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Chen C, Wang J, Kang M, Wu P, Zhu L, Fang Y, Xue Y. Identification of a novel MEF2C::SS18L1 fusion in childhood acute B-lymphoblastic leukemia. J Cancer Res Clin Oncol 2024; 150:314. [PMID: 38907739 PMCID: PMC11193691 DOI: 10.1007/s00432-024-05846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
PURPOSE Leukemia-associated fusion genes are closely related to the occurrence, development, diagnosis, and treatment of leukemia. DNA microarrays and second-generation sequencing have discovered multiple B-ALL fusion genes. We identified a novel MEF2C::SS18L1 fusion gene in a child diagnosed with B-ALL. This study investigates the oncogenicity and prognosis of this fusion gene in B-ALL. METHODS A child with B-ALL who has a MEF2C::SS18L1 fusion is reported as a newly discovered case. Compared the breakpoints, structural domains, clinical phenotypes, and differential expression genes of MEF2C::SS18L1 and MEF2D::SS18.Using "ONCOFUSE" software, the carcinogenicity of MEF2C::SS18L1 is predicted. Using whole transcriptome sequencing, we analyze the breakpoints and the secondary structure of the fusion protein. Further, we compared the structures, differentially expressed genes, and clinical phenotypes of MEF2D and MEF2C fusion genes by DESeq, GO functional enrichment, and flow cytometry immunophenotyping analysis. RESULTS Whole transcriptome sequencing identified a MEF2C::SS18L1 fusion transcript in a 3-year-old child with B-ALL. The MADS box, MEF structural domain, HJURP_C structural domain, and TAD I structural domain of MEF2C, and the QPGY structural domain of SS18L1, make up the fusion protein. "Oncofuse" found a 0.99 Bayesian probability that the fusion gene drives cancer. The breakpoint positions, fusion protein secondary structures, differentially expressed genes, and clinical characteristics of this patient were identical to those with MEF2D::SS18 fusion gene. CONCLUSION We identified a novel MEF2C::SS18L1 fusion gene in childhood ALL, which shares similar structural and clinical characteristics with MEF2D::SS18. Further studies with more samples should be conducted in future.
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Affiliation(s)
- Chuqin Chen
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Jiali Wang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Meiyun Kang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Peng Wu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Liwen Zhu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China.
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China.
| | - Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China.
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China.
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2
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Xu Y, Zhou Q, Wang X, Zhang A, Qi W, Li Y, Zheng C, Guan J, Sun T, Li J, Lu C, Shen Y, Zhao B. PELI2 regulates early B-cell progenitor differentiation and related leukemia via the IL-7R expression. Haematologica 2024; 109:1800-1814. [PMID: 38058209 PMCID: PMC11141684 DOI: 10.3324/haematol.2023.284041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
Little is known about the transition mechanisms that govern early lymphoid lineage progenitors from common lymphoid progenitors (CLP). Pellino2 (PELI2) is a newly discovered E3 ubiquitin ligase, which plays important roles in inflammation and the immune system. However, the physiological and molecular roles of PELI2 in the differentiation of immune cells are largely unknown. Here, by using a conditional knockout mouse model, we demonstrated that PELI2 is required for early B-cell development and stressed hematopoiesis. PELI2 interacted with and stabilized PU.1 via K63-polyubiquitination to regulate IL-7R expression. The defects of B-cell development induced by PELI2 deletion were restored by overexpression of PU.1. Similarly, PELI2 promoted TCF3 protein stability via K63-polyubiquitination to regulate IL-7R expression, which is required for the proliferation of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cells. These results underscore the significance of PELI2 in both normal B lymphopoiesis and malignant B-cell acute lymphoblastic leukemia via the regulation of IL-7R expression, providing a potential therapeutic approach for BCP-ALL.
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Affiliation(s)
- Yan Xu
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012
| | - Qian Zhou
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012
| | - Xiaoming Wang
- Department of Pediatrics, Qilu hospital of Shandong University, Jinan, Shandong, 250012
| | - Aijun Zhang
- Department of Pediatrics, Qilu hospital of Shandong University, Jinan, Shandong, 250012
| | - Wentao Qi
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012
| | - Yuan Li
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012
| | - Chengzu Zheng
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012
| | - Jianmin Guan
- Department of Hematology, Heze Municipal Hospital, Heze, Shandong
| | - Tao Sun
- Department of Hematology, Qilu hospital of Shandong University, Jinan, Shandong, 250012
| | - Jingxin Li
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012
| | - Chunhua Lu
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012
| | - Yuemao Shen
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012
| | - Baobing Zhao
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012.
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3
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Gökbuget N, Boissel N, Chiaretti S, Dombret H, Doubek M, Fielding A, Foà R, Giebel S, Hoelzer D, Hunault M, Marks DI, Martinelli G, Ottmann O, Rijneveld A, Rousselot P, Ribera J, Bassan R. Diagnosis, prognostic factors, and assessment of ALL in adults: 2024 ELN recommendations from a European expert panel. Blood 2024; 143:1891-1902. [PMID: 38295337 DOI: 10.1182/blood.2023020794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/02/2024] Open
Abstract
ABSTRACT Working groups of the European LeukemiaNet have published several important consensus guidelines. Acute lymphoblastic leukemia (ALL) has many different clinical and biological subgroups and the knowledge on disease biology and therapeutic options is increasing exponentially. The European Working Group for Adult ALL has therefore summarized the current state of the art and provided comprehensive consensus recommendations for diagnostic approaches, biologic and clinical characterization, prognostic factors, and risk stratification as well as definitions of endpoints and outcomes. Aspects of treatment, management of subgroups and specific situations, aftercare, and supportive care are covered in a separate publication. The present recommendation intends to provide guidance for the initial management of adult patients with ALL and to define principles as a basis for future collaborative research.
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Affiliation(s)
- Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University, University Hospital, Frankfurt, Germany
| | - Nicolas Boissel
- Hospital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Hervé Dombret
- Leukemia Department, University Hospital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Saint-Louis Research Institute, Université Paris Cité, Paris, France
| | - Michael Doubek
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | | | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Sebastian Giebel
- Department of Bone Marrow Transplantation and Onco-Hematology, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Dieter Hoelzer
- Department of Medicine II, Hematology/Oncology, Goethe University, University Hospital, Frankfurt, Germany
| | - Mathilde Hunault
- Maladies du Sang University Hospital of Angers, FHU Goal, INSERM, National Centre for Scientific Research, Angers, France
| | - David I Marks
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori Dino Amadori, Meldola, Italy
| | - Oliver Ottmann
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Philippe Rousselot
- Clinical Hematology Department, Centre Hospitalier de Versailles, Université Paris-Saclay, Versailles, France
| | - Josep Ribera
- Clinical Hematology Department, Institut Catala d'Oncologia-Hospital Germans Trias I Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Renato Bassan
- Division of Hematology, Ospedale dell'Angelo, Mestre-Venice, Italy
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4
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Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
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5
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Gutierrez-Camino A, Caron M, Richer C, Fuchs C, Illarregi U, Poncelet L, St-Onge P, Bataille AR, Tremblay-Dauphinais P, Lopez-Lopez E, Camos M, Ramirez-Orellana M, Astigarraga I, Lécuyer É, Bourque G, Martin-Guerrero I, Sinnett D. CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in TCF3::PBX1 ALL. Int J Mol Sci 2024; 25:1477. [PMID: 38338754 PMCID: PMC10855129 DOI: 10.3390/ijms25031477] [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: 11/10/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Childhood B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous disease comprising multiple molecular subgroups with subtype-specific expression profiles. Recently, a new type of ncRNA, termed circular RNA (circRNA), has emerged as a promising biomarker in cancer, but little is known about their role in childhood B-ALL. Here, through RNA-seq analysis in 105 childhood B-ALL patients comprising six genetic subtypes and seven B-cell controls from two independent cohorts we demonstrated that circRNAs properly stratified B-ALL subtypes. By differential expression analysis of each subtype vs. controls, 156 overexpressed and 134 underexpressed circRNAs were identified consistently in at least one subtype, most of them with subtype-specific expression. TCF3::PBX1 subtype was the one with the highest number of unique and overexpressed circRNAs, and the circRNA signature could effectively discriminate new patients with TCF3::PBX1 subtype from others. Our results indicated that NUDT21, an RNA-binding protein (RBP) involved in circRNA biogenesis, may contribute to this circRNA enrichment in TCF3::PBX1 ALL. Further functional characterization using the CRISPR-Cas13d system demonstrated that circBARD1, overexpressed in TCF3::PBX1 patients and regulated by NUDT21, might be involved in leukemogenesis through the activation of p38 via hsa-miR-153-5p. Our results suggest that circRNAs could play a role in the pathogenesis of childhood B-ALL.
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Affiliation(s)
- Angela Gutierrez-Camino
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Maxime Caron
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Chantal Richer
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Claire Fuchs
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Unai Illarregi
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (U.I.); (I.M.-G.)
| | - Lucas Poncelet
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Pascal St-Onge
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Alain R. Bataille
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Pascal Tremblay-Dauphinais
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Elixabet Lopez-Lopez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Mireia Camos
- Hematology Laboratory, Sant Joan de Déu Research Institute, Esplugues de Llobregat, 08950 Barcelona, Spain;
| | - Manuel Ramirez-Orellana
- Department of Pediatric Hematology and Oncology, Niño Jesús University Hospital, 28009 Madrid, Spain;
| | - Itziar Astigarraga
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Pediatrics, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Éric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada;
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (U.I.); (I.M.-G.)
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Daniel Sinnett
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
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6
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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Monovich AC, Narina S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Pruett-Miller SM, Ryan RJH, Yang JJ, Evans WE, Savic D. Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators. CELL GENOMICS 2023; 3:100442. [PMID: 38116118 PMCID: PMC10726428 DOI: 10.1016/j.xgen.2023.100442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/30/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023]
Abstract
B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of accessible chromatin sites exhibiting strong subtype enrichment and candidate TFs that maintain subtype-specific chromatin architectures. Over 9,000 genetic variants were uncovered, contributing to variability in chromatin accessibility among patient samples. Our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants that promote unique gene-regulatory networks.
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Affiliation(s)
- Kelly R Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert J Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alexander C Monovich
- Department of Pathology, University of Michigan-Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kristine R Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher S Manring
- Alliance Hematologic Malignancy Biorepository, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Elisabeth Paietta
- Department of Oncology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Mark R Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mary V Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Russell J H Ryan
- Department of Pathology, University of Michigan-Ann Arbor, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Jun J Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - William E Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA.
