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Ochodnicka-Mackovicova K, Mokry M, Haagmans M, Bradley TE, van Noesel CJM, Guikema JEJ. RAG1/2 induces double-stranded DNA breaks at non-Ig loci in the proximity of single sequence repeats in developing B cells. Eur J Immunol 2024:e2350958. [PMID: 39046890 DOI: 10.1002/eji.202350958] [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: 12/14/2023] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
In developing B cells, V(D)J gene recombination is initiated by the RAG1/2 endonuclease complex, introducing double-stranded DNA breaks (DSBs) in V, D, and J genes and resulting in the formation of the hypervariable parts of immunoglobulins (Ig). Persistent or aberrant RAG1/2 targeting is a potential threat to genome integrity. While RAG1 and RAG2 have been shown to bind various regions genome-wide, the in vivo off-target DNA damage instigated by RAG1/2 endonuclease remains less well understood. In the current study, we identified regions containing RAG1/2-induced DNA breaks in mouse pre-B cells on a genome-wide scale using a global DNA DSB detection strategy. We detected 1489 putative RAG1/2-dependent DSBs, most of which were located outside the Ig loci. DNA sequence motif analysis showed a specific enrichment of RAG1/2-induced DNA DSBs at GA- and CA-repeats and GC-rich motifs. These findings provide further insights into RAG1/2 off-target activity. The ability of RAG1/2 to introduce DSBs on the non-Ig loci during the endogenous V(D)J recombination emphasizes its genotoxic potential in developing lymphocytes.
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Affiliation(s)
- Katarina Ochodnicka-Mackovicova
- Department of Pathology, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
| | - Michal Mokry
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Martin Haagmans
- Core Facility Genomics, Department of Clinical Genetics, Amsterdam University Medical Center, The Netherlands
| | - Ted E Bradley
- Core Facility Genomics, Department of Clinical Genetics, Amsterdam University Medical Center, The Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
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2
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Ma SB, Lin W, Campbell J, Clerici K, White D, Yeung D, Gorniak M, Fleming S, Fong CY, Agarwal R. Laboratory validation and clinical utility of next-generation sequencing-based IGH/TCR clonality testing for the monitoring of measurable residual disease in acute lymphoblastic leukaemia: real-world experience at Austin Pathology. Pathology 2024:S0031-3025(24)00171-5. [PMID: 39025724 DOI: 10.1016/j.pathol.2024.04.012] [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: 01/09/2024] [Revised: 03/12/2024] [Accepted: 04/28/2024] [Indexed: 07/20/2024]
Abstract
Measurable residual disease (MRD) testing is an essential aspect of disease prognostication in acute lymphoblastic leukaemia (ALL) and informs clinical decisions. The depth of MRD clearance is highly relevant and requires assays with sufficient sensitivity. Austin Pathology is one of the few laboratories in Australia currently utilising a fully validated and National Association of Testing Authorities (NATA)-accredited ultrasensitive next-generation sequencing (NGS) platform for MRD monitoring in ALL. This technology is based on the detection of clonal rearrangement of immunoglobulin and T cell receptor genes in leukaemic cells, and is capable of achieving a limit of detection at least one to two logs below that of multiparametric flow cytometry (MFC). In this retrospective analysis, we report a clonotype detection rate of up to 85.7% at diagnosis, and a concordance rate of 78.7% in MRD results between NGS and MFC. Of the discordant samples, nearly all were NGS+/MFC-, highlighting the superior sensitivity of NGS. The enhanced sensitivity is clinically relevant, as discordant MRD results often heralded fulminant relapse, and therefore offer clinicians additional lead time and a window of opportunity to initiate pre-emptive therapy. Notwithstanding a small and heterogeneous cohort, our real-world survival data indicate an intermediate relapse risk for NGS+/MFC- patients. In light of recent approval of Medicare rebatable ALL MRD testing, we discuss how NGS can complement other techniques such as MFC in personalising management strategies. We recommend routine clonality testing by NGS at diagnosis and use a multi-modality approach for subsequent MRD monitoring.
