome transfer. FISH, PCR, multiplex ligation-dependent probe amplification, and whole exome sequencing showed that an additional chromosome 21 was successfully transferred to the recipient cells. Transcription of some but not all genes on chromosome 21 was increased, indicating tight transcriptional regulation. Nalm-6 cells with an additional chromosome 21 proliferated slightly slower compared with parental Nalm-6 and sensitivity to induction chemotherapeutics was mildly increased. The extra copy of chromosome 21 did not confer sensitivity to targeted signaling inhibitors. In conclusion, a BCPALL cell line with an additional human chromosome 21 was developed, validated, and subjected to functional studies, which showed a minor but potentially relevant effect in vitro. This cell line offers the possibility to study further the role of chromosome 21 in ALL.
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Affiliation(s)
- Femke M Hormann
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Eva J Mooij
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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18
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Zhang P, Lu R. The Molecular and Biological Function of MEF2D in Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:379-403. [PMID: 39017853 DOI: 10.1007/978-3-031-62731-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Myocyte enhancer factor 2 (MEF2) is a key transcription factor (TF) in skeletal, cardiac, and neural tissue development and includes four isoforms: MEF2A, MEF2B, MEF2C, and MEF2D. These isoforms significantly affect embryonic development, nervous system regulation, muscle cell differentiation, B- and T-cell development, thymocyte selection, and effects on tumorigenesis and leukemia. This chapter describes the multifaceted roles of MEF2 family proteins, covering embryonic development, nervous system regulation, and muscle cell differentiation. It further elucidates the contribution of MEF2 to various blood and immune cell functions. Specifically, in B-cell precursor acute lymphoblastic leukemia (BCP-ALL), MEF2D is aberrantly expressed and forms a fusion protein with BCL9, CSF1R, DAZAP1, HNRNPUL1, and SS18. These fusion proteins are closely related to the pathogenesis of leukemia. In addition, it specifically introduces the regulatory effect of MEF2D fusion protein on the proliferation and growth of B-cell acute lymphoblastic leukemia (B-ALL) cells. Finally, we detail the positive feedback loop between MEF2D and IRF8 that significantly promotes the progression of acute myeloid leukemia (AML) and the importance of the ZMYND8-BRD4 interaction in regulating the IRF8 and MYC transcriptional programs. The MEF2D-CEBPE axis is highlighted as a key transcriptional mechanism controlling the block of leukemic cell self-renewal and differentiation in AML. This chapter starts with the structure and function of MEF2 family proteins, specifically summarizing and analyzing the role of MEF2D in B-ALL and AML, mediating the complex molecular mechanisms of transcriptional regulation and exploring their implications for human health and disease.
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Affiliation(s)
- Pengcheng Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
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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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20
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Li Z, Jiang M, Wang J, Zhuo Z, Zhang S, Tan Y, Hu W, Zhang H, Meng G. Transcription factor 12-mediated self-feedback regulatory mechanism is required in DUX4 fusion leukaemia. Clin Transl Med 2023; 13:e1514. [PMID: 38115701 PMCID: PMC10731121 DOI: 10.1002/ctm2.1514] [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: 07/26/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND IGH::DUX4 is frequently observed in 4% B-cell acute lymphoblastic leukaemia patients. Regarding the IGH::DUX4-driven transactivation and alternative splicing, which are the main reasons behind this acute leukaemia outbreak, it remains unclear how transcriptional cofactors contribute to this oncogenic process. Further investigation is required to elucidate their specific role in leukaemogenesis. METHODS In order to investigate the cofactors of IGH::DUX4, integrated mining of Chromatin immunoprecipitation (ChIP)-sequencing and RNA-sequencing of leukaemia cells and patient samples were conducted. Furthermore, to elucidate the synergistic interaction between transcription factor 12 (TCF12) and IGH::DUX4, knockdown and knockout experiment, mammalian two-hybridisation assay, co-immunoprecipitation and in situ proximity ligation assays were carried out. Additionally, to further investigate the direct interaction between TCF12 and IGH::DUX4, AI-based structural simulations were utilised. Finally, to validate the synergistic role of TCF12 in promoting IGH::DUX4 leukaemia, cell proliferation, apoptosis and drug sensitivity experiments were performed. RESULTS In this study, we observed that the IGH::DUX4 target gene TCF12 might be an important cofactor/helper for this oncogenic driver. The co-expression of IGH::DUX4 and TCF12 resulted in enhanced DUX4-driven transactivation. Supportively, knockdown and knockout of TCF12 significantly reduced expression of IGH::DUX4-driven target genes in leukaemia REH (a precursor B-cell leukaemia cell line) and NALM-6 cells (a precursor B-cell leukaemia cell line). Consistently, in TCF12 knockout cells, the expression of structure-based TCF12 mutant, but not wild-type TCF12, failed to restore the TCF12-IGH::DUX4 crosstalk and the synergistic transactivation. More importantly, the breakdown in TCF12-IGH::DUX4 cooperation impaired IGH::DUX4-driven leukaemia cell survival, caused sensitivity to the chemotherapy. CONCLUSIONS Altogether, these results helped to define a previously unrecognised TCF12-mediated positive self-feedback regulatory mechanism in IGH::DUX4 leukaemia, which holds the potential to function as a pivotal drug target for the management of this particular form of leukaemia. HIGHLIGHTS Transcription factor 12 (TCF12) is a new novel cofactor in IGH::DUX4 transcriptional complexes/machinery. TCF12 mediates a positive self-feedback regulatory mechanism in IGH::DUX4-driven oncogenic transaction. IGH::DUX4-TCF12 structure/cooperation might represent a potent target/direction in future drug design against B-cell acute lymphoblastic leukaemia.
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Affiliation(s)
- Zhihui Li
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
| | - Minghao Jiang
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
| | - Junfei Wang
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
| | - Zhiyi Zhuo
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
| | - Shiyan Zhang
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
| | - Yangxia Tan
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
| | - Weiguo Hu
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
- Department of Geriatrics and Medical Center on AgingRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiP. R. China
| | - Hao Zhang
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
- Institute for Translational Brain ResearchState Key Laboratory of Medical NeurobiologyMOE Frontiers Center for Brain ScienceJinshan HospitalFudan UniversityShanghaiP. R. China
| | - Guoyu Meng
- Shanghai Institute of HematologyState Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRui‐Jin HospitalShanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP. R. China
- State Key Laboratory of PathogenesisPrevention and Treatment of High Incidence Diseases in Central Asia, First Affiliated Hospital of Xinjiang Medical UniversityXinjiangP. R. China
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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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22
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Kovach AE, Wood BL. Updates on lymphoblastic leukemia/lymphoma classification and minimal/measurable residual disease analysis. Semin Diagn Pathol 2023; 40:457-471. [PMID: 37953192 DOI: 10.1053/j.semdp.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Lymphoblastic leukemia/lymphoma (ALL/LBL), especially certain subtypes, continues to confer morbidity and mortality despite significant therapeutic advances. The pathologic classification of ALL/LBL, especially that of B-ALL, has recently substantially expanded with the identification of several distinct and prognostically important genetic drivers. These discoveries are reflected in both current classification systems, the World Health Organization (WHO) 5th edition and the new International Consensus Classification (ICC). In this article, novel subtypes of B-ALL are reviewed, including DUX4, MEF2D and ZNF384-rearranged B-ALL; the rare pediatric entity B-ALL with TLF3::HLF, now added to the classifications, is discussed; updates to the category of B-ALL with BCR::ABL1-like features (Ph-like B-ALL) are summarized; and emerging genetic subtypes of T-ALL are presented. The second half of the article details current approaches to minimal/measurable residual disease (MRD) detection in B-ALL and T-ALL and presents anticipated challenges to current approaches in the burgeoning era of antigen-directed immunotherapy.