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7
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Akin-Bali DF, Doganay Erdogan B, Aslar Oner D, Mahmud A, Tasdelen S, Kurekci E, Akar N, Ozdag Sevgili H. Genetic Profiling of Pediatric Patients with B-Cell Precursor Acute Lymphoblastic Leukemia. J Pediatr Genet 2023; 12:288-300. [PMID: 38162155 PMCID: PMC10756719 DOI: 10.1055/s-0041-1742246] [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: 08/06/2021] [Accepted: 12/09/2021] [Indexed: 10/19/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a heterogeneous leukemia subgroup. It has multiple sub-types that are likely to be classified by prognostic factors. Following a systematic literature review, this study analyzed the genes correlated with BCP-ALL prognosis ( IKZF1, PAX5, EBF1, CREBBP, CRLF2, JAK2, ERG, CXCR4, ZAP70, VLA4, NF1, NR3C1, RB1, TSLP, ZNRF1, and FOXO3A) , specifically their nucleotide variations and expression profiles in pediatric BCP-ALL samples. The study included 45 pediatric BCP-ALL patients with no cytogenetic anomaly and a control group of 10 children. The selected genes' hot-spot regions were sequenced using next-generation sequencing, while Polymorphism Phenotyping v2 and Supplemental Nutrition Assistance Program were used to identify pathogenic mutations. The expression analysis was performed using quantitative real-time polymerase chain reaction. The mutation analysis detected 328 variants (28 insertions, 47 indels, 74 nucleotide variants, 75 duplications, and 104 deletions). The most and least frequently mutated genes were IKZF1 and CREBBP , respectively. There were statistically significant differences between patients and controls for mutation distribution in eight genes ( ERG, CRLF2, CREBBP, TSLP, JAK2, ZAP70, FOXO3A, and NR3C1 ). The expression analysis revealed that JAK and ERG were significantly overexpressed in patients compared with controls (respectively, p = 0.004 and p = 0.003). This study combined genes and pathways previously analyzed in pediatric BCP-ALL into one dataset for a comprehensive analysis from the same samples to unravel candidate prognostic biomarkers. Novel mutations were identified in all of the studied genes.
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Affiliation(s)
- Dilara Fatma Akin-Bali
- Department of Medical Biology, Faculty of Medicine, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Beyza Doganay Erdogan
- Department of Biostatistic, Faculty of Medicine, Biostatistics, Ankara University, Ankara, Turkey
| | - Deniz Aslar Oner
- Atatürk Vocational School of Health Services, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Akkan Mahmud
- LÖSANTE Children's and Adult Hospital, Ankara, Turkey
| | | | - Emin Kurekci
- LÖSANTE Children's and Adult Hospital, Ankara, Turkey
| | - Nejat Akar
- Department of Pediatrics, TOBB-ETU Hospital, Ankara, Turkey
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8
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Gray ZH, Chakraborty D, Duttweiler RR, Alekbaeva GD, Murphy SE, Chetal K, Ji F, Ferman BI, Honer MA, Wang Z, Myers C, Sun R, Kaniskan HÜ, Toma MM, Bondarenko EA, Santoro JN, Miranda C, Dillingham ME, Tang R, Gozani O, Jin J, Skorski T, Duy C, Lee H, Sadreyev RI, Whetstine JR. Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell 2023; 186:4528-4545.e18. [PMID: 37788669 PMCID: PMC10591855 DOI: 10.1016/j.cell.2023.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
MLL/KMT2A amplifications and translocations are prevalent in infant, adult, and therapy-induced leukemia. However, the molecular contributor(s) to these alterations are unclear. Here, we demonstrate that histone H3 lysine 9 mono- and di-methylation (H3K9me1/2) balance at the MLL/KMT2A locus regulates these amplifications and rearrangements. This balance is controlled by the crosstalk between lysine demethylase KDM3B and methyltransferase G9a/EHMT2. KDM3B depletion increases H3K9me1/2 levels and reduces CTCF occupancy at the MLL/KMT2A locus, in turn promoting amplification and rearrangements. Depleting CTCF is also sufficient to generate these focal alterations. Furthermore, the chemotherapy doxorubicin (Dox), which associates with therapy-induced leukemia and promotes MLL/KMT2A amplifications and rearrangements, suppresses KDM3B and CTCF protein levels. KDM3B and CTCF overexpression rescues Dox-induced MLL/KMT2A alterations. G9a inhibition in human cells or mice also suppresses MLL/KMT2A events accompanying Dox treatment. Therefore, MLL/KMT2A amplifications and rearrangements are controlled by epigenetic regulators that are tractable drug targets, which has clinical implications.
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Affiliation(s)
- Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Reuben R Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gulnaz D Alekbaeva
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sedona E Murphy
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kashish Chetal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Cynthia Myers
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Renhong Sun
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monika Maria Toma
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - John N Santoro
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Christopher Miranda
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Megan E Dillingham
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA; School of Life Science and Technology, Harbin Institute of Technology, 150000 Harbin, China
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomasz Skorski
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Cihangir Duy
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA.
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9
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Leons GK, Sharma P, Gupta SK, Gupta R, Rani L, Gajendra S, Roy A, Sahoo RK. Detection of a novel SNX2 gene breakpoint in the SNX2::ABL1 fusion transcript in Ph-like B-cell acute lymphoblastic leukemia. Pediatr Blood Cancer 2023; 70:e30546. [PMID: 37414723 DOI: 10.1002/pbc.30546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023]
Affiliation(s)
- Gadha K Leons
- Laboratory Oncology Unit, Dr BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Preity Sharma
- Laboratory Oncology Unit, Dr BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjeev Kumar Gupta
- Laboratory Oncology Unit, Dr BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Rani
- Centralized Core Research Facility, Genomics Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Smeeta Gajendra
- Laboratory Oncology Unit, Dr BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Roy
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Ranjit Kumar Sahoo
- Department of Medical Oncology, Dr BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
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10
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Mukherjee S, Patra R, Behzadi P, Masotti A, Paolini A, Sarshar M. Toll-like receptor-guided therapeutic intervention of human cancers: molecular and immunological perspectives. Front Immunol 2023; 14:1244345. [PMID: 37822929 PMCID: PMC10562563 DOI: 10.3389/fimmu.2023.1244345] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023] Open
Abstract
Toll-like receptors (TLRs) serve as the body's first line of defense, recognizing both pathogen-expressed molecules and host-derived molecules released from damaged or dying cells. The wide distribution of different cell types, ranging from epithelial to immune cells, highlights the crucial roles of TLRs in linking innate and adaptive immunity. Upon stimulation, TLRs binding mediates the expression of several adapter proteins and downstream kinases, that lead to the induction of several other signaling molecules such as key pro-inflammatory mediators. Indeed, extraordinary progress in immunobiological research has suggested that TLRs could represent promising targets for the therapeutic intervention of inflammation-associated diseases, autoimmune diseases, microbial infections as well as human cancers. So far, for the prevention and possible treatment of inflammatory diseases, various TLR antagonists/inhibitors have shown to be efficacious at several stages from pre-clinical evaluation to clinical trials. Therefore, the fascinating role of TLRs in modulating the human immune responses at innate as well as adaptive levels directed the scientists to opt for these immune sensor proteins as suitable targets for developing chemotherapeutics and immunotherapeutics against cancer. Hitherto, several TLR-targeting small molecules (e.g., Pam3CSK4, Poly (I:C), Poly (A:U)), chemical compounds, phytocompounds (e.g., Curcumin), peptides, and antibodies have been found to confer protection against several types of cancers. However, administration of inappropriate doses of such TLR-modulating therapeutics or a wrong infusion administration is reported to induce detrimental outcomes. This review summarizes the current findings on the molecular and structural biology of TLRs and gives an overview of the potency and promises of TLR-directed therapeutic strategies against cancers by discussing the findings from established and pipeline discoveries.
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Affiliation(s)
- Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Alessandro Paolini
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
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11
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Burmeister T, Gröger D, Gökbuget N, Spriewald B, Starck M, Elmaagacli A, Hoelzer D, Keller U, Schwartz S. Molecular characterization of TCF3::PBX1 chromosomal breakpoints in acute lymphoblastic leukemia and their use for measurable residual disease assessment. Sci Rep 2023; 13:15167. [PMID: 37704696 PMCID: PMC10499895 DOI: 10.1038/s41598-023-42294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
The translocation t(1;19)(q23;p13) with the resulting chimeric TCF3::PBX1 gene is the third most prevalent recurrent chromosomal translocation in acute lymphoblastic leukemia and accounts for 3-5% of cases. The molecular background of this translocation has been incompletely studied, especially in adult cases. We characterized the chromosomal breakpoints of 49 patients with TCF3::PBX1 and the corresponding reciprocal PBX1::TCF3 breakpoints in 15 cases at the molecular level, thus providing an extensive molecular overview of this translocation in a well-defined study patient population. Breakpoints were found to be remarkably clustered not only in TCF3 but also in PBX1. No association with DNA repeats or putative cryptic recombination signal sequence sites was observed. A simplified detection method for breakpoint identification was developed and the feasibility of patient-specific chromosomal break sites as molecular markers for detecting measurable residual disease (MRD) was explored. A highly sensitive generic real-time PCR for MRD assessment using these breakpoint sequences was established that could serve as a useful alternative to the classical method utilizing rearranged immune gene loci. This study provides the first extensive molecular data set on the chromosomal breakpoints of the t(1;19)/TCF3::PBX1 aberration in adult ALL. Based on the obtained data a generic MRD method was developed that has several theoretical advantages, including an on average higher sensitivity and a greater stability of the molecular marker in the course of disease.
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Affiliation(s)
- Thomas Burmeister
- Department of Hematology, Oncology and Tumor Immunology, CVK, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Daniela Gröger
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicola Gökbuget
- Medical Department 2, Goethe-Universität, Frankfurt, Germany
| | - Bernd Spriewald
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Michael Starck
- I. Medical Department, München Klinik Schwabing, Munich, Germany
| | - Ahmet Elmaagacli
- Department of Hematology, Oncology, Asklepios Klinik St. Georg, Hamburg, Germany
| | - Dieter Hoelzer
- Medical Department 2, Goethe-Universität, Frankfurt, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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12
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Kourti M, Aivaliotis M, Hatzipantelis E. Proteomics in Childhood Acute Lymphoblastic Leukemia: Challenges and Opportunities. Diagnostics (Basel) 2023; 13:2748. [PMID: 37685286 PMCID: PMC10487225 DOI: 10.3390/diagnostics13172748] [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: 06/30/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children and one of the success stories in cancer therapeutics. Risk-directed therapy based on clinical, biologic and genetic features has played a significant role in this accomplishment. Despite the observed improvement in survival rates, leukemia remains one of the leading causes of cancer-related deaths. Implementation of next-generation genomic and transcriptomic sequencing tools has illustrated the genomic landscape of ALL. However, the underlying dynamic changes at protein level still remain a challenge. Proteomics is a cutting-edge technology aimed at deciphering the mechanisms, pathways, and the degree to which the proteome impacts leukemia subtypes. Advances in mass spectrometry enable high-throughput collection of global proteomic profiles, representing an opportunity to unveil new biological markers and druggable targets. The purpose of this narrative review article is to provide a comprehensive overview of studies that have utilized applications of proteomics in an attempt to gain insight into the pathogenesis and identification of biomarkers in childhood ALL.