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Affiliation(s)
- Stephen B Ma
- Austin Pathology, Heidelberg, Vic, Australia; Austin Health, Heidelberg, Vic, Australia.
| | - Wendi Lin
- Austin Pathology, Heidelberg, Vic, Australia
| | | | | | - Deborah White
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - David Yeung
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | | | - Shaun Fleming
- Alfred Health, Melbourne, Vic, Australia; Australian Centre for Blood Diseases, Monash University, Melbourne, Vic, Australia
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3
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Lao Z, Lam KY, Cheung YMC, Teng CL, Radhakrishnan V, Bhurani D, Ko BS, Goh YT. Recommendations for the treatment and management of adult B-Cell acute lymphoblastic leukemia in Asia-Pacific: Outcomes from a pilot initiative. Asia Pac J Clin Oncol 2024; 20:325-334. [PMID: 38148287 DOI: 10.1111/ajco.14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/27/2023] [Accepted: 12/07/2023] [Indexed: 12/28/2023]
Abstract
The outcomes of adult B-cell acute lymphoblastic leukemia (ALL) remain poor. Recent advancements in the field of leukemia research show potential for improved patient care. However, the adoption of research findings into clinical practice is fraught with practice- and country-specific challenges. The continued addition of new findings warrants critical evaluation for the feasibility of incorporation into clinical practice. A uniform set of evidence-based guidelines can favorably assist physicians in making optimal clinical decisions. Such a resource may also serve as a reference point for strategic planning of initiatives aimed at addressing critical barriers in the optimal management of B-cell ALL. This initiative was undertaken to seek a collaborative perspective and understand the existing challenges. Concordance-based recommendations were outlined through a systematic discussion on various aspects of treatment and management of adult B-cell ALL. The outcomes and experiences gained from this exercise will serve as a foundation for future efforts encompassing the more granular aspects of the management of B-cell ALL across the Asia-Pacific region.
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Affiliation(s)
- Zhentang Lao
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Kwong Yok Lam
- Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Yuk Man Carol Cheung
- Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Chieh-Lin Teng
- Department of Medicine, Division of Hematology/Medical Oncology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Vivek Radhakrishnan
- Division of Haematology Oncology and Haematopoietic Cell Transplantation, Tata Medical Center, Kolkata, India
| | - Dinesh Bhurani
- Department of Hematology and Bone Marrow Transplant, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi, India
| | - Bor-Sheng Ko
- Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Yeow Tee Goh
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
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4
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Altieri F, Buono L, Lanzilli M, Mirabelli P, Cianflone A, Beneduce G, De Matteo A, Parasole R, Salvatore M, Smaldone G. LINC00958 as new diagnostic and prognostic biomarker of childhood acute lymphoblastic leukaemia of B cells. Front Oncol 2024; 14:1388154. [PMID: 38884090 PMCID: PMC11176504 DOI: 10.3389/fonc.2024.1388154] [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: 02/19/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Background Paediatric acute B-cell lymphoblastic leukaemia is the most common cancer of the paediatric age. Although the advancement of scientific and technological knowledge has ensured a huge step forward in the management of this disease, there are 15%-20% cases of recurrence leading to serious complications for the patient and sometimes even death. It is therefore necessary to identify new and increasingly personalised biomarkers capable of predicting the degree of risk of B-ALL in order to allow the correct management of paediatric leukaemia patients. Methods Starting from our previously published results, we validate the expression level of LINC00958 in a cohort of 33 B-ALL and 9 T-ALL childhood patients, using in-silico public datasets as support. Expression levels of LINC00958 in B-ALL patients stratified by risk (high risk vs. standard/medium risk) and who relapsed 3 years after the first leukaemia diagnosis were also evaluated. Results We identified the lncRNA LINC00958 as a biomarker of B-ALL, capable of discriminating B-ALL from T-ALL and healthy subjects. Furthermore, we associated LINC00958 expression levels with the disease risk classification (high risk and standard risk). Finally, we show that LINC00958 can be used as a predictor of relapses in patients who are usually stratified as standard risk and thus not always targeted for marrow transplantation. Conclusions Our results open the way to new diagnostic perspectives that can be directly used in clinical practice for a better management of B-ALL paediatric patients.