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Affiliation(s)
- Alexandra E Kovach
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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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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Shakah H, Tbakhi A, Khudirat S, Abweh RA, Hasasna N, Alwhaidi A, Khoujah A, Barakat F. Flow cytometric signature of CD371-positive B-cell acute lymphoblastic leukemia. J Int Med Res 2023; 51:3000605231203842. [PMID: 37818740 PMCID: PMC10566281 DOI: 10.1177/03000605231203842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
OBJECTIVES Multiparametric flow cytometry (MFC) aids in the diagnosis and management of B-cell acute lymphoblastic leukemia (B-ALL) by establishing a baseline immunophenotype for leukemic cells and measuring minimal residual disease (MRD) throughout the course of treatment. Aberrant expression patterns of myeloid markers in B-ALL are also examined during long-term surveillance. Here, we investigated the utility of the newly described myeloid marker cluster of differentiation (CD)371 in MRD surveillance via MFC in patients with CD371-positive B-ALL. METHODS Eight-color MFC with standard panels (including CD371) was used to evaluate 238 patients with newly diagnosed B-ALL. Expression levels of key markers were retrospectively assessed at diagnosis, as well as days 15 and 33 of therapy. RESULTS CD371 was expressed in 8.4% of patients with B-ALL. CD371 positivity was associated with older age at diagnosis, higher expression levels of CD34 and CD38, and lower expression levels of CD10 and CD20. Residual leukemic cells demonstrated decreased CD10 expression and increased CD45 expression after therapy, whereas CD371 expression remained stable. CONCLUSIONS Patients with CD371-positive B-ALL exhibit a specific signature that merits further analysis, particularly because it has been associated with DUX4 rearrangement.
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Affiliation(s)
- Hind Shakah
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Abdelghani Tbakhi
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Saleh Khudirat
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Ruba Al Abweh
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Nabil Hasasna
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Alaa Alwhaidi
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Abdallah Khoujah
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center (KHCC), Jordan
| | - Fareed Barakat
- Department of Pathology and laboratory Medicine, King Hussein Cancer Center (KHCC), Jordan
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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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Kugler E, Madiwale S, Yong D, Thoms JAI, Birger Y, Sykes DB, Schmoellerl J, Drakul A, Priebe V, Yassin M, Aqaqe N, Rein A, Fishman H, Geron I, Chen CW, Raught B, Liu Q, Ogana H, Liedke E, Bourquin JP, Zuber J, Milyavsky M, Pimanda J, Privé GG, Izraeli S. The NCOR-HDAC3 co-repressive complex modulates the leukemogenic potential of the transcription factor ERG. Nat Commun 2023; 14:5871. [PMID: 37735473 PMCID: PMC10514085 DOI: 10.1038/s41467-023-41067-2] [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: 03/07/2022] [Accepted: 08/16/2023] [Indexed: 09/23/2023] Open
Abstract
The ERG (ETS-related gene) transcription factor is linked to various types of cancer, including leukemia. However, the specific ERG domains and co-factors contributing to leukemogenesis are poorly understood. Drug targeting a transcription factor such as ERG is challenging. Our study reveals the critical role of a conserved amino acid, proline, at position 199, located at the 3' end of the PNT (pointed) domain, in ERG's ability to induce leukemia. P199 is necessary for ERG to promote self-renewal, prevent myeloid differentiation in hematopoietic progenitor cells, and initiate leukemia in mouse models. Here we show that P199 facilitates ERG's interaction with the NCoR-HDAC3 co-repressor complex. Inhibiting HDAC3 reduces the growth of ERG-dependent leukemic and prostate cancer cells, indicating that the interaction between ERG and the NCoR-HDAC3 co-repressor complex is crucial for its oncogenic activity. Thus, targeting this interaction may offer a potential therapeutic intervention.
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Affiliation(s)
- Eitan Kugler
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Hematology, Davidoff Cancer Center, Rabin Medical Center, Petah Tikva, Israel
| | - Shreyas Madiwale
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Darren Yong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Julie A I Thoms
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Yehudit Birger
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA & Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Johannes Schmoellerl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Aneta Drakul
- Division of Pediatric Oncology, and Children Research Center, University Children's Hospital, Zurich, Switzerland
| | - Valdemar Priebe
- Division of Pediatric Oncology, and Children Research Center, University Children's Hospital, Zurich, Switzerland
| | - Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avigail Rein
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hila Fishman
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Ifat Geron
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Qiao Liu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Heather Ogana
- Department of Pediatrics, Division of Hematology and Oncology, Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Elisabeth Liedke
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, and Children Research Center, University Children's Hospital, Zurich, Switzerland
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - John Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
| | - Shai Izraeli
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center of Israel, Petach Tikva, Israel.
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Campolungo D, Salomé M, Biferali B, Tascini AS, Gabellini D. DUX4-r exerts a neomorphic activity that depends on GTF2I in acute lymphoblastic leukemia. SCIENCE ADVANCES 2023; 9:eadi3771. [PMID: 37713484 PMCID: PMC10881058 DOI: 10.1126/sciadv.adi3771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023]
Abstract
Translocations producing rearranged versions of the transcription factor double homeobox 4 (DUX4-r) are one of the most frequent causes of B cell acute lymphoblastic leukemia (B-ALL). DUX4-r retains the DNA binding domain of wild-type DUX4 but is truncated on the C-terminal transcription activation domain. The precise mechanism through which DUX4-r causes leukemia is unknown, and no targeted therapy is currently available. We found that the rearrangement leads to both a loss and a gain of function in DUX4-r. Loss of CBP/EP300 transcriptional coactivator interaction leads to an inability to bind and activate repressed chromatin. Concurrently, a gain of interaction with the general transcription factor 2 I (GTF2I) redirects DUX4-r toward leukemogenic targets. This neomorphic activity exposes an Achilles' heel whereby DUX4-r-positive leukemia cells are exquisitely sensitive to GTF2I targeting, which inhibits DUX4-r leukemogenic activity. Our work elucidates the molecular mechanism through which DUX4-r causes leukemia and suggests a possible therapeutic avenue tailored to this B-ALL subtype.
