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Abdelfattah NE, Elsayed GM, Soliman AH, Ebeid EN, El Ashry MS. Copy number alterations in pediatric B-cell precursor acute lymphoblastic leukemia patients and their association with patients' outcome. Ann Hematol 2025; 104:1821-1832. [PMID: 39589495 PMCID: PMC12031935 DOI: 10.1007/s00277-024-06102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Accepted: 11/14/2024] [Indexed: 11/27/2024]
Abstract
Genetic abnormalities provide diagnostic and prognostic information for pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. The aim of this study was to determine the effects of genetic CNAs and RUNX1 gene abnormalities on the outcome of pediatric BCP-ALL patients. This study included 78 de novo-BCP-ALL pediatric patients who presented to the Pediatric Oncology Department of the National Cancer Institute (NCI), Cairo University. We aimed to study the impact of copy number alteration (CNA) of 8 of the most altered genes in BCP-ALL patients, in addition to RUNX1 gene abnormalities, on patient survival and response to treatment. Multiplex ligation-dependent probe amplification (MLPA) was used to detect CNA, while RUNX1 gene alterations were detected by fluorescence in situ hybridization (FISH). CNA of the PAX5 gene was significantly associated with worse overall survival (OS) and event-free survival (EFS) (P = 0.012 and P = 0.025, respectively). An increase in the CNA of ETV6 was associated with an increase in minimal residual disease (MRD) on day 15 (P = 0.041). Although RUNX1 gene abnormalities were not a predictor of shorter OS or EFS, an interesting significant association was found between PAX5 CNA and RUNX1 gene gain and translocation (P = 0.017 and P = 0.041, respectively). PAX5 CNA is an adverse prognostic factor. ETV6 CNA is associated with high MRD on day 15.
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Affiliation(s)
- Nesma E Abdelfattah
- Clinical Pathology Department, National Cancer Institute, Cairo University, Kasr Al Eini Street, 4 Form El Khalig, Cairo, 11796, Egypt.
| | - Ghada M Elsayed
- Clinical Pathology Department, National Cancer Institute, Cairo University, Kasr Al Eini Street, 4 Form El Khalig, Cairo, 11796, Egypt
| | - Amira H Soliman
- Clinical Pathology Department, National Cancer Institute, Cairo University, Kasr Al Eini Street, 4 Form El Khalig, Cairo, 11796, Egypt
| | - Emad N Ebeid
- Pediatric Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mona S El Ashry
- Clinical Pathology Department, National Cancer Institute, Cairo University, Kasr Al Eini Street, 4 Form El Khalig, Cairo, 11796, Egypt
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2
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Paulsson K. Chromosomal Gains as a Favorable Prognostic Factor in Pediatric ALL. J Clin Oncol 2023; 41:5433-5436. [PMID: 37820292 DOI: 10.1200/jco.23.01760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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3
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Camuset M, Le Calvez B, Theisen O, Godon C, Grain A, Thomas C, Couec M, Béné MC, Rialland F, Eveillard M. Added value of molecular karyotype in childhood acute lymphoblastic leukemia. CANCER INNOVATION 2023; 2:513-523. [PMID: 38125768 PMCID: PMC10730002 DOI: 10.1002/cai2.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/02/2023] [Indexed: 12/23/2023]
Abstract
Background Thanks to an improved therapeutic regimen in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), 5 year-overall survival now exceeds 90%. Unfortunately, the 25% of children who relapse have an initial poor prognosis, potentially driven by pre-existing or emerging molecular anomalies. The latter are initially and essentially identified by cytogenetics. However, some subtle alterations are not visible through karyotyping. Methods Single nucleotide polymorphisms (SNP) array is an alternative way of chromosomal analysis allowing for a more in-depth evaluation of chromosomal modifications such as the assessment of copy number alterations (CNA) and loss of heterozygosity (LOH). This method was applied here in retrospective diagnosis/relapse paired samples from seven children with BCP-ALL and in a prospective cohort of 38 newly diagnosed childhood cases. Results In the matched study, compared to the initial karyotype, SNP array analysis reclassified two patients as poor prognosis cases. Modulation during relapse was seen for 4 CNA and 0.9 LOH. In the prospective study, SNP reclassified the 10 patients with intermediate karyotype as 7 good prognosis and 3 poor prognosis. Ultimately, in all the children tested, SNP array allowed to identify additional anomalies compared to conventional karyotype, refine its prognostic value and identify some druggable anomalies that could be used for precision medicine. Overall, the anomalies detected could be segregated in four groups respectively involved in B-cell development, cell proliferation, transcription and molecular pathways. Conclusion SNP therefore appears to be a method of choice in the integrated diagnosis of BCP ALL, especially for patients initially classified as intermediate prognosis. This complementary method of both cytogenetics and high throughput sequencing allows to obtain further classified information and can be useful in case of failure of these techniques.