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Affiliation(s)
- Maria Kourti
- Third Department of Pediatrics, School of Medicine, Aristotle University and Hippokration General Hospital, 54642 Thessaloniki, Greece
| | - Michalis Aivaliotis
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Emmanouel Hatzipantelis
- Children & Adolescent Hematology-Oncology Unit, Second Department of Pediatrics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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13
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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Yang JJ, Evans WE, Savic D. Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528493. [PMID: 36824825 PMCID: PMC9949063 DOI: 10.1101/2023.02.14.528493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
B-cell lineage acute lymphoblastic leukemia (B-ALL) is comprised of diverse molecular subtypes and while transcriptional and DNA methylation profiling of B-ALL subtypes has been extensively examined, the accompanying chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq for 10 B-ALL molecular subtypes in primary ALL cells from 154 patients. Comparisons with B-cell progenitors identified candidate B-ALL cell-of-origin and AP-1-associated cis-regulatory rewiring in B-ALL. Cis-regulatory rewiring promoted B-ALL-specific gene regulatory networks impacting oncogenic signaling pathways that perturb normal B-cell development. We also identified that over 20% of B-ALL accessible chromatin sites exhibit strong subtype enrichment, with transcription factor (TF) footprint profiling identifying candidate TFs that maintain subtype-specific chromatin architectures. Over 9000 inherited genetic variants were further uncovered that contribute to variability in chromatin accessibility among individual patient samples. Overall, our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants which promote unique gene regulatory networks that contribute to transcriptional differences among B-ALL subtypes.
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Affiliation(s)
- Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Elisabeth Paietta
- Department of Oncology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles G. Mullighan
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38105, USA
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14
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Panuciak K, Nowicka E, Mastalerczyk A, Zawitkowska J, Niedźwiecki M, Lejman M. Overview on Aneuploidy in Childhood B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:ijms24108764. [PMID: 37240110 DOI: 10.3390/ijms24108764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Recent years have brought significant progress in the treatment of B-cell acute lymphoblastic leukemia (ALL). This was influenced by both the improved schemes of conventionally used therapy, as well as the development of new forms of treatment. As a consequence, 5-year survival rates have increased and now exceed 90% in pediatric patients. For this reason, it would seem that everything has already been explored in the context of ALL. However, delving into its pathogenesis at the molecular level shows that there are many variations that still need to be analyzed in more detail. One of them is aneuploidy, which is among the most common genetic changes in B-cell ALL. It includes both hyperdiploidy and hypodiploidy. Knowledge of the genetic background is important already at the time of diagnosis, because the first of these forms of aneuploidy is characterized by a good prognosis, in contrast to the second, which is in favor of an unfavorable course. In our work, we will focus on summarizing the current state of knowledge on aneuploidy, along with an indication of all the consequences that may be correlated with it in the context of the treatment of patients with B-cell ALL.
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Affiliation(s)
- Kinga Panuciak
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Emilia Nowicka
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Angelika Mastalerczyk
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland
| | - Maciej Niedźwiecki
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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15
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Ehm P, Bettin B, Jücker M. Activated Src kinases downstream of BCR-ABL and Flt3 induces proteasomal degradation of SHIP1 by phosphorylation of tyrosine 1021. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119467. [PMID: 36958526 DOI: 10.1016/j.bbamcr.2023.119467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/03/2023] [Accepted: 03/12/2023] [Indexed: 03/25/2023]
Abstract
Within the various subtypes of ALL, patients with a BCR-ABL-positive background as well as with a genetic change in the KMT2A gene have by far the worst survival probabilities. Interestingly, both subtypes are characterized by highly activated tyrosine kinases. SHIP1 serves as an important negative regulator of the PI3K/AKT signaling pathway, which is often constitutively activated in ALL. The protein expression of SHIP1 is decreased in most T-ALL and in some subgroups of B-ALL. In this study, we analyzed the expression of SHIP1 protein in detail in the context of groups with aberrant activated tyrosine kinases, namely BCR-ABL (Ph+) and Flt3 (KMT2A translocations). We demonstrate that constitutively activated Src kinases downstream of BCR-ABL and receptor tyrosine kinases reduce the SHIP1 expression in a SHIP1-Y1021 phosphorylated-dependent manner with subsequent ubiquitin marked proteasomal degradation. Inhibition of BCR-ABL (Imatinib), Flt3 (Quizartinib) or Src-Kinase-Family (Saracatinib) leads to significant reconstitution of SHIP1 protein expression. These results further support a functional role of SHIP1 as tumor suppressor protein and could be the basis for the establishment of a targeted therapy form.
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Affiliation(s)
- Patrick Ehm
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; Research Institute Children's Cancer Center Hamburg, Hamburg and Dept. of Pediatric Oncology and Hematology, University Medical Center, Hamburg, Germany.
| | - Bettina Bettin
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
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16
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Dargenio M, Bonifacio M, Chiaretti S, Vitale A, Fracchiolla NS, Papayannidis C, Giglio F, Salutari P, Audisio E, Scappini B, Zappasodi P, Defina M, Forghieri F, Scattolin AM, Todisco E, Lunghi M, Guolo F, Del Principe MI, Annunziata M, Lazzarotto D, Cedrone M, Pasciolla C, Imovilli A, Tanasi I, Trappolini S, Cerrano M, La Starza R, Krampera M, Di Renzo N, Candoni A, Pizzolo G, Ferrara F, Foà R. Incidence, treatment and outcome of central nervous system relapse in adult acute lymphoblastic leukaemia patients treated front-line with paediatric-inspired regimens: A retrospective multicentre Campus ALL study. Br J Haematol 2023; 200:440-450. [PMID: 36335916 PMCID: PMC10098932 DOI: 10.1111/bjh.18537] [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: 08/08/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/08/2022]
Abstract
Within the Campus ALL network we analyzed the incidence, characteristics, treatment and outcome of a central nervous system (CNS) relapse in 1035 consecutive adult acute lymphoblastic leukemia (ALL) patients treated frontline with pediatric-inspired protocols between 2009 and 2020. Seventy-one patients (6.8%) experienced a CNS recurrence, more frequently in T- (28/278; 10%) than in B-ALL (43/757; 5.7%) (p = 0.017). An early CNS relapse-< 12 months from diagnosis-was observed in 41 patients. In multivariate analysis, risk factors for early CNS relapse included T-cell phenotype (p = <0.001), hyperleucocytosis >100 × 109 /L (p<0.001) and male gender (p = 0.015). Treatment was heterogeneous, including chemotherapy, radiotherapy, intrathecal therapy and novel agents. A complete remission (CR) was obtained in 39 patients (55%) with no differences among strategies. After CR, 26 patients underwent an allogenic transplant, with a significant overall survival benefit compared to non-transplanted patients (p = 0.012). After a median observation of 8 months from CNS relapse, 23 patients (32%) were alive. In multivariate analysis, the time to CNS relapse was the strongest predictor of a lower 2-year post-relapse survival (p<0.001). In conclusion, in adult ALL the outcome after a CNS relapse remains very poor. Effective CNS prophylaxis remains the best approach and allogenic transplant should be pursued when possible.
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Affiliation(s)
- Michelina Dargenio
- Ospedale Vito Fazzi, Unità Operativa di Ematologia e Trapianto, Lecce, Italy
| | - Massimiliano Bonifacio
- Dipartimento di Medicina, Sezione di Ematologia, Università e Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Sabina Chiaretti
- Divisione di Ematologia, Dipartimento di Medicina Traslazionale e di Precisione, Università Sapienza, Rome, Italy
| | - Antonella Vitale
- Divisione di Ematologia, Dipartimento di Medicina Traslazionale e di Precisione, Università Sapienza, Rome, Italy
| | | | - Cristina Papayannidis
- IRCCS Azienda Ospedaliero-Universitaria, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Fabio Giglio
- Ospedale San Raffaele, Unità Operativa di Ematologia, Milan, Italy
| | - Prassede Salutari
- Unità Operativa Complessa di Ematologia, Ospedale Civile Spirito Santo, Pescara, Italy
| | - Ernesta Audisio
- Dipartimento di Ematologia e Oncologia, AO Città della Salute e della Scienza, Torino, Italy
| | | | - Patrizia Zappasodi
- Unità Operativa di Ematologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marzia Defina
- Unità Operativa Complessa di Ematologia, AOUS, Università di Siena, Siena, Italy
| | - Fabio Forghieri
- Unità Operativa Complessa di Ematologia, AOU Policlinico, Modena, Italy
| | | | - Elisabetta Todisco
- Unità Operativa Ematologia, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Monia Lunghi
- Divisione di Ematologia, Dipartimento di Medicina Traslazionale, Università del Piemonte Orientale, Novara, Italy
| | - Fabio Guolo
- Clinica Ematologica, Dipartimento di Medicina Interna, Università degli Studi di Genova, Genoa, Italy.,Dipartimento di Oncologia e Ematologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Mario Annunziata
- Unità Operativa Complessa di Ematologia, AORN Cardarelli, Naples, Italy
| | - Davide Lazzarotto
- Clinica ematologica e centro trapianti, Azienda sanitaria universitaria Friuli Centrale, Udine, Italy
| | - Michele Cedrone
- Unità Operativa Complessa di Ematologia, Ospedale San Giovanni Addolorata, Rome, Italy
| | - Crescenza Pasciolla
- Unità Operativa di Ematologia, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | | | - Ilaria Tanasi
- Dipartimento di Medicina, Sezione di Ematologia, Università e Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Marco Cerrano
- Unità Operativa di Ematologia, Presidio Molinette-AOU Città della Salute e della Scienza, Torino, Italy
| | - Roberta La Starza
- Sezione di Ematologia e Trapianto, Università degli Studi di Perugia, A.O. Perugia, Italy
| | - Mauro Krampera
- Dipartimento di Medicina, Sezione di Ematologia, Università e Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Nicola Di Renzo
- Ospedale Vito Fazzi, Unità Operativa di Ematologia e Trapianto, Lecce, Italy
| | - Anna Candoni
- Unità Operativa Complessa di Ematologia, AORN Cardarelli, Naples, Italy
| | - Giovanni Pizzolo
- Dipartimento di Medicina, Sezione di Ematologia, Università e Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Felicetto Ferrara
- Dipartimento di Biomedicina e Prevenzione, Università degli studi Tor Vergata, Rome, Italy
| | - Robin Foà
- Divisione di Ematologia, Dipartimento di Medicina Traslazionale e di Precisione, Università Sapienza, Rome, Italy
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17
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Fernandes MB, Barata JT. IL-7 and IL-7R in health and disease: An update through COVID times. Adv Biol Regul 2023; 87:100940. [PMID: 36503870 DOI: 10.1016/j.jbior.2022.100940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
The role of IL-7 and IL-7R for normal lymphoid development and an adequately functioning immune system has been recognized for long, with severe immune deficiency and lymphoid leukemia as extreme examples of the consequences of deregulation of the IL-7-IL-7R axis. In this review, we provide an update (focusing on the past couple of years) on IL-7 and IL-7R in health and disease. We highlight the findings on IL-7/IL-7R signaling mechanisms and the, sometimes controversial, impact of IL-7 and its receptor on leukocyte biology, COVID-19, acute lymphoblastic leukemia, and different solid tumors, as well as their relevance as therapeutic tools or targets.