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Affiliation(s)
- Daniele Campolungo
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Mara Salomé
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Beatrice Biferali
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Anna Sofia Tascini
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, 20132 Milano, Italy
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy
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Tsai HK, Gogakos T, Lip V, Tsai JM, Li YD, Fisch AS, Weiss J, Yang W, Grimmett L, DiToro D, Schaefer EJ, Lindsley RC, Tran TH, Caron M, Langlois S, Sinnett D, Pikman Y, Nardi V, Kim AS, Silverman LB, Harris MH. Outlier Expression of Isoforms by Targeted or Total RNA Sequencing Identifies Clinically Significant Genomic Variants in Hematolymphoid Tumors. J Mol Diagn 2023; 25:665-681. [PMID: 37419244 PMCID: PMC10488324 DOI: 10.1016/j.jmoldx.2023.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 07/09/2023] Open
Abstract
Recognition of aberrant gene isoforms due to DNA events can impact risk stratification and molecular classification of hematolymphoid tumors. In myelodysplastic syndromes, KMT2A partial tandem duplication (PTD) was one of the top adverse predictors in the International Prognostic Scoring System-Molecular study. In B-cell acute lymphoblastic leukemia (B-ALL), ERG isoforms have been proposed as markers of favorable-risk DUX4 rearrangements, whereas deletion-mediated IKZF1 isoforms are associated with adverse prognosis and have been extended to the high-risk IKZF1plus signature defined by codeletions, including PAX5. In this limited study, outlier expression of isoforms as markers of IKZF1 intragenic or 3' deletions, DUX4 rearrangements, or PAX5 intragenic deletions were 92.3% (48/52), 90% (9/10), or 100% (9/9) sensitive, respectively, and 98.7% (368/373), 100% (35/35), or 97.1% (102/105) specific, respectively, by targeted RNA sequencing, and 84.0% (21/25), 85.7% (6/7), or 81.8% (9/11) sensitive, respectively, and 98.2% (109/111), 98.4% (127/129), or 98.7% (78/79) specific, respectively, by total RNA sequencing. Comprehensive split-read analysis identified expressed DNA breakpoints, cryptic splice sites associated with IKZF1 3' deletions, PTD of IKZF1 exon 5 spanning N159Y in B-ALL with mutated IKZF1 N159Y, and truncated KMT2A-PTD isoforms. Outlier isoforms were also effective targeted RNA markers for PAX5 intragenic amplifications (B-ALL), KMT2A-PTD (myeloid malignant cancers), and rare NOTCH1 intragenic deletions (T-cell acute lymphoblastic leukemia). These findings support the use of outlier isoform analysis as a robust strategy for detecting clinically significant DNA events.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Tasos Gogakos
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Va Lip
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Weiss
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weiping Yang
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel DiToro
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva J Schaefer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Maxime Caron
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Sylvie Langlois
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
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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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30
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Leongamornlert D, Gutiérrez-Abril J, Lee S, Barretta E, Creasey T, Gundem G, Levine MF, Arango-Ossa JE, Liosis K, Medina-Martinez JS, Zuborne Alapi K, Kirkwood AA, Clifton-Hadley L, Patrick P, Jones D, O’Neill L, Butler AP, Harrison CJ, Campbell P, Patel B, Moorman AV, Fielding AK, Papaemmanuil E. Diagnostic utility of whole genome sequencing in adults with B-other acute lymphoblastic leukemia. Blood Adv 2023; 7:3862-3873. [PMID: 36867579 PMCID: PMC10405200 DOI: 10.1182/bloodadvances.2022008992] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/12/2023] [Indexed: 03/04/2023] Open
Abstract
Genomic profiling during the diagnosis of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) in adults is used to guide disease classification, risk stratification, and treatment decisions. Patients for whom diagnostic screening fails to identify disease-defining or risk-stratifying lesions are classified as having B-other ALL. We screened a cohort of 652 BCP-ALL cases enrolled in UKALL14 to identify and perform whole genome sequencing (WGS) of paired tumor-normal samples. For 52 patients with B-other, we compared the WGS findings with data from clinical and research cytogenetics. WGS identified a cancer-associated event in 51 of 52 patients, including an established subtype defining genetic alterations that were previously missed with standard-of-care (SoC) genetics in 5 of them. Of the 47 true B-other ALL, we identified a recurrent driver in 87% (41). A complex karyotype via cytogenetics emerges as a heterogeneous group, including distinct genetic alterations associated with either favorable (DUX4-r) or poor outcomes (MEF2D-r and IGK::BCL2). For a subset of 31 cases, we integrated the findings from RNA sequencing (RNA-seq) analysis to include fusion gene detection and classification based on gene expression. Compared with RNA-seq, WGS was sufficient to detect and resolve recurrent genetic subtypes; however, RNA-seq can provide orthogonal validation of findings. In conclusion, we demonstrated that WGS can identify clinically relevant genetic abnormalities missed with SoC testing as well as identify leukemia driver events in virtually all cases of B-other ALL.