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Affiliation(s)
- Margaux Camuset
- Pediatric Oncology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Baptiste Le Calvez
- Pediatric Oncology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Olivier Theisen
- Hematology Biology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Catherine Godon
- Hematology Biology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Audrey Grain
- Pediatric Oncology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Caroline Thomas
- Pediatric Oncology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Marie‐Laure Couec
- Pediatric Oncology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Marie C. Béné
- Hematology Biology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Fanny Rialland
- Pediatric Oncology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
| | - Marion Eveillard
- Hematology Biology, CHU Nantes, Nantes UniversitéUniv Angers, INSERM, CNRS, CRCI2NANantesFrance
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Shetty D, Talker E, Dhamne C, Mohanty P, Chaubal K, Tembhare P, Patkar N, Subramanian PG, Moulik NR, Narula G, Banavali S. Copy number gain of JAK2 on marker chromosome in a case of relapsed pediatric B-ALL. Pediatr Blood Cancer 2022; 69:e29658. [PMID: 35373889 DOI: 10.1002/pbc.29658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/19/2022] [Accepted: 02/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Dhanlaxmi Shetty
- Cancer Cytogenetics Department, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - Elizabeth Talker
- Cancer Cytogenetics Department, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India
| | - Chetan Dhamne
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - Purvi Mohanty
- Cancer Cytogenetics Department, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India
| | - Kruti Chaubal
- Cancer Cytogenetics Department, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- Department of Hematopathology, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - Nikhil Patkar
- Department of Hematopathology, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - P G Subramanian
- Department of Hematopathology, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - Nirmalya Roy Moulik
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - Gaurav Narula
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
| | - Shripad Banavali
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Mumbai, India
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5
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Meléndez-Flórez MP, Valbuena DS, Cepeda S, Rangel N, Forero-Castro M, Martínez-Agüero M, Rondón-Lagos M. Profile of Chromosomal Alterations, Chromosomal Instability and Clonal Heterogeneity in Colombian Farmers Exposed to Pesticides. Front Genet 2022; 13:820209. [PMID: 35281828 PMCID: PMC8908452 DOI: 10.3389/fgene.2022.820209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/28/2022] [Indexed: 12/04/2022] Open
Abstract
Pesticides are a group of environmental pollutants widely used in agriculture to protect crops, and their indiscriminate use has led to a growing public awareness about the health hazards associated with exposure to these substances. In fact, exposure to pesticides has been associated with an increased risk of developing diseases, including cancer. In a study previously published by us, we observed the induction of specific chromosomal alterations and, in general, the deleterious effect of pesticides on the chromosomes of five individuals exposed to pesticides. Considering the importance of our previous findings and their implications in the identification of cytogenetic biomarkers for the monitoring of exposed populations, we decided to conduct a new study with a greater number of individuals exposed to pesticides. Considering the above, the aim of this study was to evaluate the type and frequency of chromosomal alterations, chromosomal variants, the level of chromosomal instability and the clonal heterogeneity in a group of thirty-four farmers occupationally exposed to pesticides in the town of Simijacá, Colombia, and in a control group of thirty-four unexposed individuals, by using Banding Cytogenetics and Molecular Cytogenetics (Fluorescence in situ hybridization). Our results showed that farmers exposed to pesticides had significantly increased frequencies of chromosomal alterations, chromosomal variants, chromosomal instability and clonal heterogeneity when compared with controls. Our results confirm the results previously reported by us, and indicate that occupational exposure to pesticides induces not only chromosomal instability but also clonal heterogeneity in the somatic cells of people exposed to pesticides. This study constitutes, to our knowledge, the first study that reports clonal heterogeneity associated with occupational exposure to pesticides. Chromosomal instability and clonal heterogeneity, in addition to reflecting the instability of the system, could predispose cells to acquire additional instability and, therefore, to an increased risk of developing diseases.