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Affiliation(s)
- Marta B Fernandes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - João T Barata
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal.
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18
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Wray JP, Deltcheva EM, Boiers C, Richardson SЕ, Chhetri JB, Brown J, Gagrica S, Guo Y, Illendula A, Martens JHA, Stunnenberg HG, Bushweller JH, Nimmo R, Enver T. Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability. Nat Commun 2022; 13:7124. [PMID: 36411286 PMCID: PMC9678885 DOI: 10.1038/s41467-022-34653-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 11/01/2022] [Indexed: 11/22/2022] Open
Abstract
The ETV6-RUNX1 onco-fusion arises in utero, initiating a clinically silent pre-leukemic state associated with the development of pediatric B-acute lymphoblastic leukemia (B-ALL). We characterize the ETV6-RUNX1 regulome by integrating chromatin immunoprecipitation- and RNA-sequencing and show that ETV6-RUNX1 functions primarily through competition for RUNX1 binding sites and transcriptional repression. In pre-leukemia, this results in ETV6-RUNX1 antagonization of cell cycle regulation by RUNX1 as evidenced by mass cytometry analysis of B-lineage cells derived from ETV6-RUNX1 knock-in human pluripotent stem cells. In frank leukemia, knockdown of RUNX1 or its co-factor CBFβ results in cell death suggesting sustained requirement for RUNX1 activity which is recapitulated by chemical perturbation using an allosteric CBFβ-inhibitor. Strikingly, we show that RUNX1 addiction extends to other genetic subtypes of pediatric B-ALL and also adult disease. Importantly, inhibition of RUNX1 activity spares normal hematopoiesis. Our results suggest that chemical intervention in the RUNX1 program may provide a therapeutic opportunity in ALL.
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Affiliation(s)
- Jason P Wray
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Elitza M Deltcheva
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Charlotta Boiers
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden
| | - Simon Е Richardson
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, CB2 0AW, UK
| | | | - John Brown
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Sladjana Gagrica
- IMED Oncology, AstraZeneca, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Yanping Guo
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
| | - Anuradha Illendula
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525, GA, Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525, GA, Nijmegen, The Netherlands
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Rachael Nimmo
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK
- Oxford Biomedica (UK) Ltd, Windrush Court, Transport Way, Oxford, OX4 6LT, UK
| | - Tariq Enver
- Department of Cancer Biology UCL Cancer Institute, UCL, London, WC1E 6DD, UK.
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 84, Lund, Sweden.
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden.
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19
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Fei F, Zhang M, Tarighat SS, Joo EJ, Yang L, Heisterkamp N. Galectin-1 and Galectin-3 in B-Cell Precursor Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms232214359. [PMID: 36430839 PMCID: PMC9694201 DOI: 10.3390/ijms232214359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Acute lymphoblastic leukemias arising from the malignant transformation of B-cell precursors (BCP-ALLs) are protected against chemotherapy by both intrinsic factors as well as by interactions with bone marrow stromal cells. Galectin-1 and Galectin-3 are lectins with overlapping specificity for binding polyLacNAc glycans. Both are expressed by bone marrow stromal cells and by hematopoietic cells but show different patterns of expression, with Galectin-3 dynamically regulated by extrinsic factors such as chemotherapy. In a comparison of Galectin-1 x Galectin-3 double null mutant to wild-type murine BCP-ALL cells, we found reduced migration, inhibition of proliferation, and increased sensitivity to drug treatment in the double knockout cells. Plant-derived carbohydrates GM-CT-01 and GR-MD-02 were used to inhibit extracellular Galectin-1/-3 binding to BCP-ALL cells in co-culture with stromal cells. Treatment with these compounds attenuated migration of the BCP-ALL cells to stromal cells and sensitized human BCP-ALL cells to vincristine and the targeted tyrosine kinase inhibitor nilotinib. Because N-glycan sialylation catalyzed by the enzyme ST6Gal1 can regulate Galectin cell-surface binding, we also compared the ability of BCP-ALL wild-type and ST6Gal1 knockdown cells to resist vincristine treatment when they were co-cultured with Galectin-1 or Galectin-3 knockout stromal cells. Consistent with previous results, stromal Galectin-3 was important for maintaining BCP-ALL fitness during chemotherapy exposure. In contrast, stromal Galectin-1 did not significantly contribute to drug resistance, and there was no clear effect of ST6Gal1-catalysed N-glycan sialylation. Taken together, our results indicate a complicated joint contribution of Galectin-1 and Galectin-3 to BCP-ALL survival, with different roles for endogenous and stromal produced Galectins. These data indicate it will be important to efficiently block both extracellular and intracellular Galectin-1 and Galectin-3 with the goal of reducing BCP-ALL persistence in the protective bone marrow niche during chemotherapy.
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Affiliation(s)
- Fei Fei
- Section of Molecular Carcinogenesis, Department of Pediatrics, Division of Hematology/Oncology and Bone Marrow Transplantation, The Saban Research Institute of Children’s Hospital, Los Angeles, CA 90027, USA
| | - Mingfeng Zhang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
| | - Somayeh S. Tarighat
- Section of Molecular Carcinogenesis, Department of Pediatrics, Division of Hematology/Oncology and Bone Marrow Transplantation, The Saban Research Institute of Children’s Hospital, Los Angeles, CA 90027, USA
| | - Eun Ji Joo
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
| | - Nora Heisterkamp
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA 91016, USA
- Correspondence: ; Tel.: +1-626-218-7503
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20
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Panobinostat (LBH589) increase survival in adult xenografic model of acute lymphoblastic leukemia with t(4;11) but promotes antagonistic effects in combination with MTX and 6MP. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:216. [PMID: 36175721 DOI: 10.1007/s12032-022-01813-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022]
Abstract
Patients diagnosed with acute lymphoblastic leukemia (ALL) bearing t(4;11)/MLL-AF4 have aggressive clinical features, poor prognosis and there is an urgent need for new therapies to improve outcomes. Panobinostat (LBH589) has been identified as a potential therapeutic agent for ALL with t(4;11) and studies suggest that the antineoplastic effects are associated with reduced MLL-AF4 fusion protein and reduced expression of HOX genes. Here, we evaluated the in vitro effects of the combination of LBH589 with methotrexate (MTX) or 6-mercaptopurine (6MP) by cell proliferation assays and Calcusyn software in ALL cell line (RS4;11); the in vivo effects of LBH589 in xenotransplanted NOD-scid IL2Rgammanull mice measuring human lymphoblasts by flow cytometry; and the expression of HOX genes by qPCR after treatment in an adult model of ALL with t(4;11). LBH589 combination with MTX or 6MP did not promote synergistic effects in RS4;11 cell line. LBH589 treatment leads to increased overall survival and reduction of blasts in xenotransplanted mice but caused no significant changes in HOXA7, HOXA9, HOXA10, and MEIS1 expression. The LBH589, alone, showed promising antineoplastic effects in vivo and may represent a potential agent for chemotherapy in ALL patients with t(4;11).
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21
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Genc DB, Akinci N, Yildirmak ZY, Vural S. Renal Ultrasonographic Abnormalities at Initial Presentation of Children Diagnosed with Acute Lymphoblastic Leukemia and Long-Term Renal Functions and Prognosis in Survivors. SISLI ETFAL HASTANESI TIP BULTENI 2022; 56:421-426. [PMID: 36304210 PMCID: PMC9580970 DOI: 10.14744/semb.2022.89646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/15/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVES The kidney is a vulnerable organ for acute lymphoblastic leukemia (ALL), by the disease, and various associated clinical pictures. This retrospective study aims to document renal ultrasound abnormalities in children with newly diagnosed ALL as well as to investigate the correlation between renal findings and clinical/laboratory/survival data. METHODS All children (age <18 years) with ALL were included in the study. An increase in size/nephromegaly (NM) or hyperechogenicity (HE) of the kidneys at first admission was accepted as a pathological renal abnormality. The clinical/laboratory findings, survival, and long-term renal functions were compared between patients with and without NM/HE. RESULTS The incidence of NM±HE was 12% in 163 patients. Enlargement of spleen, liver, or both and, hypercreatininemia was independently correlated with the presence of NM/HE. After the induction therapy, ultrasound findings were resolved in all patients, and NM/HE did not influence ALL prognosis. All survivors had normal renal functions in long term. CONCLUSION The renal ultrasound abnormalities are not uncommon in children with leukemia at admission, without a negative impact on leukemia prognosis and on long-term renal functions.
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Affiliation(s)
- Dildar Bahar Genc
- Department of Pediatric Hematology and Oncology, University of Health Sciences Türkiye, Sisli Hamidiye Etfal Training and Research Hospital, Istanbul, Türkiye
| | - Nurver Akinci
- Department of Pediatric Nephrology, University of Health Sciences Türkiye, Sisli Hamidiye Etfal Training and Research Hospital, Istanbul, Türkiye
| | - Zeynep Yildiz Yildirmak
- Department of Pediatric Hematology and Oncology, University of Health Sciences Türkiye, Sisli Hamidiye Etfal Training and Research Hospital, Istanbul, Türkiye
| | - Sema Vural
- Department of Pediatric Hematology and Oncology, University of Health Sciences Türkiye, Sisli Hamidiye Etfal Training and Research Hospital, Istanbul, Türkiye
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22
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Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution. Leukemia 2022; 36:1759-1768. [PMID: 35585141 PMCID: PMC9252914 DOI: 10.1038/s41375-022-01587-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022]
Abstract
The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia. ![]()
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23
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Bang B, Eisfeldt J, Barbany G, Harila-Saari A, Heyman M, Zachariadis V, Taylan F, Nordgren A. A somatic UBA2 variant preceded ETV6-RUNX1 in the concordant BCP-ALL of monozygotic twins. Blood Adv 2022; 6:2275-2289. [PMID: 34982829 PMCID: PMC9006272 DOI: 10.1182/bloodadvances.2021005703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Genetic analysis of leukemic clones in monozygotic twins with concordant acute lymphoblastic leukemia (ALL) has proved a unique opportunity to gain insight into the molecular phylogenetics of leukemogenesis. Using whole-genome sequencing, we characterized constitutional and somatic single nucleotide variants/insertion-deletions (indels) and structural variants in a monozygotic twin pair with concordant ETV6-RUNX1+ B-cell precursor ALL (BCP-ALL). In addition, digital PCR (dPCR) was applied to evaluate the presence of and quantify selected somatic variants at birth, diagnosis, and remission. A shared somatic complex rearrangement involving chromosomes 11, 12, and 21 with identical fusion sequences in leukemias of both twins offered direct proof of a common clonal origin. The ETV6-RUNX1 fusion detected at diagnosis was found to originate from this complex rearrangement. A shared somatic frameshift deletion in UBA2 was also identified in diagnostic samples. In addition, each leukemia independently acquired analogous deletions of 3 genes recurrently targeted in BCP-ALLs (ETV6, ATF7IP, and RAG1/RAG2), providing evidence of a convergent clonal evolution only explained by a strong concurrent selective pressure. Quantification of the UBA2 deletion by dPCR surprisingly indicated it persisted in remission. This, for the first time to our knowledge, provided evidence of a UBA2 variant preceding the well-established initiating event ETV6-RUNX1. Further, we suggest the UBA2 deletion exerted a leukemia predisposing effect and that its essential role in Small Ubiquitin-like Modifier (SUMO) attachment (SUMOylation), regulating nearly all physiological and pathological cellular processes such as DNA-repair by nonhomologous end joining, may hold a mechanistic explanation for the predisposition.