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Affiliation(s)
- Daniel Leongamornlert
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jesús Gutiérrez-Abril
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - SooWah Lee
- Department of Haematology, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Emilio Barretta
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Creasey
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gunes Gundem
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Max F. Levine
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan E. Arango-Ossa
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Konstantinos Liosis
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan S. Medina-Martinez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Krisztina Zuborne Alapi
- Department of Haematology, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Amy A. Kirkwood
- Cancer Research UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - Laura Clifton-Hadley
- Cancer Research UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - Pip Patrick
- Cancer Research UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Laura O’Neill
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam P. Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Bela Patel
- Department of Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Anthony V. Moorman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adele K. Fielding
- Department of Haematology, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Elli Papaemmanuil
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
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31
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Masih KE, Gardner RA, Chou HC, Abdelmaksoud A, Song YK, Mariani L, Gangalapudi V, Gryder BE, Wilson AL, Adebola SO, Stanton BZ, Wang C, Milewski D, Kim YY, Tian M, Cheuk ATC, Wen X, Zhang Y, Altan-Bonnet G, Kelly MC, Wei JS, Bulyk ML, Jensen MC, Orentas RJ, Khan J. A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia. Blood Adv 2023; 7:4218-4232. [PMID: 36607839 PMCID: PMC10440404 DOI: 10.1182/bloodadvances.2022008977] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
CD19 chimeric antigen receptor T-cell therapy (CD19-CAR) has changed the treatment landscape and outcomes for patients with pre-B-cell acute lymphoblastic leukemia (B-ALL). Unfortunately, primary nonresponse (PNR), sustained CD19+ disease, and concurrent expansion of CD19-CAR occur in 20% of the patients and is associated with adverse outcomes. Although some failures may be attributable to CD19 loss, mechanisms of CD19-independent, leukemia-intrinsic resistance to CD19-CAR remain poorly understood. We hypothesize that PNR leukemias are distinct compared with primary sensitive (PS) leukemias and that these differences are present before treatment. We used a multiomic approach to investigate this in 14 patients (7 with PNR and 7 with PS) enrolled in the PLAT-02 trial at Seattle Children's Hospital. Long-read PacBio sequencing helped identify 1 PNR in which 47% of CD19 transcripts had exon 2 skipping, but other samples lacked CD19 transcript abnormalities. Epigenetic profiling discovered DNA hypermethylation at genes targeted by polycomb repressive complex 2 (PRC2) in embryonic stem cells. Similarly, assays of transposase-accessible chromatin-sequencing revealed reduced accessibility at these PRC2 target genes, with a gain in accessibility of regions characteristic of hematopoietic stem cells and multilineage progenitors in PNR. Single-cell RNA sequencing and cytometry by time of flight analyses identified leukemic subpopulations expressing multilineage markers and decreased antigen presentation in PNR. We thus describe the association of a stem cell epigenome with primary resistance to CD19-CAR therapy. Future trials incorporating these biomarkers, with the addition of multispecific CAR T cells targeting against leukemic stem cell or myeloid antigens, and/or combined epigenetic therapy to disrupt this distinct stem cell epigenome may improve outcomes of patients with B-ALL.
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Affiliation(s)
- Katherine E. Masih
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge, England
- Medical Scientist Training Program, University of Miami Leonard M. Miller School of Medicine, Miami, FL
| | - Rebecca A. Gardner
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Hsien-Chao Chou
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Abdalla Abdelmaksoud
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Young K. Song
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Vineela Gangalapudi
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Berkley E. Gryder
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Ashley L. Wilson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Serifat O. Adebola
- Immunodynamics Group, Cancer and Inflammation Program, Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Benjamin Z. Stanton
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital, Columbus, OH
| | - Chaoyu Wang
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - David Milewski
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yong Yean Kim
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Meijie Tian
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Adam Tai-Chi Cheuk
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xinyu Wen
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Zhang
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Michael C. Kelly
- Center for Cancer Research Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Jun S. Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Michael C. Jensen
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rimas J. Orentas
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Radhakrishnan K, Truong L, Carmichael CL. An "unexpected" role for EMT transcription factors in hematological development and malignancy. Front Immunol 2023; 14:1207360. [PMID: 37600794 PMCID: PMC10435889 DOI: 10.3389/fimmu.2023.1207360] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The epithelial to mesenchymal transition (EMT) is a fundamental developmental process essential for normal embryonic development. It is also important during various pathogenic processes including fibrosis, wound healing and epithelial cancer cell metastasis and invasion. EMT is regulated by a variety of cell signalling pathways, cell-cell interactions and microenvironmental cues, however the key drivers of EMT are transcription factors of the ZEB, TWIST and SNAIL families. Recently, novel and unexpected roles for these EMT transcription factors (EMT-TFs) during normal blood cell development have emerged, which appear to be largely independent of classical EMT processes. Furthermore, EMT-TFs have also begun to be implicated in the development and pathogenesis of malignant hematological diseases such as leukemia and lymphoma, and now present themselves or the pathways they regulate as possible new therapeutic targets within these malignancies. In this review, we discuss the ZEB, TWIST and SNAIL families of EMT-TFs, focusing on what is known about their normal roles during hematopoiesis as well as the emerging and "unexpected" contribution they play during development and progression of blood cancers.
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Affiliation(s)
- Karthika Radhakrishnan
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Lynda Truong
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Catherine L. Carmichael
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Monash University, Faculty of Medicine, Nursing and Health Sciences, Clayton, VIC, Australia
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33
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Page EC, Heatley SL, Rehn J, Thomas PQ, Yeung DT, White DL. Gain of chromosome 21 increases the propensity for P2RY8::CRLF2 acute lymphoblastic leukemia via increased HMGN1 expression. Front Oncol 2023; 13:1177871. [PMID: 37483494 PMCID: PMC10358767 DOI: 10.3389/fonc.2023.1177871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) patients with a gain of chromosome 21, intrachromosomal amplification of chromosome 21 (iAMP21), or Down syndrome (DS), have increased expression of genes in the DS critical region (DSCR) of chromosome 21, including the high-mobility group nucleosome-binding protein 1, HMGN1. Children with DS are predisposed to develop hematologic malignancies, providing insight into the role of chromosome 21 in the development of leukemias. A 320-kb deletion in the pseudoautosomal region of the X/Y chromosome in leukemic cells, resulting in a gene fusion between the purinergic receptor and cytokine receptor-like factor-2 (P2Y Receptor Family Member 8 (P2RY8)::CRLF2), is a common feature in ~60% of DS-ALL and ~40% of iAMP21 patients, suggesting a link between chromosome 21 and P2RY8::CRLF2. In an Australian cohort of pediatric B-ALL patients with P2RY8::CRLF2 (n = 38), eight patients harbored gain of chromosome 21 (+21), and two patients had iAMP21, resulting in a significantly increased HMGN1 expression. An inducible CRISPR/Cas9 system was used to model P2RY8::CRLF2 and investigate its cooperation with HMGN1. This model was then used to validate HMGN1 as an influencing factor for P2RY8::CRLF2 development. Using Cas9 to cleave the DNA at the pseudoautosomal region without directed repair, cells expressing HMGN1 favored repair, resulting in P2RY8::CRLF2 generation, compared with cells without HMGN1. CRISPR/Cas9 P2RY8::CRLF2 cells expressing HMGN1 exhibit increased proliferation, thymic stromal lymphopoietin receptor (TSLPR) expression, and JAK/STAT signaling, consistent with cells from patients with P2RY8::CRLF2. Our patient expression data and unique CRISPR/Cas9 modeling, when taken together, suggest that HMGN1 increases the propensity for P2RY8::CRLF2 development. This has important implications for patients with DS, +21, or iAMP21.