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Affiliation(s)
| | | | | | - Peppino Mirabelli
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Alessandra Cianflone
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Giuliana Beneduce
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Antonia De Matteo
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
| | - Rosanna Parasole
- Department of Paediatric Haemato-Oncology, Santobono-Pausilipon Children's Hospital, AORN, Naples, Italy
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Komorowski L, Dabkowska A, Madzio J, Pastorczak A, Szczygiel K, Janowska M, Fidyt K, Bielecki M, Hunia J, Bajor M, Stoklosa T, Winiarska M, Patkowska E, Firczuk M. Concomitant inhibition of the thioredoxin system and nonhomologous DNA repair potently sensitizes Philadelphia-positive lymphoid leukemia to tyrosine kinase inhibitors. Hemasphere 2024; 8:e56. [PMID: 38486859 PMCID: PMC10938465 DOI: 10.1002/hem3.56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
Breakpoint cluster region-Abelson (BCR::ABL1) gene fusion is an essential oncogene in both chronic myeloid leukemia (CML) and Philadelphia-positive (Ph+) B-cell acute lymphoblastic leukemia (B-ALL). While tyrosine kinase inhibitors (TKIs) are effective in up to 95% of CML patients, 50% of Ph+ B-ALL cases do not respond to treatment or relapse. This calls for new therapeutic approaches for Ph+ B-ALL. Previous studies have shown that inhibitors of the thioredoxin (TXN) system exert antileukemic activity against B-ALL cells, particularly in combination with other drugs. Here, we present that peroxiredoxin-1 (PRDX1), one of the enzymes of the TXN system, is upregulated in Ph+ lymphoid as compared to Ph+ myeloid cells. PRDX1 knockout negatively affects the viability of Ph+ B-ALL cells and sensitizes them to TKIs. Analysis of global gene expression changes in imatinib-treated, PRDX1-deficient cells revealed that the nonhomologous end-joining (NHEJ) DNA repair is a novel vulnerability of Ph+ B-ALL cells. Accordingly, PRDX1-deficient Ph+ B-ALL cells were susceptible to NHEJ inhibitors. Finally, we demonstrated the potent efficacy of a novel combination of TKIs, TXN inhibitors, and NHEJ inhibitors against Ph+ B-ALL cell lines and primary cells, which can be further investigated as a potential therapeutic approach for the treatment of Ph+ B-ALL.
