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Lizcova L, Prihodova E, Pavlistova L, Svobodova K, Mejstrikova E, Hrusak O, Luknarova P, Janotova I, Sramkova L, Stary J, Zemanova Z. Cytogenomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals TCR rearrangements as predictive factors for exceptional prognosis. Mol Cytogenet 2024; 17:14. [PMID: 38783324 PMCID: PMC11118568 DOI: 10.1186/s13039-024-00682-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND T-cell acute lymphoblastic leukemia (T-ALL) represents a rare and clinically and genetically heterogeneous disease that constitutes 10-15% of newly diagnosed pediatric ALL cases. Despite improved outcomes of these children, the survival rate after relapse is extremely poor. Moreover, the survivors must also endure the acute and long-term effects of intensive therapy. Although recent studies have identified a number of recurrent genomic aberrations in pediatric T-ALL, none of the changes is known to have prognostic significance. The aim of our study was to analyze the cytogenomic changes and their various combinations in bone marrow cells of children with T-ALL and to correlate our findings with the clinical features of the subjects and their treatment responses. RESULTS We performed a retrospective and prospective comprehensive cytogenomic analysis of consecutive cohort of 66 children (46 boys and 20 girls) with T-ALL treated according to BFM-based protocols and centrally investigated cytogenetics and immunophenotypes. Using combinations of cytogenomic methods (conventional cytogenetics, FISH, mFISH/mBAND, arrayCGH/SNP and MLPA), we identified chromosomal aberrations in vast majority of patients (91%). The most frequent findings involved the deletion of CDKN2A/CDKN2B genes (71%), T-cell receptor (TCR) loci translocations (27%), and TLX3 gene rearrangements (23%). All chromosomal changes occurred in various combinations and were rarely found as a single abnormality. Children with aberrations of TCR loci had a significantly better event free (p = 0.0034) and overall survival (p = 0.0074), all these patients are living in the first complete remission. None of the abnormalities was an independent predictor of an increased risk of relapse. CONCLUSIONS We identified a subgroup of patients with TCR aberrations (both TRA/TRD and TRB), who had an excellent prognosis in our cohort with 5-year EFS and OS of 100%, regardless of the presence of other abnormality or the translocation partner. Our data suggest that escalation of treatment intensity, which may be considered in subsets of T-ALL is not needed for nonHR (non-high risk) patients with TCR aberrations.
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Affiliation(s)
- Libuse Lizcova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.
| | - Eva Prihodova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lenka Pavlistova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Karla Svobodova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ester Mejstrikova
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague and University Hospital Motol, Prague, Czech Republic
| | - Ondrej Hrusak
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague and University Hospital Motol, Prague, Czech Republic
| | - Pavla Luknarova
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague and University Hospital Motol, Prague, Czech Republic
| | - Iveta Janotova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague and University Hospital Motol, Prague, Czech Republic
| | - Lucie Sramkova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague and University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague and University Hospital Motol, Prague, Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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Yang R, Ai Y, Bai T, Lu XX, He G. Williams-Beuren syndrome in pediatric T-cell acute lymphoblastic leukemia: A rare case report and review of literature. Medicine (Baltimore) 2024; 103:e36976. [PMID: 38363891 PMCID: PMC10869033 DOI: 10.1097/md.0000000000036976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/22/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Williams-Beuren syndrome (WBS) is a rare genetic disorder caused by hemizygous microdeletion of contiguous genes on chromosome 7q11.23. Although the phenotype features extensive heterogeneity in severity and performance, WBS is not considered to be a predisposing factor for cancer development. Currently, hematologic cancers, mainly Burkitt lymphoma, are rarely reported in patients with WBS. Here in, we report a unique case of T-cell acute lymphoblastic leukemia in a male child with WBS. METHODS This retrospective study analyzed the clinical data of this case receiving chemotherapy were analyzed. This is a retrospective study. RESULTS The patient, who exhibited a typical WBS phenotype and presented with hemorrhagic spots. Chromosomal genome-wide chip analysis (CMA) revealed abnormalities on chromosomes 7 and 9. The fusion gene STIL-TAL1 and mutations in BCL11B, NOTCH1, and USP7 have also been found and all been associated with the occurrence of T-cell leukemia. The patient responded well to the chemotherapy. CONCLUSION To the best of our knowledge, this is the first reported case of WBS in T-cell acute lymphoblastic leukemia. We want to emphasize that the occurrence of leukemia in this patient might be related to the loss of 7q11.23 and microdeletion of 9p21.3 (including 3 TSGs), but the relationship between WBS and malignancy remains unclear. Further studies are required to clarify the relationship between WBS and malignancy.
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Affiliation(s)
- Rong Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yuan Ai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Ting Bai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiao-Xi Lu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Guoqian He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
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3
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Ampatzidou M, Papadhimitriou SI, Paisiou A, Paterakis G, Tzanoudaki M, Papadakis V, Florentin L, Polychronopoulou S. The Prognostic Effect of CDKN2A/2B Gene Deletions in Pediatric Acute Lymphoblastic Leukemia (ALL): Independent Prognostic Significance in BFM-Based Protocols. Diagnostics (Basel) 2023; 13:diagnostics13091589. [PMID: 37174980 PMCID: PMC10178600 DOI: 10.3390/diagnostics13091589] [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: 03/31/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
One of the most frequent genes affected in pediatric ALL is the CDKN2A/2B gene, acting as a secondary cooperating event and playing an important role in cell-cycle regulation and chemosensitivity. Despite its inclusion in combined CNA (copy-number alterations) classifiers, like the IKZF1plus entity and the UKALL CNA profile, the prognostic impact of the individual gene deletions outside the context of a combined CNA evaluation remains controversial. Addressing the CDKN2A/2B deletions' additive prognostic effect in current risk-stratification algorithms, we present a retrospective study of a Greek pediatric ALL cohort comprising 247 patients studied over a 24-year period (2000-2023). Herein, we provide insight regarding the correlation with disease features, MRD clearance, and independent prognostic significance for this ALL cohort treated with contemporary BFM-based treatment protocols. Within an extended follow-up time of 135 months, the presence of the CDKN2A/2B deletions (biallelic or monoallelic) was associated with inferior EFS rates (65.1% compared to 91.8% for the gene non-deleted subgroup, p < 0.001), with the relapse rate accounting for 22.2% and 5.9%, respectively (p < 0.001). The presence of the biallelic deletion was associated with the worst outcomes (EFS 57.2% vs. 89.6% in the case of any other status, monoallelic or non-deleted, p < 0.001). Survival differences were demonstrated for B-ALL cases (EFS 65.3% vs. 93.6% for the non-deleted B-ALL subgroup, p < 0.001), but the prognostic effect was not statistically significant within the T-ALL cohort (EFS 64.3 vs. 69.2, p = 0.947). The presence of the CDKN2A/2B deletions clearly correlated with inferior outcomes within all protocol-defined risk groups (standard risk (SR): EFS 66.7% vs. 100%, p < 0.001, intermediate risk (IR): EFS 77.1% vs. 97.9%, p < 0.001, high risk (HR): EFS 42.1% vs. 70.5% p < 0.001 for deleted vs non-deleted cases in each patient risk group); additionally, in this study, the presence of the deletion differentiated prognosis within both MRD-positive and -negative subgroups on days 15 and 33 of induction. In multivariate analysis, the presence of the CDKN2A/2B deletions was the most important prognostic factor for relapse and overall survival, yielding a hazard ratio of 5.2 (95% confidence interval: 2.59-10.41, p < 0.001) and 5.96 (95% confidence interval: 2.97-11.95, p < 0.001), respectively, designating the alteration's independent prognostic significance in the context of modern risk stratification. The results of our study demonstrate that the presence of the CDKN2A/2B deletions can further stratify all existing risk groups, identifying patient subgroups with different outcomes. The above biallelic deletions could be incorporated into future risk-stratification algorithms, refining MRD-based stratification. In the era of targeted therapies, future prospective controlled clinical trials will further explore the possible use of cyclin-dependent kinase inhibitors (CDKIs) in CDKN2A/2B-affected ALL pediatric subgroups.