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Affiliation(s)
- Elyse C. Page
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering, and Technology, University of Adelaide, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Susan L. Heatley
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Jacqueline Rehn
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Paul Q. Thomas
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
- SA Gene Editing Program, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - David T. Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group, Melbourne, VIC, Australia
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia
| | - Deborah L. White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering, and Technology, University of Adelaide, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
- Australasian Leukaemia and Lymphoma Group, Melbourne, VIC, Australia
- Australian and New Zealand Children’s Hematology/Oncology Group (ANZCHOG), Clayton, VIC, Australia
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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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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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Gu Z, Hu Z, Jia Z, Liu J, Mao A, Han H. MD-ALL: an Integrative Platform for Molecular Diagnosis of B-cell Acute Lymphoblastic Leukemia. RESEARCH SQUARE 2023:rs.3.rs-2798895. [PMID: 37090504 PMCID: PMC10120769 DOI: 10.21203/rs.3.rs-2798895/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) consists of dozens of subtypes defined by distinct gene expression profiles (GEPs) and various genetic lesions. With the application of transcriptome sequencing (RNA-seq), multiple novel subtypes have been identified, which lead to an advanced B-ALL classification and risk-stratification system. However, the complexity of analyzing RNA-seq data for B-ALL classification hinders the implementation of the new B-ALL taxonomy. Here, we introduce MD-ALL (Molecular Diagnosis of ALL), a user-friendly platform featuring sensitive and accurate B-ALL classification based on GEPs and sentinel genetic alterations. In this study, we systematically analyzed 2,955 B-ALL RNA-seq samples and generated a reference dataset representing all the reported B-ALL subtypes. Using multiple machine learning algorithms, we identified the feature genes and then established highly accurate models for B-ALL classification using either bulk or single-cell RNA-seq data. Importantly, this platform integrates the key genetic lesions, including sequence mutations, large-scale copy number variations, and gene rearrangements, to perform comprehensive and definitive B-ALL classification. Through validation in a hold-out cohort of 974 samples, our models demonstrated superior performance for B-ALL classification compared with alternative tools. In summary, MD-ALL is a user-friendly B-ALL classification platform designed to enable integrative, accurate, and comprehensive B-ALL subtype classification.
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Davis K, Sheikh T, Aggarwal N. Emerging molecular subtypes and therapies in acute lymphoblastic leukemia. Semin Diagn Pathol 2023; 40:202-215. [PMID: 37120350 DOI: 10.1053/j.semdp.2023.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/01/2023]
Abstract
Tremendous strides have been made in the molecular and cytogenetic classification of acute lymphoblastic leukemia based on gene expression profiling data, leading to an expansion of entities in the recent International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias and 2022 WHO Classification of Tumours: Haematolymphoid Tumors, 5th edition. This increased diagnostic and therapeutic complexity can be overwhelming, and this review compares nomenclature differences between the ICC and WHO 5th edition publications, compiles key features of each entity, and provides a diagnostic algorithmic approach. In covering B-lymphoblastic leukemia (B-ALL), we divided the entities into established (those present in the revised 4th edition WHO) and novel (those added to either the ICC or WHO 5th edition) groups. The established B-ALL entities include B-ALL with BCR::ABL1 fusion, BCR::ABL1-like features, KMT2A rearrangement, ETV6::RUNX1 rearrangement, high hyperdiploidy, hypodiploidy (focusing on near haploid and low hypodiploid), IGH::IL3 rearrangement, TCF3::PBX1 rearrangement, and iAMP21. The novel B-ALL entities include B-ALL with MYC rearrangement; DUX4 rearrangement; MEF2D rearrangement; ZNF384 or ZNF362 rearrangement, NUTM1 rearrangement; HLF rearrangement; UBTF::ATXN7L3/PAN3,CDX2; mutated IKZF1 N159Y; mutated PAX5 P80R; ETV6::RUNX1-like features; PAX5 alteration; mutated ZEB2 (p.H1038R)/IGH::CEBPE; ZNF384 rearranged-like; KMT2A-rearranged-like; and CRLF2 rearrangement (non-Ph-like). Classification of T-ALL is complex with some variability in how the subtypes are defined in recent literature. It was classified as early T-precursor lymphoblastic leukemia/lymphoma and T-ALL, NOS in the WHO revised 4th edition and WHO 5th edition. The ICC added an entity into early T-cell precursor ALL, BCL11B-activated, and also added provisional entities subclassified based on transcription factor families that are aberrantly activated.
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Affiliation(s)
- Katelynn Davis
- Department of Hematopathology, School of Medicine and UPMC, University of Pittsburgh, USA
| | | | - Nidhi Aggarwal
- Department of Hematopathology, School of Medicine and UPMC, University of Pittsburgh, USA.
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Functional damaging germline variants in ETV6, IKZF1, PAX5 and RUNX1 predisposing to B-cell precursor acute lymphoblastic leukemia. Eur J Med Genet 2023; 66:104725. [PMID: 36764385 DOI: 10.1016/j.ejmg.2023.104725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/29/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Recent genome-wide studies have demonstrated that a significant proportion of children with cancer carry predisposing germline variants, with varying incidence according to cancer type. In general, there is a lower incidence of underlying germline predisposing variants among patients with B-cell acute lymphoblastic leukemia (B-ALL) compared to other types of cancer, but higher rates may be found in patients with specific leukemia subtypes. Two categories of ALL-predisposing variants have been described: common polymorphisms, conferring low-penetrance ALL susceptibility, and rare variants, conferring high-penetrance ALL susceptibility. Variants in genes encoding hematopoietic transcription factors are an example of the latter, and include ETV6, IKZF1, PAX5 and RUNX1. Here, we present an overview of the germline variants detected in patients with B-ALL in these four genes and a summary of functional studies analyzing the impacts of these variants upon protein function, and hence their effects with regard to leukemia predisposition. Furthermore, we review specific clinical characteristics of patients with B-ALL, including specific features of the patient or family history and associated somatic genetic characteristics, which are suggestive of underlying germline alterations in one of these genes. This review may be of assistance in the interpretation of patient genetic germline findings, made even more challenging by the absence of a suggestive family history or by an unknown familial cancer history. Despite a low incidence of underlying germline alterations in ETV6, IKZF1, PAX5 and RUNX1 in patients with B-ALL, identification of an underlying ALL predisposition syndrome is relevant to the clinical management of patients and their relatives, as the latter are also at risk of developing cancer.