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Affiliation(s)
- Lukasz Komorowski
- Department of ImmunologyMedical University of WarsawWarsawPoland
- Postgraduate School of Molecular MedicineMedical University of WarsawWarsawPoland
| | - Agnieszka Dabkowska
- Department of ImmunologyMedical University of WarsawWarsawPoland
- Laboratory of Immunology, Mossakowski Medical Research InstitutePolish Academy of SciencesWarsawPoland
| | - Joanna Madzio
- Department of Pediatrics, Oncology and HematologyMedical University of LodzLodzPoland
| | - Agata Pastorczak
- Department of Pediatrics, Oncology and HematologyMedical University of LodzLodzPoland
| | - Kacper Szczygiel
- Department of ImmunologyMedical University of WarsawWarsawPoland
- Polpharma Biologics SAGdańskPoland
| | - Martyna Janowska
- Laboratory of Immunology, Mossakowski Medical Research InstitutePolish Academy of SciencesWarsawPoland
| | - Klaudyna Fidyt
- Department of ImmunologyMedical University of WarsawWarsawPoland
| | - Maksymilian Bielecki
- Department of PsychologySWPS University of Social Sciences and HumanitiesWarsawPoland
| | - Jaromir Hunia
- Department of ImmunologyMedical University of WarsawWarsawPoland
| | - Malgorzata Bajor
- Laboratory of Immunology, Mossakowski Medical Research InstitutePolish Academy of SciencesWarsawPoland
| | - Tomasz Stoklosa
- Department of Tumor Biology and GeneticsMedical University of WarsawWarsawPoland
| | - Magdalena Winiarska
- Department of ImmunologyMedical University of WarsawWarsawPoland
- Laboratory of Immunology, Mossakowski Medical Research InstitutePolish Academy of SciencesWarsawPoland
| | | | - Malgorzata Firczuk
- Department of ImmunologyMedical University of WarsawWarsawPoland
- Laboratory of Immunology, Mossakowski Medical Research InstitutePolish Academy of SciencesWarsawPoland
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6
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Shi ZY, Wang X, Chen WM, Li LD, Hao Y, Li JY, Sun K, Zhao XS, Jiang H, Jiang Q, Huang XJ, Qin YZ. ZNF384 fusion transcript levels for measurable residual disease monitoring in adult B-cell acute lymphoblastic leukemia. Hematol Oncol 2024; 42:e3251. [PMID: 38287528 DOI: 10.1002/hon.3251] [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: 08/13/2023] [Revised: 11/17/2023] [Accepted: 01/03/2024] [Indexed: 01/31/2024]
Abstract
Zinc finger protein 384 (ZNF384) rearrangement defined a novel subtype of B-cell acute lymphoblastic leukemia (B-ALL). The prognostic significance of ZNF384 fusion transcript levels represented measurable residual disease remains to be explored. ZNF384 fusions were screened out in 57 adult B-ALL patients at diagnosis by real-time quantitative polymerase chain reaction and their transcript levels were serially monitored during treatment. The reduction of ZNF384 fusion transcript levels at the time of achieving complete remission had no significant impact on survival, whereas its ≥2.5-log reduction were significantly associated with higher relapse free survival (RFS) and overall survival (OS) rates after course 1 consolidation (p = 0.022 and = 0.0083) and course 2 consolidation (p = 0.0025 and = 0.0008). Compared with chemotherapy alone, allogeneic hematopoietic stem cell transplantation (allo-HSCT) significantly improved RFS and OS of patients with <2.5-log reduction after course 1 consolidation (p < 0.0001 and = 0.0002) and course 2 consolidation (p = 0.0003 and = 0.019), whereas exerted no significant effects in patients with ≥2.5-log reduction (all p > 0.05). ZNF384 fusion transcript levels after course 1 and course 2 consolidation strongly predict relapse and survival and may guide whether receiving allo-HSCT in adult B-ALL.
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Affiliation(s)
- Zong-Yan Shi
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xu Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ling-Di Li
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yue Hao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Jin-Ying Li
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Kai Sun
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xiao-Su Zhao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Hao Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Qian Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xiao-Jun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
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7
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Li X, Le Y, Zhang Z, Nian X, Liu B, Yang X. Viral Vector-Based Gene Therapy. Int J Mol Sci 2023; 24:ijms24097736. [PMID: 37175441 PMCID: PMC10177981 DOI: 10.3390/ijms24097736] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Gene therapy is a technique involving the modification of an individual's genes for treating a particular disease. The key to effective gene therapy is an efficient carrier delivery system. Viral vectors that have been artificially modified to lose their pathogenicity are used widely as a delivery system, with the key advantages of their natural high transduction efficiency and stable expression. With decades of development, viral vector-based gene therapies have achieved promising clinical outcomes. Currently, the three key vector strategies are based on adeno-associated viruses, adenoviruses, and lentiviruses. However, certain challenges, such as immunotoxicity and "off-target", continue to exist. In the present review, the above three viral vectors are discussed along with their respective therapeutic applications. In addition, the major translational challenges encountered in viral vector-based gene therapies are summarized, and the possible strategies to address these challenges are also discussed.