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Affiliation(s)
- Benedicte Bang
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Arja Harila-Saari
- Department of Women’s and Children’s Health, Uppsala University Hospital, Uppsala, Sweden
| | - Mats Heyman
- Department of Women’s and Children’s Health, Karolinska University Hospital Solna, Stockholm, Sweden; and
| | - Vasilios Zachariadis
- Department of Oncology-Pathology, Cancer Centre Karolinska (CCK), Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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24
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In Utero Development and Immunosurveillance of B Cell Acute Lymphoblastic Leukemia. Curr Treat Options Oncol 2022; 23:543-561. [PMID: 35294722 PMCID: PMC8924576 DOI: 10.1007/s11864-022-00963-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2022] [Indexed: 11/06/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequent type of pediatric cancer with a peak incidence at 2–5 years of age. ALL frequently begins in utero with the emergence of clinically silent, preleukemic cells. Underlying leukemia-predisposing germline and acquired somatic mutations define distinct ALL subtypes that vary dramatically in treatment outcomes. In addition to genetic predisposition, a second hit, which usually occurs postnatally, is required for development of overt leukemia in most ALL subtypes. An untrained, dysregulated immune response, possibly due to an abnormal response to infection, may be an important co-factor triggering the onset of leukemia. Furthermore, the involvement of natural killer (NK) cells and T helper (Th) cells in controlling the preleukemic cells has been discussed. Identifying the cell of origin of the preleukemia-initiating event might give additional insights into potential options for prevention. Modulation of the immune system to achieve prolonged immunosurveillance of the preleukemic clone that eventually dies out in later years might present a future directive. Herein, we review the concepts of prenatal origin as well as potential preventive approaches to pediatric B cell precursor (BCP) ALL.
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Schmidt JA, Hornhardt S, Erdmann F, Sánchez-García I, Fischer U, Schüz J, Ziegelberger G. Risk Factors for Childhood Leukemia: Radiation and Beyond. Front Public Health 2021; 9:805757. [PMID: 35004601 PMCID: PMC8739478 DOI: 10.3389/fpubh.2021.805757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
Childhood leukemia (CL) is undoubtedly caused by a multifactorial process with genetic as well as environmental factors playing a role. But in spite of several efforts in a variety of scientific fields, the causes of the disease and the interplay of possible risk factors are still poorly understood. To push forward the research on the causes of CL, the German Federal Office for Radiation Protection has been organizing recurring international workshops since 2008 every two to three years. In November 2019 the 6th International Workshop on the Causes of CL was held in Freising and brought together experts from diverse disciplines. The workshop was divided into two main parts focusing on genetic and environmental risk factors, respectively. Two additional special sessions addressed the influence of natural background radiation on the risk of CL and the progress in the development of mouse models used for experimental studies on acute lymphoblastic leukemia, the most common form of leukemia worldwide. The workshop presentations highlighted the role of infections as environmental risk factor for CL, specifically for acute lymphoblastic leukemia. Major support comes from two mouse models, the Pax5+/- and Sca1-ETV6-RUNX1 mouse model, one of the major achievements made in the last years. Mice of both predisposed models only develop leukemia when exposed to common infections. These results emphasize the impact of gene-environment-interactions on the development of CL and warrant further investigation of such interactions - especially because genetic predisposition is detected with increasing frequency in CL. This article summarizes the workshop presentations and discusses the results in the context of the international literature.
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Affiliation(s)
- Janine-Alison Schmidt
- Department of Effects and Risks of Ionizing and Non-ionizing Radiation, Federal Office for Radiation Protection (BfS), Neuherberg, Germany
| | - Sabine Hornhardt
- Department of Effects and Risks of Ionizing and Non-ionizing Radiation, Federal Office for Radiation Protection (BfS), Neuherberg, Germany
| | - Friederike Erdmann
- Division of Childhood Cancer Epidemiology, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Environment and Lifestyle Epidemiology Branch, International Agency for Research on Cancer, World Health Organization (IARC/WHO), Lyon, France
| | - Isidro Sánchez-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Joachim Schüz
- Environment and Lifestyle Epidemiology Branch, International Agency for Research on Cancer, World Health Organization (IARC/WHO), Lyon, France
| | - Gunde Ziegelberger
- Department of Effects and Risks of Ionizing and Non-ionizing Radiation, Federal Office for Radiation Protection (BfS), Neuherberg, Germany
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Molecular Genetics of Pre-B Acute Lymphoblastic Leukemia Sister Cell Lines during Disease Progression. Curr Issues Mol Biol 2021; 43:2147-2156. [PMID: 34940123 PMCID: PMC8929001 DOI: 10.3390/cimb43030149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 11/26/2022] Open
Abstract
For many years, immortalized tumor cell lines have been used as reliable tools to understand the function of oncogenes and tumor suppressor genes. Today, we know that tumors can comprise subclones with common and with subclone-specific genetic alterations. We sequenced DNA and RNA of sequential sister cell lines obtained from patients with pre-B acute lymphoblastic leukemia at different phases of the disease. All five pairs of cell lines carry alterations that are typical for this disease: loss of tumor suppressors (CDKN2A, CDKN2B), expression of fusion genes (ETV6-RUNX1, BCR-ABL1, MEF2D-BCL9) or of genes targeted by point mutations (KRAS A146T, NRAS G12C, PAX5 R38H). MEF2D-BCL9 and PAX R38H mutations in cell lines have hitherto been undescribed, suggesting that YCUB-4 (MEF2D-BCL9), PC-53 (PAX R38H) and their sister cell lines will be useful models to elucidate the function of these genes. All aberrations mentioned above occur in both sister cell lines, demonstrating that the sisters derive from a common ancestor. However, we also found mutations that are specific for one sister cell line only, pointing to individual subclones of the primary tumor as originating cells. Our data show that sequential sister cell lines can be used to study the clonal development of tumors and to elucidate the function of common and clone-specific mutations.
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Xu H, Yu H, Jin R, Wu X, Chen H. Genetic and Epigenetic Targeting Therapy for Pediatric Acute Lymphoblastic Leukemia. Cells 2021; 10:cells10123349. [PMID: 34943855 PMCID: PMC8699354 DOI: 10.3390/cells10123349] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/06/2021] [Accepted: 11/25/2021] [Indexed: 12/31/2022] Open
Abstract
Acute lymphoblastic leukemia is the most common malignancy in children and is characterized by numerous genetic and epigenetic abnormalities. Epigenetic mechanisms, including DNA methylations and histone modifications, result in the heritable silencing of genes without a change in their coding sequence. Emerging studies are increasing our understanding of the epigenetic role of leukemogenesis and have demonstrated the potential of DNA methylations and histone modifications as a biomarker for lineage and subtypes classification, predicting relapse, and disease progression in acute lymphoblastic leukemia. Epigenetic abnormalities are relatively reversible when treated with some small molecule-based agents compared to genetic alterations. In this review, we conclude the genetic and epigenetic characteristics in ALL and discuss the future role of DNA methylation and histone modifications in predicting relapse, finally focus on the individual and precision therapy targeting epigenetic alterations.
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Fregona V, Bayet M, Gerby B. Oncogene-Induced Reprogramming in Acute Lymphoblastic Leukemia: Towards Targeted Therapy of Leukemia-Initiating Cells. Cancers (Basel) 2021; 13:cancers13215511. [PMID: 34771671 PMCID: PMC8582707 DOI: 10.3390/cancers13215511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Acute lymphoblastic leukemia is a heterogeneous disease characterized by a diversity of genetic alterations, following a sophisticated and controversial organization. In this review, we present and discuss the concepts exploring the cellular, molecular and functional heterogeneity of leukemic cells. We also review the emerging evidence indicating that cell plasticity and oncogene-induced reprogramming should be considered at the biological and clinical levels as critical mechanisms for identifying and targeting leukemia-initiating cells. Abstract Our understanding of the hierarchical structure of acute leukemia has yet to be fully translated into therapeutic approaches. Indeed, chemotherapy still has to take into account the possibility that leukemia-initiating cells may have a distinct chemosensitivity profile compared to the bulk of the tumor, and therefore are spared by the current treatment, causing the relapse of the disease. Therefore, the identification of the cell-of-origin of leukemia remains a longstanding question and an exciting challenge in cancer research of the last few decades. With a particular focus on acute lymphoblastic leukemia, we present in this review the previous and current concepts exploring the phenotypic, genetic and functional heterogeneity in patients. We also discuss the benefits of using engineered mouse models to explore the early steps of leukemia development and to identify the biological mechanisms driving the emergence of leukemia-initiating cells. Finally, we describe the major prospects for the discovery of new therapeutic strategies that specifically target their aberrant stem cell-like functions.
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Diedrich JD, Dong Q, Ferguson DC, Bergeron BP, Autry RJ, Qian M, Yang W, Smith C, Papizan JB, Connelly JP, Hagiwara K, Crews KR, Pruett-Miller SM, Pui CH, Yang JJ, Relling MV, Evans WE, Savic D. Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks. Leukemia 2021; 35:3078-3091. [PMID: 33714976 PMCID: PMC8435544 DOI: 10.1038/s41375-021-01209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematopoietic malignancy comprised of molecular subtypes largely characterized by aneuploidy or recurring chromosomal rearrangements. Despite extensive information on the ALL transcriptome and methylome, there is limited understanding of the ALL chromatin landscape. We therefore mapped accessible chromatin in 24 primary ALL cell biospecimens comprising three common molecular subtypes (DUX4/ERG, ETV6-RUNX1 and hyperdiploid) from patients treated at St. Jude Children's Research Hospital. Our findings highlight extensive chromatin reprogramming in ALL, including the identification ALL subtype-specific chromatin landscapes that are additionally modulated by genetic variation. Chromatin accessibility differences between ALL and normal B-cells implicate the activation of B-cell repressed chromatin domains and detail the disruption of normal B-cell development in ALL. Among ALL subtypes, we uncovered roles for basic helix-loop-helix, homeodomain and activator protein 1 transcription factors in promoting subtype-specific chromatin accessibility and distinct gene regulatory networks. In addition to chromatin subtype-specificity, we further identified over 3500 DNA sequence variants that alter the ALL chromatin landscape and contribute to inter-individual variability in chromatin accessibility. Collectively, our data suggest that subtype-specific chromatin landscapes and gene regulatory networks impact ALL biology and contribute to transcriptomic differences among ALL subtypes.