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Fischer A, Lersch R, de Andrade Krätzig N, Strong A, Friedrich MJ, Weber J, Engleitner T, Öllinger R, Yen HY, Kohlhofer U, Gonzalez-Menendez I, Sailer D, Kogan L, Lahnalampi M, Laukkanen S, Kaltenbacher T, Klement C, Rezaei M, Ammon T, Montero JJ, Schneider G, Mayerle J, Heikenwälder M, Schmidt-Supprian M, Quintanilla-Martinez L, Steiger K, Liu P, Cadiñanos J, Vassiliou GS, Saur D, Lohi O, Heinäniemi M, Conte N, Bradley A, Rad L, Rad R. In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution. CELL GENOMICS 2023; 3:100276. [PMID: 36950387 PMCID: PMC10025556 DOI: 10.1016/j.xgen.2023.100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 03/10/2023]
Abstract
In contrast to mono- or biallelic loss of tumor-suppressor function, effects of discrete gene dysregulations, as caused by non-coding (epi)genome alterations, are poorly understood. Here, by perturbing the regulatory genome in mice, we uncover pervasive roles of subtle gene expression variation in cancer evolution. Genome-wide screens characterizing 1,450 tumors revealed that such quasi-insufficiency is extensive across entities and displays diverse context dependencies, such as distinct cell-of-origin associations in T-ALL subtypes. We compile catalogs of non-coding regions linked to quasi-insufficiency, show their enrichment with human cancer risk variants, and provide functional insights by engineering regulatory alterations in mice. As such, kilo-/megabase deletions in a Bcl11b-linked non-coding region triggered aggressive malignancies, with allele-specific tumor spectra reflecting gradual gene dysregulations through modular and cell-type-specific enhancer activities. Our study constitutes a first survey toward a systems-level understanding of quasi-insufficiency in cancer and gives multifaceted insights into tumor evolution and the tissue-specific effects of non-coding mutations.
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Affiliation(s)
- Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Robert Lersch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Mathias J. Friedrich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Hsi-Yu Yen
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Ursula Kohlhofer
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - David Sailer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Liz Kogan
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Saara Laukkanen
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Majdaddin Rezaei
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Tim Ammon
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Juan J. Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Julia Mayerle
- Medical Department II, University Hospital, LMU Munich, Munich, Germany
| | - Mathias Heikenwälder
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), 33193 Oviedo, Spain
| | - George S. Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Olli Lohi
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Nathalie Conte
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
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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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41
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Yu CH, Jou ST, Su YH, Coustan-Smith E, Wu G, Cheng CN, Lu MY, Lin KH, Wu KH, Chen SH, Huang FL, Chang HH, Wang JL, Yen HJ, Li MJ, Chou SW, Ho WL, Liu YL, Chang CC, Lin ZS, Lin CY, Chen HY, Ni YL, Lin DT, Lin SW, Yang JJ, Ni YH, Pui CH, Yu SL, Yang YL. Clinical impact of minimal residual disease and genetic subtypes on the prognosis of childhood acute lymphoblastic leukemia. Cancer 2023; 129:790-802. [PMID: 36537587 DOI: 10.1002/cncr.34606] [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: 10/11/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND This study analyzed data from two consecutive protocols for children newly diagnosed with acute lymphoblastic leukemia (ALL) to determine the clinical impact of minimal/measurable residual disease (MRD) and recently identified tumor genetic subtypes. METHODS Genetic subtypes were determined by sequential approaches including DNA indexing, reverse transcriptase-polymerase chain reaction, multiplex ligation-dependent probe amplification, and RNA-sequencing. MRD was assessed by flow cytometry. The Taiwan Pediatric Oncology Group TPOG-ALL-2013 study enrolled patients who received MRD-directed therapy. RESULTS The 5-year event-free survival (EFS) and overall survival rates in the 2013 cohort were 77.8% and 86.9% compared to those of the 2002 cohort, which were 62.4% and 76.5%. Among patients treated with MRD-guided therapy, those with ETV6-RUNX1 fusion and high hyperdiploidy had the highest 5-year EFS (91.4% and 89.6%, respectively). The addition of dasatinib improved outcomes in patients with BCR-ABL1 ALL. Recently identified subtypes like DUX4-rearranged, ZNF384-rearranged, MEF2D-rearranged, and PAX5alt subtypes were frequently positive for MRD after remission induction, and these patients consequently received intensified chemotherapy. Treatment intensification according to the MRD improved the outcomes of patients presenting DUX4 rearrangements. In high-risk or very-high-risk subtypes, the TPOG-ALL-2013 regimen did not confer significant improvements compared to TPOG-ALL-2002, and the outcomes of BCR-ABL1-like, MEF2D-rearranged, and KMT2A-rearranged ALL subtypes (in addition to those of T-cell ALL) were not sufficiently good. Novel agents or approaches are needed to improve the outcomes for these patients. CONCLUSIONS The TPOG-ALL-2013 study yielded outcomes superior to those of patients treated in the preceding TPOG-ALL-2002 study. This study provides important data to inform the design of future clinical trials in Taiwan. PLAIN LANGUAGE SUMMARY MRD-directed therapy improved the outcomes for pediatric ALL, especially standard-risk patients. Genomic analyses and MRD might be used together for risk-directed therapy of childhood ALL. Our work provides important data to inform the design of future clinical trials in Taiwan.
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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.,Institute of Statistical Science Academia Sinica, 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
| | | | - Elane Coustan-Smith
- Department of Pediatrics, Yong, Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chao-Neng Cheng
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan.,Department of Pediatrics, College of Medicine, National Cheng Kung University, Tainan, 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
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Shu-Huey Chen
- Department of Pediatrics, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan
| | - Fang-Liang Huang
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, 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
| | - 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 University, 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
| | - Wan-Ling Ho
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yen-Lin Liu
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chia-Ching Chang
- 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
| | - 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 and the University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Yen-Hsuan Ni
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan.,Department of Pediatrics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital and the University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - 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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42
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Bomken S, Enshaei A, Schwalbe EC, Mikulasova A, Dai Y, Zaka M, Fung KTM, Bashton M, Lim H, Jones L, Karataraki N, Winterman E, Ashby C, Attarbaschi A, Bertrand Y, Bradtke J, Buldini B, Burke GAA, Cazzaniga G, Gohring G, De Groot-Kruseman HA, Haferlach C, Nigro LL, Parihar M, Plesa A, Seaford E, Sonneveld E, Strehl S, Van der Velden VHJ, Rand V, Hunger SP, Harrison CJ, Bacon CM, Van Delft FW, Loh ML, Moppett J, Vormoor J, Walker BA, Moorman AV, Russell LJ. Molecular characterization and clinical outcome of B-cell precursor acute lymphoblastic leukemia with IG-MYC rearrangement. Haematologica 2023; 108:717-731. [PMID: 35484682 PMCID: PMC9973471 DOI: 10.3324/haematol.2021.280557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
Rarely, immunophenotypically immature B-cell precursor acute lymphoblastic leukemia (BCP-ALL) carries an immunoglobulin- MYC rearrangement (IG-MYC-r). This can result in diagnostic confusion with Burkitt lymphoma/leukemia and use of individualized treatment schedules of unproven efficacy. Here we compare the molecular characteristics of these conditions and investigate historic clinical outcome data. We identified 90 cases registered in a national BCP-ALL clinical trial/registry. When present, diagnostic material underwent cytogenetic, exome, methylome and transcriptome analyses. The outcomes analyzed were 3-year event-free survival and overall survival. IG-MYC-r was identified in diverse cytogenetic backgrounds, co-existing with either established BCP-ALL-specific abnormalities (high hyperdiploidy, n=3; KMT2A-rearrangement, n=6; iAMP21, n=1; BCR-ABL1, n=1); BCL2/BCL6-rearrangements (n=15); or, most commonly, as the only defining feature (n=64). Within this final group, precursor-like V(D)J breakpoints predominated (8/9) and KRAS mutations were common (5/11). DNA methylation identified a cluster of V(D)J-rearranged cases, clearly distinct from Burkitt leukemia/lymphoma. Children with IG-MYC-r within that subgroup had a 3-year event-free survival of 47% and overall survival of 60%, representing a high-risk BCP-ALL. To develop effective management strategies this group of patients must be allowed access to contemporary, minimal residual disease-adapted, prospective clinical trial protocols.
