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Gil JV, Miralles A, de las Heras S, Such E, Avetisyan G, Díaz-González Á, Santiago M, Fuentes C, Fernández JM, Lloret P, Navarro I, Montesinos P, Llop M, Barragán E. Comprehensive detection of CRLF2 alterations in acute lymphoblastic leukemia: a rapid and accurate novel approach. Front Mol Biosci 2024; 11:1362081. [PMID: 38370004 PMCID: PMC10869515 DOI: 10.3389/fmolb.2024.1362081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
Introduction: Acute lymphoblastic leukemia (ALL) is a prevalent childhood cancer with high cure rate, but poses a significant medical challenge in adults and relapsed patients. Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL) is a high-risk subtype, with approximately half of cases characterized by CRLF2 overexpression and frequent concomitant IKZF1 deletions. Methods: To address the need for efficient, rapid, and cost-effective detection of CRLF2 alterations, we developed a novel RT-qPCR technique combining SYBR Green and highresolution melting analysis on a single plate. Results: The method successfully identified CRLF2 expression, P2RY8::CRLF2 fusions, and CRLF2 and JAK2 variants, achieving a 100% sensitivity and specificity. Application of this method across 61 samples revealed that 24.59% exhibited CRLF2 overexpression, predominantly driven by IGH::CRLF2 (73.33%). High Resolution Melting analysis unveiled concurrent CRLF2 or JAK2 variants in 8.19% of samples, as well as a dynamic nature of CRLF2 alterations during disease progression. Discussion: Overall, this approach provides an accurate identification of CRLF2 alterations, enabling improved diagnostic and facilitating therapeutic decision-making.
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Affiliation(s)
- José Vicente Gil
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Alberto Miralles
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Sandra de las Heras
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Esperanza Such
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Madrid, Spain
| | - Gayane Avetisyan
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Álvaro Díaz-González
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Marta Santiago
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Carolina Fuentes
- Accredited Research Group on Clinical and Translational Cancer Research, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Onco-Hematology Unit, Pediatrics Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - José María Fernández
- Accredited Research Group on Clinical and Translational Cancer Research, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Onco-Hematology Unit, Pediatrics Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Pilar Lloret
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Irene Navarro
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Pau Montesinos
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Marta Llop
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Biology Unit, Clinical Analysis Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Eva Barragán
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Biology Unit, Clinical Analysis Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
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Rezayee F, Eisfeldt J, Skaftason A, Öfverholm I, Sayyab S, Syvänen AC, Maqbool K, Lilljebjörn H, Johansson B, Olsson-Arvidsson L, Pietras CO, Staffas A, Palmqvist L, Fioretos T, Cavelier L, Fogelstrand L, Nordlund J, Wirta V, Rosenquist R, Barbany G. Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia. Front Oncol 2023; 13:1217712. [PMID: 37664045 PMCID: PMC10470829 DOI: 10.3389/fonc.2023.1217712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods. Methods For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL. Results Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions. Discussion The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.
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Affiliation(s)
- Fatemah Rezayee
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ingegerd Öfverholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Shumaila Sayyab
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann Christine Syvänen
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Khurram Maqbool
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | | | - Anna Staffas
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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