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Affiliation(s)
| | - Duvan Sebastián Valbuena
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Sebastián Cepeda
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Nelson Rangel
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Maribel Forero-Castro
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - María Martínez-Agüero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
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6
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Copy Number Changes and Allele Distribution Patterns of Chromosome 21 in B Cell Precursor Acute Lymphoblastic Leukemia. Cancers (Basel) 2021; 13:cancers13184597. [PMID: 34572826 PMCID: PMC8465600 DOI: 10.3390/cancers13184597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 01/12/2023] Open
Abstract
Chromosome 21 is the most affected chromosome in childhood acute lymphoblastic leukemia. Many of its numerical and structural abnormalities define diagnostically and clinically important subgroups. To obtain an overview about their types and their approximate genetic subgroup-specific incidence and distribution, we performed cytogenetic, FISH and array analyses in a total of 578 ALL patients (including 26 with a constitutional trisomy 21). The latter is the preferred method to assess genome-wide large and fine-scale copy number abnormalities (CNA) together with their corresponding allele distribution patterns. We identified a total of 258 cases (49%) with chromosome 21-associated CNA, a number that is perhaps lower-than-expected because ETV6-RUNX1-positive cases (11%) were significantly underrepresented in this array-analyzed cohort. Our most interesting observations relate to hyperdiploid leukemias with tetra- and pentasomies of chromosome 21 that develop in constitutionally trisomic patients. Utilizing comparative short tandem repeat analyses, we were able to prove that switches in the array-derived allele patterns are in fact meiotic recombination sites, which only become evident in patients with inborn trisomies that result from a meiosis 1 error. The detailed analysis of such cases may eventually provide important clues about the respective maldistribution mechanisms and the operative relevance of chromosome 21-specific regions in hyperdiploid leukemias.
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Mao J, Xue L, Wang H, Zhu Y, Wang J, Zhao L. A New Treatment Strategy for Early T-Cell Precursor Acute Lymphoblastic Leukemia: A Case Report and Literature Review. Onco Targets Ther 2021; 14:3795-3802. [PMID: 34168464 PMCID: PMC8219029 DOI: 10.2147/ott.s312494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023] Open
Abstract
Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is an aggressive and extremely fatal subtype of T-cell acute lymphoblastic leukemia (T-ALL), characterized by the similar transcriptional and immunophenotypic profiles to those of early T-cell precursors and positive expressions of myeloid antigens. Besides, the gene expression profile in ETP-ALL is similar to that in myeloid malignancies. The clinical characteristics, treatments and prognoses of ETP-ALL are significantly heterogeneous. In the present study, we reported a 43-year-old female patient who lacked terminal deoxynucleotidyl transferase (TDT) expression in immunophenotype and displayed mutations of fms-like tyrosine kinase-internal tandem duplication (FLT3-ITD), paired-box domain 5 (PAX5) and SH2B adaptor protein 3 (SH2B3) (PAX5 and SH2B3, the genes critical to B cell identity and function), which represent myeloid and precursor B-lineage associated gene mutations, respectively. It was a rare T-ALL or T-lineage case. Because of multiple poor prognostic factors in this case, conventional induction regimens, like hyper-CVAD (cyclophosphamide, vincristine, doxorubicin, dexamethasone), were invalid. The patient showed inadequate response, suggesting that this treatment was not employed on the basis of the immunophenotype. FLAG-IDA regimen (fludarabine, cytarabine [Ara-C], granulocyte-colony stimulating factor [G-CSF] and idarubicin), which is usually applied to eliminate leukemia cells, was administered combining with sorafenib as an effective induction chemotherapy. The case achieved long-term survival following the allogeneic hematopoietic stem cell transplantation (allo-HSCT). We recommend that adult ETP-ALL patients can be treated with a myeloid-oriented chemotherapy (as frontline induction treatment) along with gene-targeting inhibitors, followed by allo-HSCT.