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Affiliation(s)
- Simon Bomken
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne.
| | - Amir Enshaei
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Edward C Schwalbe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne
| | - Yunfeng Dai
- Department of Biostatistics, Colleges of Medicine, Public Health and Health Professions, University of Florida, Gainesville, Florida
| | - Masood Zaka
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK; National Horizons Centre, Teesside University, Darlington
| | - Kent T M Fung
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne
| | - Huezin Lim
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Lisa Jones
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Nefeli Karataraki
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Emily Winterman
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Cody Ashby
- Department of Biomedical Informatics / Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Yves Bertrand
- Department of Institute of Hematology Oncology Pediatric (IHOP), Hospices Civils de Lyon, Lyon
| | - Jutta Bradtke
- Institute of Pathology, Department Cytogenetics, University Hospital Giessen and Marburg
| | | | - G A Amos Burke
- Department of Paediatric Haematology, Oncology, and Palliative Care, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge
| | - Giovanni Cazzaniga
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; Centro Ricerca Tettamanti, University of Milano-Bicocca, Monza
| | - Gudrun Gohring
- Department of Human Genetics, Hannover Medical School, Hannover
| | - Hesta A De Groot-Kruseman
- Dutch Childhood Oncology Group (DCOG), Utrecht, The Netherlands; Princess Maxima Center for Pediatric Oncology, Utrecht
| | | | - Luca Lo Nigro
- Head of Cytogenetic-Cytofluorimetric-Molecular Biology Laboratory, Center of Pediatric Hematology Oncology, Azienda Policlinico "G. Rodolico - San Marco", Catania
| | - Mayur Parihar
- Department of Cytogenetics and Laboratory Haematology, Tata Medical Centre, Kolkata, India
| | - Adriana Plesa
- Hematology and Flow cytometry Laboratory, Lyon Sud University Hospital, Hospices Civils de Lyon, Lyon
| | - Emma Seaford
- Department of Paediatric Oncology, Bristol Royal Hospital for Children, Bristol
| | | | - Sabine Strehl
- St. Anna Children's Cancer Research Institute, Vienna
| | | | - Vikki Rand
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK; National Horizons Centre, Teesside University, Darlington
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Christine J Harrison
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Chris M Bacon
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne
| | - Frederik W Van Delft
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - John Moppett
- Department of Paediatric Oncology, Bristol Royal Hospital for Children, Bristol
| | - Josef Vormoor
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; Princess Maxima Center for Pediatric Oncology, Utrecht
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN
| | - Anthony V Moorman
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Lisa J Russell
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne.
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43
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Kovach AE, Raca G. Modern Classification and Management of Pediatric B-cell Leukemia and Lymphoma. Surg Pathol Clin 2023; 16:249-266. [PMID: 37149359 DOI: 10.1016/j.path.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Although pediatric hematopathology overlaps with that of adults, certain forms of leukemia and lymphoma, and many types of reactive conditions affecting the bone marrow and lymph nodes, are unique to children. As part of this series focused on lymphomas, this article (1) details the novel subtypes of lymphoblastic leukemia seen primarily in children and described since the 2017 World Health Organization classification and (2) discusses unique concepts in pediatric hematopathology, including nomenclature changes and evaluation of surgical margins in selected lymphomas.
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Affiliation(s)
- Alexandra E Kovach
- Division of Laboratory Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.
| | - Gordana Raca
- Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA; Division of Genomic Medicine, Department of Pathology and Laboratory Medicine, Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
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44
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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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45
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Zhang X, Hou Z, Huang D, Wang F, Gao B, Zhang C, Zhou D, Lou J, Wang H, Gao Y, Kang Z, Lu Y, Liu Q, Yan J. Single-cell heterogeneity and dynamic evolution of Ph-like acute lymphoblastic leukemia patient with novel TPR-PDGFRB fusion gene. Exp Hematol Oncol 2023; 12:19. [PMID: 36797781 PMCID: PMC9936632 DOI: 10.1186/s40164-023-00380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a refractory and recurrent subtype of B-cell ALL enriched with kinase-activating rearrangements. Incomplete understanding of the heterogeneity within the tumor cells presents a major challenge for the diagnosis and therapy of Ph-like ALL. Here, we exhibited a comprehensive cell atlas of one Ph-like ALL patient with a novel TPR-PDGFRB fusion gene at diagnosis and relapse by using single-cell RNA sequencing (scRNA-seq). Twelve heterogeneous B-cell clusters, four with strong MKI67 expression indicating highly proliferating B cells, were identified. A relapse-enriched B-cell subset associated with poor prognosis was discovered, implicating the transcriptomic evolution during disease progression. Integrative single-cell analysis was performed on Ph-like ALL and Ph+ ALL patients, and revealed Ph-like specific B-cell subpopulations and shared malignant B cells characterized by the ectopic expression of the inhibitory receptor CLEC2D. Collectively, scRNA-seq of Ph-like ALL with a novel TPR-PDGFRB fusion gene provides valuable insights into the underlying heterogeneity associated with disease progression and offers useful information for the development of immunotherapeutic techniques in the future.
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Affiliation(s)
- Xuehong Zhang
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China. .,Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
| | - Zhijie Hou
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China ,grid.411971.b0000 0000 9558 1426Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Dan Huang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Furong Wang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Beibei Gao
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Chengtao Zhang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Dong Zhou
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jiacheng Lou
- grid.452828.10000 0004 7649 7439Department of Neurosurgery, the Second Hospital of Dalian Medical University, Dalian, China
| | - Haina Wang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Yuan Gao
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhijie Kang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Ying Lu
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China. .,Institute of Dermatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Quentin Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China. .,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jinsong Yan
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China.