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Affiliation(s)
- Mirella Ampatzidou
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Stefanos I Papadhimitriou
- Laboratory of Hematology, Unit of Molecular Cytogenetics, "G. Gennimatas" General Hospital, 11527 Athens, Greece
| | - Anna Paisiou
- Bone Marrow Transplantation Unit, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Georgios Paterakis
- Laboratory of Flow Cytometry, Department of Immunology, "G. Gennimatas" General Hospital, 11527 Athens, Greece
| | - Marianna Tzanoudaki
- Department of Immunology, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Vassilios Papadakis
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Lina Florentin
- Alfa Laboratory Diagnostic Center, YGEIA Hospital, 11524 Athens, Greece
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
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Eisa YA, Guo Y, Yang FC. The Role of PHF6 in Hematopoiesis and Hematologic Malignancies. Stem Cell Rev Rep 2023; 19:67-75. [PMID: 36008597 DOI: 10.1007/s12015-022-10447-4] [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] [Accepted: 08/11/2022] [Indexed: 01/29/2023]
Abstract
Epigenetic regulation of gene expression represents an important mechanism in the maintenance of stem cell function. Alterations in epigenetic regulation contribute to the pathogenesis of hematological malignancies. Plant homeodomain finger protein 6 (PHF6) is a member of the plant homeodomain (PHD)-like zinc finger family of proteins that is involved in transcriptional regulation through the modification of the chromatin state. Germline mutation of PHF6 is the causative genetic alteration of the X-linked mental retardation Borjeson-Forssman-Lehmann syndrome (BFLS). Somatic mutations in PHF6 are identified in human leukemia, such as adult T-cell acute lymphoblastic leukemia (T-ALL, ~ 38%), pediatric T-ALL (~ 16%), acute myeloid leukemia (AML, ~ 3%), chronic myeloid leukemia (CML, ~ 2.5%), mixed phenotype acute leukemia (MPAL, ~ 20%), and high-grade B-cell lymphoma (HGBCL, ~ 3%). More recent studies imply an oncogenic effect of PHF6 in B-cell acute lymphoblastic leukemia (B-ALL) and solid tumors. These data demonstrate that PHF6 could act as a double-edged sword, either a tumor suppressor or an oncogene, in a lineage-dependent manner. However, the underlying mechanisms of PHF6 in normal hematopoiesis and leukemogenesis remain largely unknown. In this review, we summarize current knowledge of PHF6, emphasizing the role of PHF6 in hematological malignancies. Epigenetic regulation of PHF6 in B-ALL. PHF6 maintains a chromatin structure that is permissive to B-cell identity genes, but not T-cell-specific genes (left). Loss of PHF6 leads to aberrant expression of B-cell- and T-cell-specific genes resulting from lineage promiscuity and binding of T-cell transcription factors (right).
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Affiliation(s)
- Yusra A Eisa
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Ying Guo
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Feng-Chun Yang
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA. .,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA.
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5
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Catarino TA, Pacheco-Leyva I, Al-Dalali F, Ghezzo MN, Fernandes MT, Costa T, Dos Santos NR. Cdkn2a inactivation promotes malignant transformation of mouse immature thymocytes before the β-selection checkpoint. Exp Hematol 2022; 116:30-36. [PMID: 36240953 DOI: 10.1016/j.exphem.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/14/2022] [Accepted: 10/02/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Telmo A Catarino
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ivette Pacheco-Leyva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Faiza Al-Dalali
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
| | | | | | - Telma Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Nuno R Dos Santos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Centre for Biomedical Research, University of Algarve, Faro, Portugal.
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6
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Elderdery AY, Alhamidi AH, Elkhalifa AME, Althobiti MM, Eltayeb Omer N, Alsugoor MH, Alsuhaymi N, Atebien EM, Hamza SMA, Alzahrani B, Alanazi F, Subbiah SK, Mok PL. Synthesis, Characterization, and Antimicrobial and Antiproliferative Effects of CuO-TiO 2-Chitosan-Escin Nanocomposites on Human Leukemic MOLT4 Cells. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12213753. [PMID: 36364538 PMCID: PMC9655830 DOI: 10.3390/nano12213753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/15/2022] [Accepted: 10/19/2022] [Indexed: 05/13/2023]
Abstract
Nanocomposites comprised of CuO-TiO2-chitosan-escin, which has adjustable physicochemical properties, provide a solution for therapeutic selectivity in cancer treatment. By controlling the intrinsic signaling primarily through the mitochondrial signaling pathway, we desired nanocomposites with enhanced anticancer activity by containing CuO-TiO2-chitosan-escin. The metal oxides CuO and TiO2, the natural polymer chitosan, and a phytochemical compound escin were combined to form CuO-TiO2-chitosan-escin nanocomposites. The synthesized nanocomposites were confirmed and characterized using FTIR spectroscopy, TEM, and UV-Vis absorption spectroscopy. A human leukemia cell line (MOLT-4) was used to assess the efficacy and selectivity of nanocomposites. Based on a cytotoxicity study, CuO-TiO2-chitosan-escin nanocomposites had inhibition concentrations (IC50) of 13.68, 8.9, and 7.14 µg/mL against human T lymphoblast cells after 24, 48, and 72 h of incubation, respectively. Compared with untreated MOLT-4 cells, CuO-TiO2-chitosan-escin nanocomposite-treated cells significantly increased (p < 0.05) caspase-3, -8, and -9 and decreased the levels of antioxidant enzymes GR, SOD, and GSH. Furthermore, MDA for lipid peroxidase and ROS levels significantly increased (p < 0.05) in the treated cells than in the untreated cells. Remarkably, CuO-TiO2-chitosan-escin nanocomposite-mediated control of cell cycles were mainly achieved through the activation of caspase-3, -8, and -9.
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Affiliation(s)
- Abozer Y. Elderdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia
- Health Sciences Research Unit, Jouf University, Sakaka 42421, Saudi Arabia
- Correspondence: (A.Y.E.); (P.L.M.)
| | - Abdulaziz H. Alhamidi
- Clinical Laboratory Sciences Department, College of Applied Medical Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed M. E. Elkhalifa
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh 13316, Saudi Arabia
| | - Maryam M. Althobiti
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Shaqra 15572, Saudi Arabia
| | | | - Mahdi H. Alsugoor
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Makkah 21912, Saudi Arabia
| | - Naif Alsuhaymi
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Makkah 21912, Saudi Arabia
| | - Entesar M. Atebien
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Shaqra 15572, Saudi Arabia
| | - Siddiqa M. A. Hamza
- College of Medicine, Department of Pathology, Umm Alqura University Algunfuda, Mecca 24382, Saudi Arabia
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia
| | - Fehaid Alanazi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences-AlQurayyat, Jouf University, Sakaka 42421, Saudi Arabia
| | - Suresh Kumar Subbiah
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Chennai 600073, India
| | - Pooi Ling Mok
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: (A.Y.E.); (P.L.M.)