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Affiliation(s)
- Xuedan Li
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Yang Le
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Zhegang Zhang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Xuanxuan Nian
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Bo Liu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Xiaoming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
- China National Biotech Group Company Limited, Beijing 100029, China
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8
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Kim Z, Lee JH. Neurofibromatosis Symptom-Lacking B-Cell Lineage Acute Lymphoblastic Leukemia with Only an NF1 Gene Pathogenic Variant. Diagnostics (Basel) 2023; 13:diagnostics13081486. [PMID: 37189588 DOI: 10.3390/diagnostics13081486] [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: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Next-generation sequencing technology has improved molecular genetic analysis, and many molecular genetic studies have been utilized for diagnostic classification, risk stratification, and prognosis prediction of acute lymphoblastic leukemia (ALL). Inactivation of neurofibromin or Nf1, a protein derived from the NF1 gene, causes Ras pathway regulation failure, which is related to leukemogenesis. Pathogenic variants of the NF1 gene in B-cell lineage ALL are uncommon, and in this study, we reported a pathogenic variant that is not registered in any public database. The patient diagnosed with B-cell lineage ALL had no clinical symptoms of neurofibromatosis. Studies on the biology, diagnosis, and treatment of this uncommon disease, as well as other related hematologic neoplasms, such as acute myeloid leukemia and juvenile myelomonocytic leukemia, were reviewed. Biological studies included epidemiological differences among age intervals and pathways for leukemia, such as the Ras pathway. Diagnostic studies included cytogenetic, FISH, and molecular tests for leukemia-related genes and ALL classification, such as Ph-like ALL or BCR-ABL1-like ALL. Treatment studies included pathway inhibitors and chimeric antigen cell receptor T-cells. Resistance mechanisms related to leukemia drugs were also investigated. We believe that these literature reviews will enhance medical care for the uncommon diagnosis of B-cell lineage ALL.
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Affiliation(s)
- Zehwan Kim
- Department of Laboratory Medicine, College of Medicine, Yeungnam University, Daegu 42415, Republic of Korea
| | - Jong Ho Lee
- Department of Laboratory Medicine, College of Medicine, Yeungnam University, Daegu 42415, Republic of Korea
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9
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Mukae J, Sadato D, Toya T, Watanabe S, Hirama C, Konuma R, Shimizu H, Najima Y, Kobayashi T, Kato M, Ohki K, Oboki K, Harada H, Ohashi K, Deguchi T, Harada Y, Doki N. Labile CD22 and CD19 expression in a case of Philadelphia chromosome-like acute lymphoblastic leukemia. Leuk Lymphoma 2022; 63:3261-3264. [PMID: 36102781 DOI: 10.1080/10428194.2022.2116936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Junichi Mukae
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Daichi Sadato
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takashi Toya
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Satoru Watanabe
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Chizuko Hirama
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Ryosuke Konuma
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Hiroaki Shimizu
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Yuho Najima
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Takeshi Kobayashi
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keisuke Oboki
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hironori Harada
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.,School of Life Sciences, Laboratory of Oncology, Tokyo University of Pharmacy & Life Sciences, Tokyo, Japan
| | - Kazuteru Ohashi
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Takao Deguchi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yuka Harada
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Noriko Doki
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
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10