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Affiliation(s)
- Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Maoxiang Qian
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James B Papizan
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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Oliveira T, Zhang M, Joo EJ, Abdel-Azim H, Chen CW, Yang L, Chou CH, Qin X, Chen J, Alagesan K, Almeida A, Jacob F, Packer NH, von Itzstein M, Heisterkamp N, Kolarich D. Glycoproteome remodeling in MLL-rearranged B-cell precursor acute lymphoblastic leukemia. Am J Cancer Res 2021; 11:9519-9537. [PMID: 34646384 PMCID: PMC8490503 DOI: 10.7150/thno.65398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/03/2021] [Indexed: 01/13/2023] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi-omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets. Methods: We have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers. Results: MLL-r cells feature an extensive remodeling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodeling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodeling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology. Conclusions: Apart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Mingfeng Zhang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Eun Ji Joo
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Hisham Abdel-Azim
- Division of Hematology/Oncology and Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Chih-Hsing Chou
- Division of Hematology/Oncology and Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Andreia Almeida
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Francis Jacob
- Glyco-Oncology, Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Nicolle H Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Nora Heisterkamp
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA.,✉ Corresponding authors: Equal contributions of Nora Heisterkamp, E-mail: ; and Daniel Kolarich, E-mail:
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia.,✉ Corresponding authors: Equal contributions of Nora Heisterkamp, E-mail: ; and Daniel Kolarich, E-mail:
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Why Do Children with Acute Lymphoblastic Leukemia Fare Better Than Adults? Cancers (Basel) 2021; 13:cancers13153886. [PMID: 34359787 PMCID: PMC8345615 DOI: 10.3390/cancers13153886] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
It is a new and exciting time for acute lymphoblastic leukemia (ALL). While nearly 50 years ago, only one in nine children with ALL survived with chemotherapy, nowadays nearly 90% of children have a chance of long-term survival. Adults with ALL, as well as the special category of adolescents and young adult (AYA) patients, are catching up with the new developments seen in children, but still their prognosis is much worse. A plethora of factors are regarded as responsible for the differences in treatment response, such as age, ethnicity, disease biology, treatment regimens and toxicities, drug tolerance and resistance, minimal residual disease evaluation, hematopoietic stem cell transplantation timing and socio-economic factors. Taking these factors into account, bringing pediatric-like protocols to adult patient management and incorporating new agents into frontline treatment could be the key to improve the survival rates in adults and AYA.
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Zerkalenkova E, Lebedeva S, Borkovskaia A, Soldatkina O, Plekhanova O, Tsaur G, Maschan M, Maschan A, Novichkova G, Olshanskaya Y. BTK, NUTM2A, and PRPF19 Are Novel KMT2A Partner Genes in Childhood Acute Leukemia. Biomedicines 2021; 9:biomedicines9080924. [PMID: 34440129 PMCID: PMC8391293 DOI: 10.3390/biomedicines9080924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/29/2023] Open
Abstract
Chromosomal rearrangements of the human KMT2A/MLL gene are associated with acute leukemias, especially in infants. KMT2A is rearranged with a big variety of partner genes and in multiple breakpoint locations. Detection of all types of KMT2A rearrangements is an essential part of acute leukemia initial diagnostics and follow-up, as it has a strong impact on the patients’ outcome. Due to their high heterogeneity, KMT2A rearrangements are most effectively uncovered by next-generation sequencing (NGS), which, however, requires a thorough prescreening by cytogenetics. Here, we aimed to characterize uncommon KMT2A rearrangements in childhood acute leukemia by conventional karyotyping, FISH, and targeted NGS on both DNA and RNA level with subsequent validation. As a result of this comprehensive approach, three novel KMT2A rearrangements were discovered: ins(X;11)(q26;q13q25)/KMT2A-BTK, t(10;11)(q22;q23.3)/KMT2A-NUTM2A, and inv(11)(q12.2q23.3)/KMT2A-PRPF19. These novel KMT2A-chimeric genes expand our knowledge of the mechanisms of KMT2A-associated leukemogenesis and allow tracing the dynamics of minimal residual disease in the given patients.
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Affiliation(s)
- Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
- Correspondence:
| | - Svetlana Lebedeva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Aleksandra Borkovskaia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Olga Soldatkina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Olga Plekhanova
- Regional Children Hospital 1, Pediatric Oncology and Hematology Center, Research Institute of Medical Cell Technologies, Ural Federal University Named after the First President of Russia BN Yeltsin, 620149 Ekaterinburg, Russia; (O.P.); (G.T.)
| | - Grigory Tsaur
- Regional Children Hospital 1, Pediatric Oncology and Hematology Center, Research Institute of Medical Cell Technologies, Ural Federal University Named after the First President of Russia BN Yeltsin, 620149 Ekaterinburg, Russia; (O.P.); (G.T.)
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Aleksey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
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Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemia. Sci Rep 2021; 11:13158. [PMID: 34162911 PMCID: PMC8222245 DOI: 10.1038/s41598-021-92448-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional gene regulation, including that by RNA binding proteins (RBPs), has recently been described as an important mechanism in cancer. We had previously identified a set of RBPs that were highly dysregulated in B-cell acute lymphoblastic leukemia (B-ALL) with MLL translocations, which carry a poor prognosis. Here, we sought to functionally characterize these dysregulated RBP genes by performing a focused CRISPR dropout screen in B-ALL cell lines, finding dependencies on several genes including EIF3E, EPRS and USO1. Validating our findings, CRISPR/Cas9-mediated disruption of USO1 in MLL-translocated B-ALL cells reduced cell growth, promoted cell death, and altered the cell cycle. Transcriptomic analysis of USO1-deficient cells revealed alterations in pathways related to mTOR signaling, RNA metabolism, and targets of MYC. In addition, USO1-regulated genes from these experimental samples were significantly and concordantly correlated with USO1 expression in primary samples collected from B-ALL patients. Lastly, we found that loss of Uso1 inhibited colony formation of MLL-transformed in primary bone marrow cells from Cas9-EGFP mice. Together, our findings demonstrate an approach to performing focused sub-genomic CRISPR screens and highlight a putative RBP vulnerability in MLL-translocated B-ALL, thus identifying potential therapeutic targets in this disease.
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Genomic Analyses of Pediatric Acute Lymphoblastic Leukemia Ph+ and Ph-Like-Recent Progress in Treatment. Int J Mol Sci 2021; 22:ijms22126411. [PMID: 34203891 PMCID: PMC8232636 DOI: 10.3390/ijms22126411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) with t(9;22)(q34;q11.2) is a very rare malignancy in children. Approximately 3-5% of pediatric ALL patients present with the Philadelphia chromosome. Previously, children with Ph+ had a poor prognosis, and were considered for allogeneic stem cell transplantation (allo-HSCT) in their first remission (CR1). Over the last few years, the treatment of childhood ALL has significantly improved due to standardized research protocols. Hematopoietic stem cell transplantation (HSCT) has been the gold standard therapy in ALL Ph+ patients, but recently first-generation tyrosine kinase inhibitor (TKI)-imatinib became a major milestone in increasing overall survival. Genomic analyses give the opportunity for the investigation of new fusions or mutations, which can be used to establish effective targeted therapies. Alterations of the IKZF1 gene are present in a large proportion of pediatric and adult ALL Ph+ cases. IKZF1 deletions are present in ~15% of patients without BCR-ABL1 rearrangements. In BCR-ABL1-negative cases, IKZF1 deletions have been shown to have an independent prognostic impact, carrying a three-fold increased risk of treatment failure. The prognostic significance of IKZF1 gene aberrations in pediatric ALL Ph+ is still under investigation. More research should focus on targeted therapies and immunotherapy, which is not associated with serious toxicity in the same way as classic chemotherapy, and on the improvement of patient outcomes. In this review, we provide a molecular analysis of childhood ALL with t(9;22)(q34;q11.2), including the Ph-like subtype, and of treatment strategies.
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Chen D, Camponeschi A, Nordlund J, Marincevic‐Zuniga Y, Abrahamsson J, Lönnerholm G, Fogelstrand L, Mårtensson I. RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children. Cancer Med 2021; 10:3997-4003. [PMID: 33987955 PMCID: PMC8209579 DOI: 10.1002/cam4.3928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 12/05/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) can be classified into subtypes according to the genetic aberrations they display. For instance, the translocation t(12;21)(p13;q22), representing the ETV6-RUNX1 fusion gene (ER), is present in a quarter of BCP-ALL cases. However, around 10% of the cases lack classifying chromosomal abnormalities (B-other). In pediatric ER BCP-ALL, rearrangement mediated by RAG (recombination-activating genes) has been proposed as the predominant driver of oncogenic rearrangement. Herein we analyzed almost 1600 pediatric BCP-ALL samples to determine which subtypes express RAG. We demonstrate that RAG1 mRNA levels are especially high in the ETV6-RUNX1 (ER) subtype and in a subset of B-other samples. We also define 31 genes that are co-expressed with RAG1 (RAG1-signature) in the ER subtype, a signature that also identifies this subset of B-other samples. Moreover, this subset also shares leukemia and pro-B gene expression signatures as well as high levels of the ETV6 target genes (BIRC7, WBP1L, CLIC5, ANGPTL2) with the ER subtype, indicating that these B-other cases are the recently identified ER-like subtype. We validated our results in a cohort where ER-like has been defined, which confirmed expression of the RAG1-signature in this recently described subtype. Taken together, our results demonstrate that the RAG1-signature identifies the ER-like subtype. As there are no definitive genetic markers to identify this novel subtype, the RAG1-signature represents a means to screen for this leukemia in children.
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Affiliation(s)
- Dongfeng Chen
- Institute of Life SciencesJiangsu UniversityZhenjiangChina
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Alessandro Camponeschi
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Jessica Nordlund
- Department of Medical SciencesMolecular Medicine and Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Yanara Marincevic‐Zuniga
- Department of Medical SciencesMolecular Medicine and Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Jonas Abrahamsson
- Department of PediatricsInstitute of Clinical SciencesSahlgrenska University HospitalGothenburgSweden
| | - Gudmar Lönnerholm
- Department of Women and Children’s HealthUppsala UniversityUppsalaSweden
| | - Linda Fogelstrand
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
- Department of Clinical Chemistry and Transfusion MedicineUniversity of GothenburgGothenburgSweden
| | - Inga‐Lill Mårtensson
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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36
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Andrew B, Attilio O, Sumit G, Vijay T, Reshad GS, Osvaldo P. A rare case of B cell lymphoblastic leukemia with inv(7)(p15q34) with review of literature. Leuk Res Rep 2021; 15:100250. [PMID: 34150490 PMCID: PMC8192865 DOI: 10.1016/j.lrr.2021.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 05/04/2021] [Accepted: 05/23/2021] [Indexed: 11/23/2022] Open
Abstract
The inv(7)(p15q34) chromosomal abnormality which juxtaposes part of the HOXA gene cluster on 7p15 to the TCRβ locus on 7q34, has been described in a subset of cases of T-cell lymphoblastic leukemia, but its presence in cases of B-cell lymphoblastic leukemia is virtually unknown. Herewith, we report a case of a B-cell lymphoblastic leukemia with inv(7)(p15q34). The patient received standard induction chemotherapy, which failed to produce remission. After treatment with blinatumomab, a bispecific T-cell engager, the follow-up bone marrow biopsy showed no evidence of persistent/ relapsed B-cell lymphoblastic leukemia. The unique cytogenetics of this case may have contributed to its resistance of standard induction chemotherapy.