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7
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Feng J, Guo Y, Yang W, Zou Y, Zhang L, Chen Y, Zhang Y, Zhu X, Chen X. Childhood Acute B-Lineage Lymphoblastic Leukemia With CDKN2A/B Deletion Is a Distinct Entity With Adverse Genetic Features and Poor Clinical Outcomes. Front Oncol 2022; 12:878098. [PMID: 35712467 PMCID: PMC9195293 DOI: 10.3389/fonc.2022.878098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
To further emphasize the clinical-genetic features and prognosis of CDKN2A/B deletions in childhood acute lymphoblastic leukemia (ALL), we retrospectively analyzed 819 consecutive B-ALL patients treated with the Chinese Children's Cancer Group ALL-2015 (CCCG-ALL-2015) protocol, and fluorescence in situ hybridization (FISH) analysis on CDKN2A/B deletion was available for 599 patients. The prevalence of CDKN2A/B gene deletions was 20.2% (121/599) of B-ALL. CDKN2A/B deletions were significantly associated with older age, higher leukocyte counts, a higher percentage of hepatosplenomegaly, and a higher frequency of BCR-ABL (p < 0.05). Those patients achieved similar minimal residual disease (MRD) clearance and complete remission compared to patients without CDKN2A/B deletion. The CDKN2A/B deletions were correlated with inferior outcomes, including a 3-year event-free survival (EFS) rate (69.8 ± 4.6 vs. 89.2 ± 1.6%, p = 0.000) and a 3-year overall survival (OS) rate (89.4% ± 2.9% vs. 94.7% ± 1.1%, p = 0.037). In multivariable analysis, CDKN2A/B deletion was still an independent prognostic factor for EFS in total cohorts (p < 0.05). We also detected a multiplicative interaction between CDKN2A/B deletions and TP53 deletion on dismal prognosis (p-interaction < 0.05). In conclusion, CDKN2A/B deletion is associated with distinct characteristics and serves as a poor prognostic factor in pediatric ALL, especially in TP53 deletion carriers.
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Affiliation(s)
- Jing Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ye Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wenyu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yumei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaojuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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8
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Mansur MB, Furness CL, Nakjang S, Enshaei A, Alpar D, Colman SM, Minto L, Irving J, Poole BV, Noronha EP, Savola S, Iqbal S, Gribben J, Pombo-de-Oliveira MS, Ford TM, Greaves MF, van Delft FW. The genomic landscape of teenage and young adult T-cell acute lymphoblastic leukemia. Cancer Med 2021; 10:4864-4873. [PMID: 34080325 PMCID: PMC8290240 DOI: 10.1002/cam4.4024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/09/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Treatment on risk adapted intensive pediatric protocols has improved outcome for teenagers and young adults (TYA) with T-cell acute lymphoblastic leukemia (T-ALL). Understanding the biology of disease in this age group and the genetic basis of relapse is a key goal as patients with relapsed/refractory disease have poor outcomes with conventional chemotherapy and novel molecular targets are required. This study examines the question of whether TYA T-ALL has a specific biological-molecular profile distinct from pediatric or adult T-ALL. METHODS Genomic characterization was undertaken of a retrospective discovery cohort of 80 patients aged 15-26 years with primary or relapsed T-ALL, using a combination of Genome-Wide Human SNP Array 6.0, targeted gene mutation and promoter methylation analyses. Findings were confirmed by MLPA, real-time quantitative PCR, and FISH. Whole Exome Sequencing was performed in 4 patients with matched presentation and relapse to model clonal evolution. A prevalence analysis was performed on a final data set of 1,792 individual cases to identify genetic lesions with age specific frequency patterns, including 972 pediatric (1-14 years), 439 TYA (15-24 years) and 381 adult (≥25 years) cases. These cases were extracted from 19 publications with comparable genomic data identified through a PubMed search. RESULTS Genomic characterization of this large cohort of TYA T-ALL patients identified recurrent isochromosome 7q i(7q) in our discovery cohort (n = 3). Prevalence analysis did not identify any age specific genetic abnormalities. Genomic analysis of 6 pairs of matched presentation - relapsed T-ALL established that all relapses were clonally related to the initial leukemia. Whole exome sequencing analysis revealed recurrent, targetable, mutations disrupting NOTCH, PI3K/AKT/mTOR, FLT3, NRAS as well as drug metabolism pathways. CONCLUSIONS All genetic aberrations in TYA T-ALL occurred with an incidence similar or intermediate to that reported in the pediatric and adult literature, demonstrating that overall TYA T-ALL exhibits a transitional genomic profile. Analysis of matched presentation - relapse supported the hypothesis that relapse is driven by the Darwinian evolution of sub-clones associated with drug resistance (NT5C2 and TP53 mutations) and re-iterative mutation of known key T-ALL drivers, including NOTCH1.
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Affiliation(s)
- Marcela B Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Division of Clinical Research, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Amir Enshaei
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Donat Alpar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sue M Colman
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Lynne Minto
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Julie Irving
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Beth V Poole
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Elda P Noronha
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Suvi Savola
- Oncogenetics, MRC-Holland, Amsterdam, The Netherlands
| | - Sameena Iqbal
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Tony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mel F Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Frederik W van Delft
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
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9
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Wang HP, Zhou YL, Huang X, Zhang Y, Qian JJ, Li JH, Li XY, Li CY, Lou YJ, Mai WY, Meng HT, Yu WJ, Tong HY, Jin J, Zhu HH. CDKN2A deletions are associated with poor outcomes in 101 adults with T-cell acute lymphoblastic leukemia. Am J Hematol 2021; 96:312-319. [PMID: 33306218 DOI: 10.1002/ajh.26069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
The identification of genetic risk subgroups of T-cell acute lymphoblastic leukemia (T-ALL) may provide evidence for risk stratification and individualized treatment. We investigated the characteristics and prognostic value of tumor suppressor gene CDKN2A deletions in 101 patients with T-ALL. The CDKN2A deletion was present in 23% (23/101) of T-ALL by fluorescence in situ hybridization (FISH). The most common type of CDKN2A deletion was homozygous deletion (70%, 16/23). A lower frequency of CDKN2A deletion was found in patients with early T-cell precursor (ETP) ALL than in patients with non-ETP-ALL (10.4% vs 34.0%; P = .008). Deletion of CDKN2A was significantly associated with younger age (P = .001), higher white blood cell (WBC) count (P < .001) and higher lactate dehydrogenase (LDH) level (P = .002). Patients with CDKN2A deletion had lower 2-year overall survival (OS) and event-free survival (EFS) rates than patients without CDKN2A deletion (2-year OS: 18.6% ± 8.9% vs 47.4% ± 6.2%, P = .032; EFS: 16.4 ± 8.3 vs 38.6 ± 5.9%, P = .022). In multivariable analysis, CDKN2A deletion was an independent adverse prognostic factor for OS (P = .016). In conclusion, adult T-ALL patients with CDKN2A deletion had a poor prognosis, and these patients might benefit from intensive chemotherapy or allogeneic hematopoietic stem-cell transplantation.
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Affiliation(s)
- Huan-Ping Wang
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Yi-Le Zhou
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Xin Huang
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Yi Zhang
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Jie-Jing Qian
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Jian-Hu Li
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Xue-Ying Li
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Chen-Ying Li
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Yin-Jun Lou
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Wen-Yuan Mai
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Hai-Tao Meng
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Wen-Juan Yu
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Hong-Yan Tong
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Jie Jin
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Hong-Hu Zhu
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
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10
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González-Gil C, Ribera J, Ribera JM, Genescà E. The Yin and Yang-Like Clinical Implications of the CDKN2A/ARF/CDKN2B Gene Cluster in Acute Lymphoblastic Leukemia. Genes (Basel) 2021; 12:genes12010079. [PMID: 33435487 PMCID: PMC7827355 DOI: 10.3390/genes12010079] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant clonal expansion of lymphoid hematopoietic precursors that exhibit developmental arrest at varying stages of differentiation. Similar to what occurs in solid cancers, transformation of normal hematopoietic precursors is governed by a multistep oncogenic process that drives initiation, clonal expansion and metastasis. In this process, alterations in genes encoding proteins that govern processes such as cell proliferation, differentiation, and growth provide us with some of the clearest mechanistic insights into how and why cancer arises. In such a scenario, deletions in the 9p21.3 cluster involving CDKN2A/ARF/CDKN2B genes arise as one of the oncogenic hallmarks of ALL. Deletions in this region are the most frequent structural alteration in T-cell acute lymphoblastic leukemia (T-ALL) and account for roughly 30% of copy number alterations found in B-cell-precursor acute lymphoblastic leukemia (BCP-ALL). Here, we review the literature concerning the involvement of the CDKN2A/B genes as a prognosis marker of good or bad response in the two ALL subtypes (BCP-ALL and T-ALL). We compare frequencies observed in studies performed on several ALL cohorts (adult and child), which mainly consider genetic data produced by genomic techniques. We also summarize what we have learned from mouse models designed to evaluate the functional involvement of the gene cluster in ALL development and in relapse/resistance to treatment. Finally, we examine the range of possibilities for targeting the abnormal function of the protein-coding genes of this cluster and their potential to act as anti-leukemic agents in patients.