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Rehn J, Mayoh C, Heatley SL, McClure BJ, Eadie LN, Schutz C, Yeung DT, Cowley MJ, Breen J, White DL. RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). PLoS Genet 2022; 18:e1010300. [PMID: 36251721 PMCID: PMC9612819 DOI: 10.1371/journal.pgen.1010300] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/27/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia (ALL) have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early. However, integrating RNA-seq in a clinical setting requires rapid detection and accurate reporting of clinically relevant alterations. Here we present RaScALL, an implementation of the k-mer based variant detection tool km, capable of identifying more than 100 prognostically significant lesions observed in ALL, including gene fusions, single nucleotide variants and focal gene deletions. We compared genomic alterations detected by RaScALL and those reported by alignment-based de novo variant detection tools in a study cohort of 180 Australian patient samples. Results were validated using 100 patient samples from a published North American cohort. RaScALL demonstrated a high degree of accuracy for reporting subtype defining genomic alterations. Gene fusions, including difficult to detect fusions involving EPOR and DUX4, were accurately identified in 98% of reported cases in the study cohort (n = 164) and 95% of samples (n = 63) in the validation cohort. Pathogenic sequence variants were correctly identified in 75% of tested samples, including all cases involving subtype defining variants PAX5 p.P80R (n = 12) and IKZF1 p.N159Y (n = 4). Intragenic IKZF1 deletions resulting in aberrant transcript isoforms were also detectable with 98% accuracy. Importantly, the median analysis time for detection of all targeted alterations averaged 22 minutes per sample, significantly shorter than standard alignment-based approaches. The application of RaScALL enables rapid identification and reporting of previously identified genomic alterations of known clinical relevance.
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Affiliation(s)
- Jacqueline Rehn
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Chelsea Mayoh
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Susan L Heatley
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
| | - Barbara J McClure
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura N Eadie
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Caitlin Schutz
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - David T Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia
| | - Mark J Cowley
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - James Breen
- Black Ochre Data Labs, Telethon Kids Institute, Adelaide, South Australia, Australia
- Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Deborah L White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
- Australian Genomics Health Alliance (AGHA), Parkville, Victoria, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
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11
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Zhang L, Habeebu SSM, Li W. Prognostic and Predictive Biomarkers in Precursor B-cell Acute Lymphoblastic Leukemia. Leukemia 2022. [DOI: 10.36255/exon-publications-leukemia-biomarkers-lymphoblastic-leukemia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Uckun FM, Qazi S. Tyrosine kinases in KMT2A/MLL-rearranged acute leukemias as potential therapeutic targets to overcome cancer drug resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:902-916. [PMID: 36627892 PMCID: PMC9771742 DOI: 10.20517/cdr.2022.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/25/2022] [Accepted: 09/26/2022] [Indexed: 12/23/2022]
Abstract
Aim: The main goal of this study was to elucidate at the transcript level the tyrosine kinase expression profiles of primary leukemia cells from mixed lineage leukemia 1 gene rearranged (KMT2A/MLL-R+) acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) patients. Methods: We evaluated protein tyrosine kinase (PTK) gene expression profiles of primary leukemic cells in KMT2A/MLL-R+ AML and ALL patients using publicly available archived datasets. Results: Our studies provided unprecedented evidence that the genetic signatures of KMT2A/MLL-R+ AML and ALL cells are characterized by transcript-level overexpression of specific PTK. In infants, children and adults with KMT2A/MLL-R+ ALL, as well as pediatric patients with KMT2A/MLL-R+ AML, the gene expression levels for FLT3, BTK, SYK, JAK2/JAK3, as well as several SRC family PTK were differentially amplified. In adults with KMT2A/MLL-R+ AML, the gene expression levels for SYK, JAK family kinase TYK2, and the SRC family kinases FGR and HCK were differentially amplified. Conclusion: These results provide new insights regarding the clinical potential of small molecule inhibitors of these PTK, many of which are already FDA/EMA-approved for other indications, as components of innovative multi-modality treatment platforms against KMT2A/MLL-R+ acute leukemias.
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Affiliation(s)
- Fatih M. Uckun
- Correspondence to: Dr. Fatih M. Uckun, Ares Pharmaceuticals, 12590 Ethan Ave N, St. Paul, MN 55110, USA. E-mail:
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