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Affiliation(s)
- Bernhisel Andrew
- Medical student, Paul Foster School of Medicine, Texas Tech Health Sciences Center at El Paso, TX
| | - Orazi Attilio
- Department of Pathology, Texas Tech Health Sciences Center at El Paso, TX
| | - Guar Sumit
- Department of Internal Medicine, Texas Tech Health Sciences Center at El Paso, TX
| | - Tonk Vijay
- Department of Pediatrics, Texas Tech Health Sciences Center at Lubbock, TX
| | | | - Padilla Osvaldo
- Department of Pathology, Texas Tech Health Sciences Center at El Paso, TX
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37
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Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL. Blood 2021; 136:2319-2333. [PMID: 32573712 DOI: 10.1182/blood.2019004090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
Karyotype is an important prognostic factor in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but the underlying pharmacogenomics remain unknown. Asparaginase is an integral component in current chemotherapy for childhood BCP-ALL. Asparaginase therapy depletes serum asparagine. Normal hematopoietic cells can produce asparagine by asparagine synthetase (ASNS) activity, but ALL cells are unable to synthesize adequate amounts of asparagine. The ASNS gene has a typical CpG island in its promoter. Thus, methylation of the ASNS CpG island could be one of the epigenetic mechanisms for ASNS gene silencing in BCP-ALL. To gain deep insights into the pharmacogenomics of asparaginase therapy, we investigated the association of ASNS methylation status with asparaginase sensitivity. The ASNS CpG island is largely unmethylated in normal hematopoietic cells, but it is allele-specifically methylated in BCP-ALL cells. The ASNS gene is located at 7q21, an evolutionally conserved imprinted gene cluster. ASNS methylation in childhood BCP-ALL is associated with an aberrant methylation of the imprinted gene cluster at 7q21. Aberrant methylation of mouse Asns and a syntenic imprinted gene cluster is also confirmed in leukemic spleen samples from ETV6-RUNX1 knockin mice. In 3 childhood BCP-ALL cohorts, ASNS is highly methylated in BCP-ALL patients with favorable karyotypes but is mostly unmethylated in BCP-ALL patients with poor prognostic karyotypes. Higher ASNS methylation is associated with higher L-asparaginase sensitivity in BCP-ALL through lower ASNS gene and protein expression levels. These observations demonstrate that silencing of the ASNS gene as a result of aberrant imprinting is a pharmacogenetic mechanism for the leukemia-specific activity of asparaginase therapy in BCP-ALL.
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38
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Sharma G, Boby E, Nidhi T, Jain A, Singh J, Singh A, Chattopadhyay P, Bakhshi S, Chopra A, Palanichamy JK. Diagnostic Utility of IGF2BP1 and Its Targets as Potential Biomarkers in ETV6-RUNX1 Positive B-Cell Acute Lymphoblastic Leukemia. Front Oncol 2021; 11:588101. [PMID: 33708624 PMCID: PMC7940665 DOI: 10.3389/fonc.2021.588101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/08/2021] [Indexed: 01/22/2023] Open
Abstract
Around 85% of childhood Acute Lymphoblastic Leukemia (ALL) are of B-cell origin and characterized by the presence of different translocations including BCR-ABL1, ETV6-RUNX1, E2A-PBX1, and MLL fusion proteins. The current clinical investigations used to identify ETV6-RUNX1 translocation include FISH and fusion transcript specific PCR. In the current study we assessed the utility of IGF2BP1, an oncofetal RNA binding protein, that is over expressed specifically in ETV6-RUNX1 translocation positive B-ALL to be used as a diagnostic marker in the clinic. Further, public transcriptomic and Crosslinked Immunoprecipitation (CLIP) datasets were analyzed to identify the putative targets of IGF2BP1. We also studied the utility of using the mRNA expression of two such targets, MYC and EGFL7 as potential diagnostic markers separately or in conjunction with IGF2BP1. We observed that the expression of IGF2BP1 alone measured by RT-qPCR is highly sensitive and specific to be used as a potential biomarker for the presence of ETV6-RUNX1 translocation in future.
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Affiliation(s)
- Gunjan Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Elza Boby
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Thakur Nidhi
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Ayushi Jain
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Jay Singh
- Department of Laboratory Oncology, Dr. B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Archna Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Sameer Bakhshi
- Department of Medical Oncology, Dr. B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Chopra
- Department of Laboratory Oncology, Dr. B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
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39
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Abstract
Classifying the hematological malignancies by assigning cells to their normal counterpart and describing the nature of disease progression are entirely reliant on an accurate picture for the development of the multifarious types of blood and immune cells. In recent years, our understanding of the complex relationships between the various hematopoietic stem cell-derived cell lineages has undergone substantial revision. There has been similar progress in how we describe the nature of the "target" cells that genetic insults transform to give rise to the hematological malignancies. Here I describe how both longstanding and new information has influenced classifying, for diagnosis, the hematological malignancies.
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Affiliation(s)
- Geoffrey Brown
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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40
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Su H, Wang M, Pang X, Guan F, Li X, Cheng Y. When Glycosylation Meets Blood Cells: A Glance of the Aberrant Glycosylation in Hematological Malignancies. Rev Physiol Biochem Pharmacol 2021; 180:85-117. [PMID: 34031738 DOI: 10.1007/112_2021_60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Among neoplasia-associated epigenetic alterations, changes in cellular glycosylation have recently received attention as a key component of hematological malignancy progression. Alterations in glycosylation appear to not only directly impact cell growth and survival, but also alter the adhesion of tumor cells and their interactions with the microenvironment, facilitating cancer-induced immunomodulation and eventual metastasis. Changes in glycosylation arise from altered expression of glycosyltransferases, enzymes that catalyze the transfer of saccharide moieties to a wide range of acceptor substrates, such as proteins, lipids, and other saccharides in the endoplasmic reticulum (ER) and Golgi apparatus. Novel glycan structures in hematological malignancies represent new targets for the diagnosis and treatment of blood diseases. This review summarizes studies of the aberrant expression of glycans commonly found in hematological malignancies and their potential mechanisms and defines the specific roles of glycans as drivers or passengers in the development of hematological malignancies.
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Affiliation(s)
- Huining Su
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Mimi Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xingchen Pang
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Science, Northwest University, Xi'an, China
| | - Feng Guan
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Science, Northwest University, Xi'an, China
| | - Xiang Li
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Science, Northwest University, Xi'an, China.
| | - Ying Cheng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.
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41
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Tebbi CK, Badiga A, Sahakian E, Powers JJ, Achille AN, Patel S, Migone F. Exposure to a mycovirus containing Aspergillus Flavus reproduces acute lymphoblastic leukemia cell surface and genetic markers in cells from patients in remission and not controls. Cancer Treat Res Commun 2020; 26:100279. [PMID: 33348275 DOI: 10.1016/j.ctarc.2020.100279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/27/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022]
Abstract
The etiology of acute lymphoblastic leukemia (ALL) remains unknown. A recent "two-hit" model for the occurrence of precursor B cell acute lymphoblastic leukemia propose that this disease arises through a two-step process, including predisposing genetic mutation and exposure to infections. While several genetic mutations are proposed, no infection category has been suggested. We have isolated a certain Aspergillus Flavus from residence of an ALL patient. This organism contains mycovirus and does not produce aflatoxin. The supernatant of culture of this mycovirus containing Aspergillus Flavus (SAF) was tested on the PBMCs of ALL patients in remission and controls. Cell surface phenotypes and genetic markers were examined. The effects of its combination with Epstein-Barr virus (EBV) was also investigated. For the SAF, positive and negative controls were aflatoxin and culture of Mycocladus corymbifer, respectively. Controls for ALL were sickle cell patients undergoing exchange transfusion. Incubation of the PMBCs from ALL patients in remission, or controls, with SAF resulted in re-development of ALL cell surface phenotypes and genetic markers in ALL patients in remission and not controls. These differentiating effects were not seen with aflatoxin or culture of Mycocladus Corymbifer. Addition of EBV did not alter effects of SAF. Currently, there are no techniques to discriminately reproduce characteristic leukemic genetic markers and cell surface phenotypes in cells from ALL patients in remission and not controls. These studies may provide a test for recognition of ALL patients in remission and new prospects for the investigation of leukemogenesis.
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Affiliation(s)
- Cameron K Tebbi
- Florida Pediatric Hematology/Oncology and Children's Cancer Research Group Laboratory, 13719 North Nebraska Avenue, Tampa, Florida, 33613 USA.
| | - Aruna Badiga
- Children's Cancer Research Group Laboratory, 13719 North Nebraska Avenue, Tampa, Florida, 33613 USA
| | - Eva Sahakian
- Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida, 33612 USA
| | - John J Powers
- Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida, 33612 USA
| | - Alex N Achille
- Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612 USA
| | - Saumil Patel
- Tampa General Hospital, 1 Tampa General Circle, Tampa, Florida, 33606 USA
| | - Felicia Migone
- Children's Cancer Research Group Laboratory, 13719 North Nebraska Avenue, Tampa, Florida, 33613 USA
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42
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Abstract
Although we are just beginning to understand the mechanisms that regulate the epigenome, aberrant epigenetic programming has already emerged as a hallmark of hematologic malignancies including acute myeloid leukemia (AML) and B-cell lymphomas. Although these diseases arise from the hematopoietic system, the epigenetic mechanisms that drive these malignancies are quite different. Yet, in all of these tumors, somatic mutations in transcription factors and epigenetic modifiers are the most commonly mutated set of genes and result in multilayered disruption of the epigenome. Myeloid and lymphoid neoplasms generally manifest epigenetic allele diversity, which contributes to tumor cell population fitness regardless of the underlying genetics. Epigenetic therapies are emerging as one of the most promising new approaches for these patients. However, effective targeting of the epigenome must consider the need to restore the various layers of epigenetic marks, appropriate biological end points, and specificity of therapeutic agents to truly realize the potential of this modality.