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Affiliation(s)
- Celia González-Gil
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
| | - Jordi Ribera
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
| | - Josep Maria Ribera
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, 08916 Badalona, Spain
| | - Eulàlia Genescà
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
- Correspondence: ; Tel.: +34-93-557-28-08
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11
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Khodzhaev K, Ng OH, Tugcu D, Erbilgin Y, Ng YY, Celkan T, Timur C, Karakas Z, Ozdemir GN, Yıldırmak Y, Sayitoglu M. High
TUBB2A
expression in childhood T‐ALL is correlated with the clinical outcome. Int J Lab Hematol 2020. [DOI: 10.1111/ijlh.13235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Khusan Khodzhaev
- Genetics Department Aziz Sancar Institute of Experimental Medicine Istanbul University Istanbul Turkey
- Istanbul University Institute of Health Sciences Istanbul Turkey
| | - Ozden Hatirnaz Ng
- Department of Medical Biology School of Medicine Acibadem Mehmet Ali Aydinlar University Istanbul Turkey
| | - Deniz Tugcu
- Pediatric Hematology Oncology Department Istanbul Faculty of Medicine Istanbul University Istanbul Turkey
| | - Yucel Erbilgin
- Genetics Department Aziz Sancar Institute of Experimental Medicine Istanbul University Istanbul Turkey
| | - Yuk Yin Ng
- Genetics and Bioengineering Department Istanbul Bilgi University Istanbul Turkey
| | - Tiraje Celkan
- Pediatric Hematology Oncology Department Istanbul University‐Cerrahpasa Faculty of Medicine Istanbul Turkey
| | - Cetin Timur
- Pediatric Hematology Oncology Department Seven Hill Hospital Istanbul Turkey
| | - Zeynep Karakas
- Pediatric Hematology Oncology Department Istanbul Faculty of Medicine Istanbul University Istanbul Turkey
| | - Gul Nihal Ozdemir
- Pediatric Hematology Oncology Department Istanbul University‐Cerrahpasa Faculty of Medicine Istanbul Turkey
- Pediatric Hematology Division Istanbul Kanuni Sultan Suleyman Education and Research Hospital Istanbul Turkey
| | - Yıldız Yıldırmak
- Pediatric Hematology Division Ministry of Health Sisli Etfal Education and Research Hospital Istanbul Turkey
| | - Muge Sayitoglu
- Genetics Department Aziz Sancar Institute of Experimental Medicine Istanbul University Istanbul Turkey
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12
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Lejman M, Włodarczyk M, Styka B, Pastorczak A, Zawitkowska J, Taha J, Sędek Ł, Skonieczka K, Braun M, Haus O, Szczepański T, Młynarski W, Kowalczyk JR. Advantages and Limitations of SNP Array in the Molecular Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2020; 10:1184. [PMID: 32766158 PMCID: PMC7379740 DOI: 10.3389/fonc.2020.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge regarding the association of whole-genome copy number abnormalities (CNAs) in childhood T-ALL with the course of leukemia and its outcome. The aim of this study was to identify the pattern of whole-genome CNAs in 86 newly diagnosed childhood T-ALL cases using a high-density single-nucleotide polymorphism array. We analyzed the presence of whole-genome CNAs with respect to immunophenotype, clinical features, and treatment outcomes. A total of 769 CNAs, including trisomies, duplications, deletions, and segmental loss of heterozygosity, were detected in 86 analyzed samples. Gain or loss of chromosomal regions exceeding 10 Mb occurred in 46 cases (53%), including six cases (7%) with complex chromosomal alterations. We observed that microdeletions in selected genes (e.g., FIP1L1 and PDGFRB) were related to the clinical features. Interestingly, 13% of samples have a duplication of the two loci (MYB and AIH1—6q23.3), which never occurred alone. Single-nucleotide polymorphism array significantly improved the molecular characterization of pediatric T-ALL. Further studies with larger cohorts of patients may contribute to the selection of prognostic CNAs in this group of patients.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Borys Styka
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Agata Pastorczak
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Joanna Taha
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Łukasz Sędek
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Skonieczka
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Łódz, Łódź, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Tomasz Szczepański
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Wojciech Młynarski
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
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13
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Jang W, Park J, Kwon A, Choi H, Kim J, Lee GD, Han E, Jekarl DW, Chae H, Han K, Yoon JH, Lee S, Chung NG, Cho B, Kim M, Kim Y. CDKN2B downregulation and other genetic characteristics in T-acute lymphoblastic leukemia. Exp Mol Med 2019; 51:1-15. [PMID: 30635552 PMCID: PMC6329696 DOI: 10.1038/s12276-018-0195-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/14/2023] Open
Abstract
We identified principal genetic alterations in 97.1% (99/102) of patients with T-acute lymphoblastic leukemia (T-ALL) using integrative genetic analyses, including massive parallel sequencing and multiplex ligation-dependent probe amplification (MLPA). A total of 133 mutations were identified in the following genes in descending order: NOTCH1 (66.7%), FBXW7 (19.6%), PHF6 (15.7%), RUNX1 (12.7%), NRAS (10.8%), and DNMT3A (9.8%). Copy number alterations were most frequently detected in CDKN2B, CDKN2A, and genes on 9p21.3 in T-ALL (45.1%). Gene expression data demonstrated the downregulation of CDKN2B in most cases of T-ALL, whereas CDKN2A downregulation was mainly restricted to deletions. Additional quantitative methylation analysis demonstrated that CDKN2B downregulation stemmed from deletion and hypermethylation. Analysis of 64 patients with CDKN2B hypermethylation indicated an association with an older age of onset and early T cell precursor ALL, which involved very early arrest of T cell differentiation. Genes associated with methylation and myeloid neoplasms, including DNMT3A and NRAS, were more commonly mutated in T-ALL with CDKN2B hypermethylation. In particular, a CDKN2B biallelic deletion or high methylation level (≥45%), the age of onset, and the GATA3 and SH2B3 mutations were factors associated with a poor prognosis. This study clarifies that one of the most important genetic events in T-ALL, namely, CDKN2B downregulation, occurs mechanistically via deletion and hypermethylation. Different susceptible genetic backgrounds exist based on the CDKN2B downregulation mechanism.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungja Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Ho Yoon
- Department of Hematology, Leukemia Research Institute, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seok Lee
- Department of Hematology, Leukemia Research Institute, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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14
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Papenhausen P, Kelly CA, Zhang Z, Tepperberg J, Burnside RD, Schwartz S. Multidisciplinary analysis of pediatric T-ALL: 9q34 gene fusions. Cancer Genet 2018; 231-232:1-13. [PMID: 30803551 DOI: 10.1016/j.cancergen.2018.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 12/13/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is not as frequently reported as the B-cell counterpart (B-ALL), only occurring in about 15% of pediatric cases with a typically heterogeneous etiology. Approximately 8% of childhood T-ALL cases have rearrangements involving the ABL1 tyrosine kinase gene at 9q34.12; although a t(9;22), resulting in a fusion of ABL1 with the BCR gene at 22q11.23 is a common occurrence in B-ALL, it is not a typical finding in T-ALL. A subset of 10 of 40 documented cases of T-ALL analyzed over a 5-year period is presented, each having gene rearrangements within band 9q34 that resulted in fusions other than BCR/ABL1. These cases included fusions involving ABL1, SET (9q34.11), NUP214 (9q34.13), SPTAN1 (9p34.11), and TNRC6B (22q13.1). Among the 10 cases are: six SET/NUP214 fusions, two ABL1/NUP214 fusions (one of which was associated with episomal amplification) and novel SPTAN1/ABL1 and TNRC6B/ABL1 fusions. The evaluations of these clones were each significantly aided by FISH analysis, which directed subsequent microarray and anchored multiplex PCR testing for fusion confirmations.