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46
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Lampson BL, Gupta A, Tyekucheva S, Mashima K, Petráčková A, Wang Z, Wojciechowska N, Shaughnessy CJ, Baker PO, Fernandes SM, Shupe S, Machado JH, Fardoun R, Kim AS, Brown JR. Rare Germline ATM Variants Influence the Development of Chronic Lymphocytic Leukemia. J Clin Oncol 2023; 41:1116-1128. [PMID: 36315919 PMCID: PMC9928739 DOI: 10.1200/jco.22.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Germline missense variants of unknown significance in cancer-related genes are increasingly being identified with the expanding use of next-generation sequencing. The ataxia telangiectasia-mutated (ATM) gene on chromosome 11 has more than 1,000 germline missense variants of unknown significance and is a tumor suppressor. We aimed to determine if rare germline ATM variants are more frequent in chronic lymphocytic leukemia (CLL) compared with other hematologic malignancies and if they influence the clinical characteristics of CLL. METHODS We identified 3,128 patients (including 825 patients with CLL) in our hematologic malignancy clinic who had received clinical-grade sequencing of the entire coding region of ATM. We ascertained the comparative frequencies of germline ATM variants in categories of hematologic neoplasms, and, in patients with CLL, we determined whether these variants affected CLL-associated characteristics such as somatic 11q deletion. RESULTS Rare germline ATM variants are present in 24% of patients with CLL, significantly greater than that in patients with other lymphoid malignancies (16% prevalence), myeloid disease (15%), or no hematologic neoplasm (14%). Patients with CLL with germline ATM variants are younger at diagnosis and twice as likely to have 11q deletion. The ATM variant p.L2307F is present in 3% of patients with CLL, is associated with a three-fold increase in rates of somatic 11q deletion, and is a hypomorph in cell-based assays. CONCLUSION Germline ATM variants cluster within CLL and affect the phenotype of CLL that develops, implying that some of these variants (such as ATM p.L2307F) have functional significance and should not be ignored. Further studies are needed to determine whether these variants affect the response to therapy or account for some of the inherited risk of CLL.
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Affiliation(s)
- Benjamin L. Lampson
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aditi Gupta
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Kiyomi Mashima
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna Petráčková
- Department of Immunology, Palacký University, Olomouc, Czech Republic
| | - Zixu Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Natalia Wojciechowska
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Current Address: Wrocław Medical University, Wrocław, Poland
| | - Conner J. Shaughnessy
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter O. Baker
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Stacey M. Fernandes
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha Shupe
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John-Hanson Machado
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rayan Fardoun
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jennifer R. Brown
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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Multi-Omic Approaches to Classify, Predict, and Treat Acute Leukemias. Cancers (Basel) 2023; 15:cancers15041049. [PMID: 36831391 PMCID: PMC9954455 DOI: 10.3390/cancers15041049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, in which nearly 5% of the cases are diagnosed before the first year of age [...].
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Targeting Pim kinases in hematological cancers: molecular and clinical review. Mol Cancer 2023; 22:18. [PMID: 36694243 PMCID: PMC9875428 DOI: 10.1186/s12943-023-01721-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Decades of research has recognized a solid role for Pim kinases in lymphoproliferative disorders. Often up-regulated following JAK/STAT and tyrosine kinase receptor signaling, Pim kinases regulate cell proliferation, survival, metabolism, cellular trafficking and signaling. Targeting Pim kinases represents an interesting approach since knock-down of Pim kinases leads to non-fatal phenotypes in vivo suggesting clinical inhibition of Pim may have less side effects. In addition, the ATP binding site offers unique characteristics that can be used for the development of small inhibitors targeting one or all Pim isoforms. This review takes a closer look at Pim kinase expression and involvement in hematopoietic cancers. Current and past clinical trials and in vitro characterization of Pim kinase inhibitors are examined and future directions are discussed. Current studies suggest that Pim kinase inhibition may be most valuable when accompanied by multi-drug targeting therapy.
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Merlini A, Pavese V, Manessi G, Rabino M, Tolomeo F, Aliberti S, D’Ambrosio L, Grignani G. Targeting cyclin-dependent kinases in sarcoma treatment: Current perspectives and future directions. Front Oncol 2023; 13:1095219. [PMID: 36741019 PMCID: PMC9893281 DOI: 10.3389/fonc.2023.1095219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Effective treatment of advanced/metastatic bone and soft tissue sarcomas still represents an unmet medical need. Recent advances in targeted therapies have highlighted the potential of cyclin-dependent kinases (CDK) inhibitors in several cancer types, including sarcomas. CDKs are master regulators of the cell cycle; their dysregulation is listed among the "hallmarks of cancer" and sarcomas are no exception to the rule. In this review, we report both the molecular basis, and the potential therapeutic implications for the use of CDK inhibitors in sarcoma treatment. What is more, we describe and discuss the possibility and biological rationale for combination therapies with conventional treatments, target therapy and immunotherapy, highlighting potential avenues for future research to integrate CDK inhibition in sarcoma treatment.
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Affiliation(s)
- Alessandra Merlini
- Candiolo Cancer Institute, IRCCS-FPO, Turin, Italy,Department of Oncology, University of Turin, Turin, Italy
| | - Valeria Pavese
- Department of Oncology, University of Turin, Turin, Italy
| | - Giulia Manessi
- Department of Oncology, University of Turin, Turin, Italy
| | - Martina Rabino
- Department of Oncology, University of Turin, Turin, Italy
| | | | | | - Lorenzo D’Ambrosio
- Department of Oncology, University of Turin, Turin, Italy,Medical Oncology, Azienda Ospedaliera Universitaria San Luigi Gonzaga, Turin, Italy,*Correspondence: Lorenzo D’Ambrosio,
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50
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Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu SCA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJ. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia. Blood Cancer Discov 2023; 4:34-53. [PMID: 36350827 PMCID: PMC9820540 DOI: 10.1158/2643-3230.bcd-21-0224] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
Distal enhancers play critical roles in sustaining oncogenic gene-expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+/- like B-ALL "signature" genes, including the likely leukemogenic driver EPOR. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of repeat enhancer-activated genes. Together, our findings reveal an epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene-expression program of ETV6-RUNX1+/- like B-ALL. SIGNIFICANCE We find a unifying mechanism underlying a leukemia subtype-defining gene-expression signature that relies on repetitive elements with poor conservation between humans and rodents. The ability of ETV6 to antagonize promiscuous, nonphysiologic ERG activity may shed light on other roles of these key regulators in hematolymphoid development and human disease. See related commentary by Mercher, p. 2. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Rohan Kodgule
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua W. Goldman
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | | | - Travis Saari
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Athalee R. Aguilar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Cody N. Hall
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Niharika Rajesh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Juhi Gupta
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shih-Chun A. Chu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Li Ye
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Aishwarya Gurumurthy
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ashwin Iyer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Noah A. Brown
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mark Y. Chiang
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Marcin P. Cieslik
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Russell J.H. Ryan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
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