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Affiliation(s)
- Cihangir Duy
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Wendy Béguelin
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
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43
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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44
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Zerkalenkova E, Mikhaylova E, Lebedeva S, Illarionova O, Baidun L, Kashpor S, Osipova E, Maschan M, Maschan A, Novichkova G, Olshanskaya Y, Popov A. Quantification of
NG2
‐positivity for the precise prediction of
KMT2A
gene rearrangements in childhood acute leukemia. Genes Chromosomes Cancer 2020; 60:88-99. [DOI: 10.1002/gcc.22915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 01/19/2023] Open
Affiliation(s)
- Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Ekaterina Mikhaylova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Svetlana Lebedeva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Olga Illarionova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | | | - Svetlana Kashpor
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Elena Osipova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Alexey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology Moscow Russia
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45
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Vincristine and prednisone regulates cellular and exosomal miR-181a expression differently within the first time diagnosed and the relapsed leukemia B cells. Leuk Res Rep 2020; 14:100221. [PMID: 33094092 PMCID: PMC7568182 DOI: 10.1016/j.lrr.2020.100221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
We explored the effect of vincristine and prednisone on cellular and exosomal miR-181a expression in first time diagnosed leukemia and relapsed leukemia. Vincristine and prednisone induced apoptosis/pro-apoptotic genes in first time diagnosed leukemia, and suppressed the cellular and exosomal miR-181a expression. In contrast, vincristine and prednisone could not induce apoptosis/pro-apoptotic genes in relapsed leukemia, and could not change the expression of cellular or exosomal miR-181a. In conclusion, the non-suppressive nature of miR-181a in relapsed leukemia might contribute to the chemo-resistance and this suggests a potential role of miR-181a-inhibitor along with the chemotherapy in the treatment of relapsed leukemia.
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46
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Oshima K, Zhao J, Pérez-Durán P, Brown JA, Patiño-Galindo JA, Chu T, Quinn A, Gunning T, Belver L, Ambesi-Impiombato A, Tosello V, Wang Z, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Balbin M, Nicolas C, Gastier-Foster JM, Devidas M, Loh ML, Paietta E, Tallman MS, Rowe JM, Litzow M, Minden MD, Meijerink J, Rabadan R, Ferrando A. Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2020; 1:1113-1127. [PMID: 33796864 DOI: 10.1038/s43018-020-00124-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multi-agent combination chemotherapy can be curative in acute lymphoblastic leukemia (ALL). Still, patients with primary refractory disease or with relapsed leukemia have a very poor prognosis. Here we integrate an in-depth dissection of the mutational landscape across diagnostic and relapsed pediatric and adult ALL samples with genome-wide CRISPR screen analysis of gene-drug interactions across seven ALL chemotherapy drugs. By combining these analyses, we uncover diagnostic and relapse-specific mutational mechanisms as well as genetic drivers of chemoresistance. Functionally, our data identifies common and drug-specific pathways modulating chemotherapy response and underscores the effect of drug combinations in restricting the selection of resistance-driving genetic lesions. In addition, by identifying actionable targets for the reversal of chemotherapy resistance, these analyses open novel therapeutic opportunities for the treatment of relapse and refractory disease.
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Affiliation(s)
- Koichi Oshima
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Junfei Zhao
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Pablo Pérez-Durán
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Juan Angel Patiño-Galindo
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Timothy Chu
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Thomas Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Alberto Ambesi-Impiombato
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Present address: PsychoGenics, Paramus, NJ, USA
| | | | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Maria Luisa Sulis
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Motohiro Kato
- Department of Hematology-Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuyoshi Koh
- Department of Hematology-Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Maddalena Paganin
- Fondazione Città della Speranza, Istituto di Ricerca Pediatrica, Padova, Italy.,Haematology-Oncology Division, Department of Woman's and Child's Health, University Hospital of Padua, Padua, Italy
| | - Giuseppe Basso
- Haematology-Oncology Division, Department of Woman's and Child's Health, University Hospital of Padua, Padua, Italy.,Present address: IIGM Italian Institute of Genomic Medicine, Turin, Italy
| | - Milagros Balbin
- Molecular Oncology Laboratory, Instituto Universitario de Oncologia del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Concepcion Nicolas
- Hematology Service, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Departments of Pathology and Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA.,Children's Oncology Group, Arcadia, CA, USA
| | - Meenakshi Devidas
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.,Present address: Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | | | - Martin S Tallman
- Department of Hematologic Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Mark D Minden
- Department of Oncology/Hematology, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Jules Meijerink
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.,Department of Pediatrics, Columbia University, New York, NY, USA
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47
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Wafa A, Jarjour RA, Alolabi D, Liehr T, Hamdan O, Melo JB, Carreira IM, Othman MAK, Al-Achkar W. A new childhood ALL case with an extremely complex karyotype and acute spontaneous tumor lysis syndrome. Mol Cytogenet 2020; 13:44. [PMID: 32944079 PMCID: PMC7488544 DOI: 10.1186/s13039-020-00512-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B cell precursor acute lymphoblastic leukemia (B-ALL) is the most common malignancy of childhood, with, after corresponding treatment, an overall complete remission rate of 90%. Approximately 75% of B-ALL cases harbor recurrent abnormalities, including so-called complex karyotypes (CK). Tumor lysis syndrome (TLS) is a metabolic abnormality which may arise during cancer therapy and also, extremely rarely, as spontaneous TLS before initiation of chemotherapy in patients with ALL. CASE PRESENTATION Here we report a 9-year-old male, diagnosed with a de novo pre-B-ALL according to the WHO classification. Cytogenetic, molecular cytogenetic approaches and array comparative genomic hybridization analyses revealed a unique CK involving five chromosomes. It included four yet unreported chromosomal aberrations: a der(11)t(7;11)(p22.1;q24.2), a der(18)t(7;18)(q21.3;p11.22), del(11)(q24.2q25) and dup(18)(q11.1q23). Unfortunately, the patient died 3 months after the initial diagnosis. CONCLUSIONS To the best of our knowledge, a comparable childhood ALL case was not previously reported. Thus, the combination of the here seen chromosomal aberrations in childhood primary ALL seems to indicate for an extremely adverse prognosis.
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Affiliation(s)
- Abdulsamad Wafa
- Department of Molecular Biology and Biotechnology, Human Genetics Division, Atomic Energy Commission, Damascus, Syria
| | - Rami A. Jarjour
- Department of Molecular Biology and Biotechnology, Human Genetics Division, Atomic Energy Commission, Damascus, Syria
| | - Doaa Alolabi
- Department of Hematology, Damascus Children University Hospital, Ministry of High Education, Damascus, Syria
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - Othman Hamdan
- Department of Hematology, Damascus Children University Hospital, Ministry of High Education, Damascus, Syria
| | - Joana B. Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- CIMAGO-Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M. Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- CIMAGO-Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | | | - Walid Al-Achkar
- Department of Molecular Biology and Biotechnology, Human Genetics Division, Atomic Energy Commission, Damascus, Syria
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Plasma of Acute Lymphoblastic Leukemia Patients React to the Culture of a Mycovirus Containing Aspergillus flavus. J Pediatr Hematol Oncol 2020; 42:350-358. [PMID: 32576782 DOI: 10.1097/mph.0000000000001845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children and is also seen in adults. Currently, no plasma-based test for the detection of ALL is available. We have cultured the home of a patient with ALL and isolated a mycovirus containing Aspergillus flavus. This culture was subjected to electron microscopy, purification, and mass spectrometry. Using enzyme-linked immunosorbent assay technique, plasma of patients with ALL and long-term survivors of this disease were tested for antibodies, utilizing supernatant of the culture of this organism. The results were compared with 3 groups of controls, including healthy individuals, patients with sickle cell disease, and solid tumors. Using electron microscopy, the isolated A. flavus contained mycovirus particles. In chemical analysis, this organism did not produce any aflatoxin. Using an enzyme-linked immunosorbent assay technique, the supernatant of the culture of the mycovirus containing A. flavus could differentiate ALL patients from each group of controls (P<0.001). These studies provide a new technique for the detection of ALL and may add information for future research regarding leukemogenesis.
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Szczepanek J. Role of microRNA dysregulation in childhood acute leukemias: Diagnostics, monitoring and therapeutics: A comprehensive review. World J Clin Oncol 2020; 11:348-369. [PMID: 32855905 PMCID: PMC7426929 DOI: 10.5306/wjco.v11.i6.348] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that regulate the expression of genes by sequence-specific binding to mRNA to either promote or block its translation; they can also act as tumor suppressors (e.g., let-7b, miR-29a, miR-99, mir-100, miR-155, and miR-181) and/or oncogenes (e.g., miR-29a, miR-125b, miR-143-p3, mir-155, miR-181, miR-183, miR-196b, and miR-223) in childhood acute leukemia (AL). Differentially expressed miRNAs are important factors associated with the initiation and progression of AL. As shown in many studies, they can be used as noninvasive diagnostic and prognostic biomarkers, which are useful in monitoring early stages of AL development or during therapy (e.g., miR-125b, miR-146b, miR-181c, and miR-4786), accurate classification of different cellular or molecular AL subgroups (e.g., let-7b, miR-98, miR-100, miR-128b, and miR-223), and identification and development of new therapeutic agents (e.g., mir-10, miR-125b, miR-203, miR-210, miR-335). Specific miRNA patterns have also been described for commonly used AL therapy drugs (e.g., miR-125b and miR-223 for doxorubicin, miR-335 and miR-1208 for prednisolone, and miR-203 for imatinib), uncovering miRNAs that are associated with treatment response. In the current review, the role of miRNAs in the development, progression, and therapy monitoring of pediatric ALs will be presented and discussed.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń 87100, Poland
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Mei E, Wei X, Gao J, Tian X, Li W, Liu L, Qian C. Association of TLX1 gene polymorphisms with the risk of acute lymphoblastic leukemia and B lineage acute lymphoblastic leukemia in Han Chinese children. J Clin Lab Anal 2020; 34:e23414. [PMID: 32488880 PMCID: PMC7521250 DOI: 10.1002/jcla.23414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Background Studies on gene polymorphism association are centered on childhood acute lymphoblastic leukemia (ALL), a common hematological malignancy in children younger than 16 years. Single‐nucleotide polymorphisms (SNPs) in some genes, such as ARID5B and CDKN2B, are associated with the risk of childhood ALL. T‐cell leukemia homeobox 1 (TLX1), a member of the HOX gene family, was identified based on its abnormal expression in T‐lineage leukemia. This study aimed to determine whether TLX1 is associated with B‐ALL and which SNP plays a significant role in ALL. Methods A total of 217 cases of ALL and 241 controls were included in this study. Six tag SNPs (rs75329544, rs946328, rs12415670, rs2075879, rs17113735, and rs1051723) were selected, and genotyping was carried out on Sequenom MassARRAY platform. Results Rs17113735 was possibly the risk locus associated with increased risk for ALL, whereas rs946328 was possibly associated with decreased risk for ALL. Moreover, rs17113735 was likely to be the risk locus for B‐cell ALL (B‐ALL), and rs2075879 was associated with decreased risk for B‐ALL (P < .05). All SNPs in the two sample types (ALL and B‐ALL samples) demonstrated linkage disequilibrium except between rs75329544 and rs2075879. Haplotype analysis showed no significant difference between the cases and controls in the two sample types. Conclusion TLX1 gene polymorphisms are associated with ALL (rs17113735 and rs946328) and possibly play a significant role in B‐ALL (rs17113735 and rs2075879). This work provides a reference for the diagnosis and therapy of this disease.
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Affiliation(s)
- Endian Mei
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Xubin Wei
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Jiadong Gao
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Xiaolong Tian
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Wei Li
- Department of Clinical Laboratory, School of Medicine, Children's Hospital, Zhejiang University, Hangzhou, China
| | - Li Liu
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Cheng Qian
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
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