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Affiliation(s)
- Peter Papenhausen
- Laboratory Corporation of America, 1904 TW Alexander Drive, Research Triangle Park, NC 27709, United States.
| | - Carla A Kelly
- Laboratory Corporation of America, 1904 TW Alexander Drive, Research Triangle Park, NC 27709, United States.
| | - Zhenxi Zhang
- Laboratory Corporation of America, 3400 Computer Drive, Westborough, MA 01581, United States.
| | - James Tepperberg
- Laboratory Corporation of America, 1904 TW Alexander Drive, Research Triangle Park, NC 27709, United States.
| | - Rachel D Burnside
- Laboratory Corporation of America, 1904 TW Alexander Drive, Research Triangle Park, NC 27709, United States.
| | - Stuart Schwartz
- Laboratory Corporation of America, 1904 TW Alexander Drive, Research Triangle Park, NC 27709, United States.
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15
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Olsson L, Lundin-Ström KB, Castor A, Behrendtz M, Biloglav A, Norén-Nyström U, Paulsson K, Johansson B. Improved cytogenetic characterization and risk stratification of pediatric acute lymphoblastic leukemia using single nucleotide polymorphism array analysis: A single center experience of 296 cases. Genes Chromosomes Cancer 2018; 57:604-607. [PMID: 30203896 DOI: 10.1002/gcc.22664] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/14/2018] [Accepted: 06/18/2018] [Indexed: 01/21/2023] Open
Abstract
Single nucleotide polymorphism array (SNP-A) analyses are increasingly being introduced in routine genetic diagnostics of acute lymphoblastic leukemia (ALL). Despite this, only few studies that have compared the diagnostic value of SNP-A with conventional chromosome banding have been published. We here report such a comparison of 296 ALL cases, the largest series to date. Only genomic imbalances >5 Mb and microdeletions targeting the BTG1, CDKN2A/B, EBF1, ERG, ETV6, IKZF1, PAX5, and RB1 genes and the pseudoautosomal region 1 (PAR1) were ascertained, in agreement with recent guidelines. Of 36 T-cell ALL cases, the karyotypes of 24 cases (67%) were revised by SNP-A analyses that either revealed additional imbalances >5 Mb or better characterized the changes found by G-banding. Of 260 B-cell precursor (BCP) ALL cases, SNP-A analyses identified additional copy number alterations, including the above-mentioned microdeletions, or better characterized the imbalances found by G-banding in 236 (91%) cases. Furthermore, the cytogenetic subtype classification of 41/260 (16%) BCP ALL cases was revised based on the SNP-A findings. Of the subtype revisions, 12/41 (29%) had clinical implications as regards risk stratifying cytogenetic groups or genotype-specific minimal residual disease stratification. We conclude that SNP-A analyses dramatically improve the cytogenetic characterization of both T-cell and BCP ALL and also provide important information pertinent to risk stratification of BCP ALL.
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Affiliation(s)
- Linda Olsson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Kristina B Lundin-Ström
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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16
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He Z, Liao Z, Chen S, Li B, Yu Z, Luo G, Yang L, Zeng C, Li Y. Downregulated miR-17, miR-29c, miR-92a and miR-214 may be related to BCL11B overexpression in T cell acute lymphoblastic leukemia. Asia Pac J Clin Oncol 2018; 14:e259-e265. [PMID: 29749698 DOI: 10.1111/ajco.12979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/23/2018] [Indexed: 12/31/2022]
Abstract
AIM BCL11B overexpression is a characteristic of most T cell acute lymphoblastic leukemia (T-ALL) cases, and downregulated BCL11B in leukemic T cells inhibits cell proliferation and induces apoptosis. The purpose of this study was to analyze the miRNA expression pattern that may be related to BCL11B regulation in T-ALL. METHODS Quantitative real-time PCR was used to detect the miRNAs miR-17-3p, miR-17-5p, miR-29c-3p, miR-92a-3p, miR-214-3p and miR-214-5p, the BCL11B expression level in peripheral blood mononuclear cells which was obtained from 17 de novo and untreated T-ALL patients, and 15 healthy individuals (HIs) served as control. Correlations between the relative miRNA expression levels and BCL11B were analyzed. RESULTS Based on the computational prediction that certain miRNAs bind the BCL11B 3'-UTR, miR-17-3p, miR-17-5p, miR-29c-3p, miR-92a-3p, miR-214-3p and miR-214-5p were found to be candidates for regulating BCL11B. The expression levels of the six miRNAs were decreased compared with HIs, and with the exception of miR-17-5p, statistically significant differences in expression levels were found in the T-ALL group. Moreover, while significantly higher BCL11B expression was found in the T-ALL group, a negative trend in the correlation level for all six miRNAs could be found in all groups; however, statistical significance was only found for miR-214-3p in the T-ALL group. CONCLUSION miRNA downregulation together with BCL11B upregulation suggests that miR-17, miR-29c, miR-92a and miR-214 might be involved in BCL11B regulation. The therapeutic promise of regulating the expression of these miRNAs for T-ALL therapy may be considered in the future.
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Affiliation(s)
- Zifan He
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Ziwei Liao
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Shaohua Chen
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Bo Li
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Zhi Yu
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Gengxin Luo
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Lijian Yang
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Chengwu Zeng
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Yangqiu Li
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.,Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
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17
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Hoff FW, Hu CW, Qiu Y, Ligeralde A, Yoo SY, Scheurer ME, de Bont ESJM, Qutub AA, Kornblau SM, Horton TM. Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance. Mol Cancer Res 2018; 16:1263-1274. [PMID: 29669823 DOI: 10.1158/1541-7786.mcr-17-0730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/21/2018] [Accepted: 03/30/2018] [Indexed: 12/13/2022]
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, and the second leading cause of pediatric cancer-related death in developed countries. While the cure rate for newly diagnosed ALL is excellent, the genetic heterogeneity and chemoresistance of leukemia cells at relapse makes individualized curative treatment plans difficult. We hypothesize that genetic events would coalesce into a finite number of protein signatures that could guide the design of individualized therapy. Custom reverse-phase protein arrays were produced from pediatric ALL (n = 73) and normal CD34+ (n = 10) samples with 194 validated antibodies. Proteins were allocated into 31 protein functional groups (PFG) to analyze them in the context of other proteins, based on known associations from the literature. The optimal number of protein clusters was determined for each PFG. Protein networks showed distinct transition states, revealing "normal-like" and "leukemia-specific" protein patterns. Block clustering identified strong correlation between various protein clusters that formed 10 protein constellations. Patients that expressed similar recurrent combinations of constellations comprised 7 distinct signatures, correlating with risk stratification, cytogenetics, and laboratory features. Most constellations and signatures were specific for T-cell ALL or pre-B-cell ALL; however, some constellations showed significant overlap. Several signatures were associated with Hispanic ethnicity, suggesting that ethnic pathophysiologic differences likely exist. In addition, some constellations were enriched for "normal-like" protein clusters, whereas others had exclusively "leukemia-specific" patterns.Implications: Recognition of proteins that have universally altered expression, together with proteins that are specific for a given signature, suggests targets for directed combinatorial inhibition or replacement to enable personalized therapy. Mol Cancer Res; 16(8); 1263-74. ©2018 AACRSee related article by Hoff et al., p. 1275.
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Affiliation(s)
- Fieke W Hoff
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.,Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Chenyue W Hu
- Department of Bioengineering, Rice University, Houston, Texas
| | - Yihua Qiu
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Suk-Young Yoo
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael E Scheurer
- Department of Pediatrics and Department of Epidemiology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston TX
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Amina A Qutub
- Department of Bioengineering, Rice University, Houston, Texas
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.
| | - Terzah M Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children's Cancer Center, Houston, Texas
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18
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Szarzyńska-Zawadzka B, Kosmalska M, Sędek Ł, Sonsala A, Twardoch M, Kowalczyk JR, Szczepański T, Witt M, Dawidowska M. Cost-effective screening of DNMT3A coding sequence identifies somatic mutation in pediatric T-cell acute lymphoblastic leukemia. Eur J Haematol 2017; 99:514-519. [PMID: 28905428 DOI: 10.1111/ejh.12964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND OBJECTIVES In pediatric T-cell acute lymphoblastic leukemia (T-ALL), risk assignment schemes preclude reliable prediction of outcome, and thus, new prognostic factors are needed. Mutations in DNMT3A are candidate prognostic and classification markers in adults with acute myeloid leukemia (AML) and T-ALL and thus were considered as candidates prognostic markers in pediatric T-ALL. PATIENTS AND METHODS DNMT3A mutational status was investigated in 74 pediatric T-ALL samples collected at diagnosis. We applied high-resolution melt (HRM) analysis and Sanger sequencing to study the hotspot position (R882) within catalytic MTase domain and exons coding for other functional domains of the protein, known to be mutated in the wide spectrum of hematological malignancies. RESULTS We demonstrate a low frequency of mutations in DNMT3A coding sequence in pediatric T-ALL (1.4%, n = 1/74). We identified missense mutation, p.Ala644Thr, which has not been described previously in pediatric T-ALL, but is recurrent in adults with T-ALL and AML. CONCLUSIONS Low frequency of DNMT3A mutations in pediatric T-ALL is in striking contrast to adult T-ALL and renders the necessity for the search of other candidate prognostic markers. Combined Sanger sequencing-HRM approach offers a cost-effective option for genotyping DNMT3A coding sequence, with potential clinical application in other hematological malignancies.
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Affiliation(s)
| | - Maria Kosmalska
- Institute of Human Genetics Polish Academy of Sciences, Poznań, Poland
| | - Łukasz Sędek
- Department of Microbiology and Immunology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Alicja Sonsala
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Magdalena Twardoch
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Cytogenetic Laboratory, Children's University Hospital, Medical University of Lublin, Lublin, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Michał Witt
- Institute of Human Genetics Polish Academy of Sciences, Poznań, Poland
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19
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Guo C, Huang Y, Yu J, Liu L, Gong X, Huang M, Jiang C, Liao Y, Huang L, Yang G, Li J. The impacts of single nucleotide polymorphisms in genes of cell cycle and NF-kB pathways on the efficacy and acute toxicities of radiotherapy in patients with nasopharyngeal carcinoma. Oncotarget 2017; 8:25334-25344. [PMID: 28445979 PMCID: PMC5421934 DOI: 10.18632/oncotarget.15835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Radiotherapy is one of the primary choices for the treatment of nasopharyngeal carcinoma (NPC) and may result in severe radiotoxicities on normal tissues. Single nucleotide polymorphisms (SNPs) in genes of cell cycle and NF-κB pathways have been linked with the prognoses of various cancers. The aim of this study was to explore whether SNPs of genes involved in cell cycle and NF-κB pathways are associated with responses to radiotherapy in NPC patients. We selected 3 SNPs in cell cycle pathway and 5 SNPs in NF-κB pathway and genotyped them in 154 NPC patients treated with radiotherapy. Multivariate logistic regression was used to determine the association of these 8 SNPs with the responses to radiotherapy. We observed that cyclin-dependent kinase inhibitor gene CDKN2A rs3088440 was significantly related with a poorer treatment efficacy on the primary tumor and cervical lymph node after radiotherapy, and also with a decreased risk of grade 3-4 acute radiation-induced myelosuppression. In some subgroups, cyclin D1 gene CCND1 rs9344 and inhibitor of κB kinase gene IKBKB rs12676482 were related with the grade 3-4 acute radiation-induced myelosuppression, and CCND1 rs9344 was also associated with grade 3-4 acute radiation-induced oral mucositis. The current results reveal that SNPs in genes of cell cycle pathwayand NF-κB pathway have the potential to predict the clinical responses to radiotherapy for NPC patients.
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Affiliation(s)
- Chengxian Guo
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yuling Huang
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Jingjing Yu
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Lijuan Liu
- Department of Pharmacy, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Xiaochang Gong
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Min Huang
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Chunling Jiang
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Yulu Liao
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Lihua Huang
- Center for Medical Experiments, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Guoping Yang
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jingao Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, China
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20
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Skalska-Sadowska J, Dawidowska M, Szarzyńska-Zawadzka B, Jarmuż-Szymczak M, Czerwińska-Rybak J, Machowska L, Derwich K. Translocation t(8;14)(q24;q11) with concurrent PTEN alterations and deletions of STIL/TAL1 and CDKN2A/B in a pediatric case of acute T-lymphoblastic leukemia: A genetic profile associated with adverse prognosis. Pediatr Blood Cancer 2017; 64. [PMID: 27759908 DOI: 10.1002/pbc.26266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 12/28/2022]
Abstract
We report a pediatric case of acute T-lymphoblastic leukemia (T-ALL) with NOTCH1wt , FBXW7wt , STIL/TAL1, and PTEN (exons 2, 3, 4, 5) monoallelic deletions, biallelic CDKN2A/B deletion, and a minor t(8;14)(q24;q11)-positive subclone. Undetectable by a flow cytometric minimal residual disease assay, the t(8;14)(q24;q11) subclone expanded as detected by fluorescence in situ hybridization from 5% at diagnosis to 26% before consolidation and 100% at relapse bearing a monoallelic deletion (exons 2, 3) with a new frameshift mutation of PTEN and the same set of remaining molecular alterations. This case documents an unfavorable prognostic potential of a co-occurrence of this set of molecular genetic events and addresses risk stratification in T-ALL.
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Affiliation(s)
- Jolanta Skalska-Sadowska
- Department of Pediatric Oncology, Hematology and Transplantology, University of Medical Sciences, Poznań, Poland
| | | | | | - Małgorzata Jarmuż-Szymczak
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland.,Department of Hematology and Bone Marrow Transplantation, University of Medical Sciences, Poznań, Poland
| | - Joanna Czerwińska-Rybak
- Department of Hematology and Bone Marrow Transplantation, University of Medical Sciences, Poznań, Poland
| | - Ludomiła Machowska
- Department of Pediatric Oncology, Hematology and Transplantology, University of Medical Sciences, Poznań, Poland
| | - Katarzyna Derwich
- Department of Pediatric Oncology, Hematology and Transplantology, University of Medical Sciences, Poznań, Poland
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21
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Zhou L, Zheng H, Huang X, Zhu L, Wu S, Zeng C, Yang L, Chen S, Luo G, Du X, Li Y. Different genetic alteration of A20
in a Sézary syndrome case with Vα2-Jα22
T cell clone. Asia Pac J Clin Oncol 2017; 14:e116-e123. [PMID: 28296250 DOI: 10.1111/ajco.12672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Lingling Zhou
- Key Laboratory for Regenerative Medicine of Ministry of Education; Jinan University; Guangzhou China
- Institute of Hematology, School of Medicine; Jinan University; Guangzhou China
| | - Haitao Zheng
- Institute of Hematology, School of Medicine; Jinan University; Guangzhou China
| | - Xin Huang
- Department of Hematology; Guangdong General Hospital (Guangdong Academy of Medical Sciences); Guangzhou China
| | - Lihua Zhu
- Department of Rheumatism and Immunology; First Affiliated Hospital; Jinan University; Guangzhou China
| | - Suijing Wu
- Department of Hematology; Guangdong General Hospital (Guangdong Academy of Medical Sciences); Guangzhou China
| | - Chengwu Zeng
- Key Laboratory for Regenerative Medicine of Ministry of Education; Jinan University; Guangzhou China
- Institute of Hematology, School of Medicine; Jinan University; Guangzhou China
| | - Lijian Yang
- Institute of Hematology, School of Medicine; Jinan University; Guangzhou China
| | - Shaohua Chen
- Institute of Hematology, School of Medicine; Jinan University; Guangzhou China
| | - Gengxin Luo
- Department of Hematology; First Affiliated Hospital; Jinan University; Guangzhou China
| | - Xin Du
- Department of Hematology; Guangdong General Hospital (Guangdong Academy of Medical Sciences); Guangzhou China
| | - Yangqiu Li
- Key Laboratory for Regenerative Medicine of Ministry of Education; Jinan University; Guangzhou China
- Institute of Hematology, School of Medicine; Jinan University; Guangzhou China
- Department of Hematology; First Affiliated Hospital; Jinan University; Guangzhou China
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22
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The NOTCH1-MYC highway toward T-cell acute lymphoblastic leukemia. Blood 2017; 129:1124-1133. [PMID: 28115368 DOI: 10.1182/blood-2016-09-692582] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a highly proliferative hematologic malignancy that results from the transformation of immature T-cell progenitors. Aberrant cell growth and proliferation in T-ALL lymphoblasts are sustained by activation of strong oncogenic drivers promoting cell anabolism and cell cycle progression. Oncogenic NOTCH signaling, which is activated in more than 65% of T-ALL patients by activating mutations in the NOTCH1 gene, has emerged as a major regulator of leukemia cell growth and metabolism. T-ALL NOTCH1 mutations result in ligand-independent and sustained NOTCH1-receptor signaling, which translates into activation of a broad transcriptional program dominated by upregulation of genes involved in anabolic pathways. Among these, the MYC oncogene plays a major role in NOTCH1-induced transformation. As result, the oncogenic activity of NOTCH1 in T-ALL is strictly dependent on MYC upregulation, which makes the NOTCH1-MYC regulatory circuit an attractive therapeutic target for the treatment of T-ALL.
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23
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Karrman K, Johansson B. Pediatric T-cell acute lymphoblastic leukemia. Genes Chromosomes Cancer 2016; 56:89-116. [PMID: 27636224 DOI: 10.1002/gcc.22416] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/06/2016] [Indexed: 12/29/2022] Open
Abstract
The most common pediatric malignancy is acute lymphoblastic leukemia (ALL), of which T-cell ALL (T-ALL) comprises 10-15% of cases. T-ALL arises in the thymus from an immature thymocyte as a consequence of a stepwise accumulation of genetic and epigenetic aberrations. Crucial biological processes, such as differentiation, self-renewal capacity, proliferation, and apoptosis, are targeted and deranged by several types of neoplasia-associated genetic alteration, for example, translocations, deletions, and mutations of genes that code for proteins involved in signaling transduction, epigenetic regulation, and transcription. Epigenetically, T-ALL is characterized by gene expression changes caused by hypermethylation of tumor suppressor genes, histone modifications, and miRNA and lncRNA abnormalities. Although some genetic and gene expression patterns have been associated with certain clinical features, such as immunophenotypic subtype and outcome, none has of yet generally been implemented in clinical routine for treatment decisions. The recent advent of massive parallel sequencing technologies has dramatically increased our knowledge of the genetic blueprint of T-ALL, revealing numerous fusion genes as well as novel gene mutations. The challenges now are to integrate all genetic and epigenetic data into a coherent understanding of the pathogenesis of T-ALL and to translate the wealth of information gained in the last few years into clinical use in the form of improved risk stratification and targeted therapies. Here, we provide an overview of pediatric T-ALL with an emphasis on the acquired genetic alterations that result in this disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kristina Karrman
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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24
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Carrasco Salas P, Fernández L, Vela M, Bueno D, González B, Valentín J, Lapunzina P, Pérez-Martínez A. The role of CDKN2A/B deletions in pediatric acute lymphoblastic leukemia. Pediatr Hematol Oncol 2016; 33:415-422. [PMID: 27960642 DOI: 10.1080/08880018.2016.1251518] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CDKN2A/B genes in the 9p21 chromosomal region are frequently involved in human cancer, including pediatric acute lymphoblastic leukemia (ALL). These genes encode 3 proteins that belong to the RB1 and TP53 pathways and act as tumor suppressors by regulating the G1/S checkpoint of the cell cycle. The prognostic value of deletions in the CDKN2A/B locus in ALL is controversial in part due to the limitations of the methodologies used. Further studies with advanced technologies are needed for elucidation. Future studies would also highlight whether CDK4/CDK6 selective inhibitors might be useful therapies for children with these genetic aberrations.
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Affiliation(s)
- P Carrasco Salas
- a Laboratory of Molecular Pediatric Hemato-Oncology , Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz , Madrid , Spain
| | - L Fernández
- b Clinical Research Program , Cancer Research National Centre , Madrid , Spain
| | - M Vela
- c Innate Immune Research Group, IdiPAZ , Madrid , Spain
| | - D Bueno
- d Department of Pediatric Hemato-Oncology and Stem Cell Transplantation , Hospital Infantil Universitario La Paz , Madrid , Spain
| | - B González
- d Department of Pediatric Hemato-Oncology and Stem Cell Transplantation , Hospital Infantil Universitario La Paz , Madrid , Spain
| | - J Valentín
- c Innate Immune Research Group, IdiPAZ , Madrid , Spain
| | - P Lapunzina
- a Laboratory of Molecular Pediatric Hemato-Oncology , Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz , Madrid , Spain
| | - A Pérez-Martínez
- a Laboratory of Molecular Pediatric Hemato-Oncology , Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz , Madrid , Spain.,c Innate Immune Research Group, IdiPAZ , Madrid , Spain.,d Department of Pediatric Hemato-Oncology and Stem Cell Transplantation , Hospital Infantil Universitario La Paz , Madrid , Spain
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25
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Zhu L, Zhou L, Wang L, Li Z, Lu S, Yang L, Chen S, Li B, Wu X, Zhou Y, Li Y. A20 SNP rs77191406 may be related to secondary cancer for rheumatoid arthritis and systemic lupus erythematosus patients. Asia Pac J Clin Oncol 2016; 12:409-414. [PMID: 27435953 DOI: 10.1111/ajco.12577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 12/21/2022]
Abstract
AIM An increased risk for malignancy for rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) patients may be related to factors that play a critical role in the regulation of T-cell activation. A20 is an important negative immunoregulatory factor that was found to be associated with lymphoma and the development of numerous solid tumors. Previous studies have implicated the A20 locus in RA susceptibility. In this study, we investigated polymorphisms in the A20 3' UTR and explored whether there was an association between these polymorphisms and malignancy risk in autoimmune diseases. METHODS PCR and sequencing were used to identify A20 gene polymorphisms in peripheral blood mononuclear cells (PBMCs) from 99 RA cases, 37 SLE cases and 99 healthy individuals. Pearson's Chi square test was used for statistical analysis. RESULTS Only one SNP (rs77191406) and one new mutation (20132 A>G) in A20 gene were identified in RA and SLE patients and healthy individuals. Heterozygous rs77191406 was identified in just 1 of 99 RA patients and 2 of 37 SLE patients. More importantly, a RA patient who was heterozygous for rs77191406 developed colon cancer 10 years after the RA diagnosis. Similarly, two SLE patients carrying rs77191406 (heterozygous) had severe disease or developed bladder cancer 5 years after SLE diagnosis. CONCLUSIONS These findings suggest that rs77191406 may be a prognostic marker for a high risk for rapid malignancy progression, poor survival and refractory disease and a new molecular marker associated with autoimmune diseases transforming into a secondary cancer.
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Affiliation(s)
- Lihua Zhu
- Departments of Rheumatism and Immunology, Guangzhou, China.,Institute of Hematology, Medical College, Guangzhou, China
| | - Lingling Zhou
- Institute of Hematology, Medical College, Guangzhou, China.,Key Laboratory for Regenerative Medicine of Ministry of Education, Guangzhou, China
| | - Liang Wang
- Departments of Oncology, Guangzhou, China
| | - Zhaoxia Li
- Departments of Rheumatism and Immunology, Guangzhou, China.,Institute of Hematology, Medical College, Guangzhou, China
| | - Shuai Lu
- Institute of Hematology, Medical College, Guangzhou, China.,Key Laboratory for Regenerative Medicine of Ministry of Education, Guangzhou, China
| | - Lijian Yang
- Institute of Hematology, Medical College, Guangzhou, China
| | - Shaohua Chen
- Institute of Hematology, Medical College, Guangzhou, China
| | - Bo Li
- Institute of Hematology, Medical College, Guangzhou, China
| | - Xiuli Wu
- Institute of Hematology, Medical College, Guangzhou, China
| | - Yi Zhou
- Departments of Rheumatism and Immunology, Guangzhou, China
| | - Yangqiu Li
- Institute of Hematology, Medical College, Guangzhou, China.,Key Laboratory for Regenerative Medicine of Ministry of Education, Guangzhou, China.,Departments of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
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26
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Xu L, Weng J, Huang X, Zeng C, Chen S, Geng S, Yang L, Wu S, Huang S, Du X, Li Y. Persistent donor derived Vδ4 T cell clones may improve survival for recurrent T cell acute lymphoblastic leukemia after HSCT and DLI. Oncotarget 2016; 7:42943-42952. [PMID: 27356746 PMCID: PMC5189998 DOI: 10.18632/oncotarget.10260] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/13/2016] [Indexed: 02/05/2023] Open
Abstract
The outcome for T-cell acute lymphoblastic leukemia (T-ALL) in relapse after hematopoietic stem cell transplantation (HSCT) is quite poor, while, both donor lymphocytes infusion (DLI) and adoptively infusion of γδ T cells in leukemia patients after HSCT have demonstrated good results in prolonging survival time of patients. Here, we reported a T-ALL case who experienced three relapses and received HSCT and DLI with an overall survival (OS) time lasting for more than seven years. Based on our previous identification of a leukemic and reactive clone in this patient, continual γδ T cell repertoire monitoring affirmed that the same Vδ5 leukemic clone existed in most samples from the patient, particularly including a sample taken at the time of the third T-ALL relapse, while it could not be detected in the donor sample. In addition, an identical Vδ4 monoclonal T cell that proliferated in the recipient for several years was confirmed to come from the donor graft, and its expression level significantly increased in third leukemia recurrence. These results indicate that clonally expanded Vδ4 T cells may represent a reconstituted γδ T cell repertoire after HSCT, which also hints to a relatively better outcome for this case. Based on this case study, we recommend DLI should be as a treatment strategy for patients who achieve CR or relapse from HSCT. Moreover, dynamically monitoring the TCR repertoire in patients who receive HSCT will benefit in supervising of malignant clone evolution and residue, identifying T cell clones mediate anti-infection, GvHD or GvL.
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MESH Headings
- Blood Donors
- Clone Cells/immunology
- Clone Cells/metabolism
- Gene Expression/immunology
- Graft vs Host Disease/etiology
- Graft vs Host Disease/immunology
- Hematopoietic Stem Cell Transplantation/adverse effects
- Hematopoietic Stem Cell Transplantation/methods
- Humans
- Immunotherapy, Adoptive/methods
- Lymphocyte Transfusion/methods
- Neoplasm Recurrence, Local
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/therapy
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Survival Analysis
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/transplantation
- Treatment Outcome
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Affiliation(s)
- Ling Xu
- Institute of Hematology, Jinan University, Guangzhou, China
| | - Jianyu Weng
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xin Huang
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chengwu Zeng
- Institute of Hematology, Jinan University, Guangzhou, China
| | - Shaohua Chen
- Institute of Hematology, Jinan University, Guangzhou, China
| | - Suxia Geng
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lijian Yang
- Institute of Hematology, Jinan University, Guangzhou, China
| | - Suijing Wu
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Suming Huang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Xin Du
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yangqiu Li
- Institute of Hematology, Jinan University, Guangzhou, China
- Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, China
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
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27
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Olsson L, Zettermark S, Biloglav A, Castor A, Behrendtz M, Forestier E, Paulsson K, Johansson B. The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes. Br J Haematol 2016; 174:292-301. [PMID: 27022003 DOI: 10.1111/bjh.14056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/22/2016] [Indexed: 01/07/2023]
Abstract
Cytogenetic analyses of a consecutive series of 67 paediatric (median age 8 years; range 0-17) de novo acute myeloid leukaemia (AML) patients revealed aberrations in 55 (82%) cases. The most common subgroups were KMT2A rearrangement (29%), normal karyotype (15%), RUNX1-RUNX1T1 (10%), deletions of 5q, 7q and/or 17p (9%), myeloid leukaemia associated with Down syndrome (7%), PML-RARA (7%) and CBFB-MYH11 (5%). Single nucleotide polymorphism array (SNP-A) analysis and exon sequencing of 100 genes, performed in 52 and 40 cases, respectively (39 overlapping), revealed ≥1 aberration in 89%; when adding cytogenetic data, this frequency increased to 98%. Uniparental isodisomies (UPIDs) were detected in 13% and copy number aberrations (CNAs) in 63% (median 2/case); three UPIDs and 22 CNAs were recurrent. Twenty-two genes were targeted by focal CNAs, including AEBP2 and PHF6 deletions and genes involved in AML-associated gene fusions. Deep sequencing identified mutations in 65% of cases (median 1/case). In total, 60 mutations were found in 30 genes, primarily those encoding signalling proteins (47%), transcription factors (25%), or epigenetic modifiers (13%). Twelve genes (BCOR, CEBPA, FLT3, GATA1, KIT, KRAS, NOTCH1, NPM1, NRAS, PTPN11, SMC3 and TP53) were recurrently mutated. We conclude that SNP-A and deep sequencing analyses complement the cytogenetic diagnosis of paediatric AML.
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Affiliation(s)
- Linda Olsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Sofia Zettermark
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Castor
- Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Mikael Behrendtz
- Department of Paediatrics, Linköping University Hospital, Linköping, Sweden
| | - Erik Forestier
- Department of Medical Bioscience, University of Umeå, Umeå, Sweden
| | - Kajsa Paulsson
- 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, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
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28
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Song J, Shao H. SNP Array in Hematopoietic Neoplasms: A Review. MICROARRAYS 2015; 5:microarrays5010001. [PMID: 27600067 PMCID: PMC5003446 DOI: 10.3390/microarrays5010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/13/2015] [Accepted: 12/14/2015] [Indexed: 12/03/2022]
Abstract
Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.
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Affiliation(s)
- Jinming Song
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| | - Haipeng Shao
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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