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Affiliation(s)
- Jianping Mao
- Department of Hematology, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, The Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, People's Republic of China
| | - Lianguo Xue
- Department of Hematology, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, The Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, People's Republic of China
| | - Haiqing Wang
- Department of Laboratory medicine, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, The Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, People's Republic of China
| | - Yuanxin Zhu
- Department of Hematology, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, The Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, People's Republic of China
| | - Juan Wang
- Department of Pediatrics, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, The Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, People's Republic of China
| | - Lidong Zhao
- Department of Hematology, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, The Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang Clinical College of Nanjing Medical University, Lianyungang, People's Republic of China
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8
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Moura‐Castro LH, Peña‐Martínez P, Castor A, Galeev R, Larsson J, Järås M, Yang M, Paulsson K. Sister chromatid cohesion defects are associated with chromosomal copy number heterogeneity in high hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2021; 60:410-417. [PMID: 33368842 PMCID: PMC8247877 DOI: 10.1002/gcc.22933] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 11/25/2022] Open
Abstract
High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. The main driver event of this disease is a nonrandom aneuploidy consisting of gains of whole chromosomes but without overt evidence of chromosomal instability (CIN). Here, we investigated the frequency and severity of defective sister chromatid cohesion-a phenomenon related to CIN-in primary pediatric ALL. We found that a large proportion (86%) of hyperdiploid cases displayed aberrant cohesion, frequently severe, to compare with 49% of ETV6/RUNX1-positive ALL, which mostly displayed mild defects. In hyperdiploid ALL, cohesion defects were associated with increased chromosomal copy number heterogeneity, which could indicate increased CIN. Furthermore, cohesion defects correlated with RAD21 and NCAPG mRNA expression, suggesting a link to reduced cohesin and condensin levels in hyperdiploid ALL. Knockdown of RAD21 in an ALL cell line led to sister chromatid cohesion defects, aberrant mitoses, and increased heterogeneity in chromosomal copy numbers, similar to what was seen in primary hyperdiploid ALL. In summary, our study shows that aberrant sister chromatid cohesion is frequent but heterogeneous in pediatric high hyperdiploid ALL, ranging from mild to very severe defects, and possibly due to low cohesin or condensin levels. Cases with high levels of aberrant chromosome cohesion displayed increased chromosomal copy number heterogeneity, possibly indicative of increased CIN. These abnormalities may play a role in the clonal evolution of hyperdiploid pediatric ALL.
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Affiliation(s)
| | - Pablo Peña‐Martínez
- Department of Laboratory Medicine, Division of Clinical GeneticsLund UniversityLundSweden
| | - Anders Castor
- Department of Pediatrics, Skåne University HospitalLund UniversityLundSweden
| | - Roman Galeev
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell CenterLund UniversityLundSweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell CenterLund UniversityLundSweden
| | - Marcus Järås
- Department of Laboratory Medicine, Division of Clinical GeneticsLund UniversityLundSweden
| | - Minjun Yang
- Department of Laboratory Medicine, Division of Clinical GeneticsLund UniversityLundSweden
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical GeneticsLund UniversityLundSweden
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Baptiste M, Moinuddeen SS, Soliz CL, Ehsan H, Kaneko G. Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning. Genes (Basel) 2021; 12:722. [PMID: 34065872 PMCID: PMC8151328 DOI: 10.3390/genes12050722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022] Open
Abstract
Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person's variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.
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Affiliation(s)
| | | | | | | | - Gen Kaneko
- School of Arts & Sciences, University of Houston-Victoria, Victoria, TX 77901, USA; (M.B.); (S.S.M.); (C.L.S.); (H.E.)
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10
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13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking. Blood 2021; 136:946-956. [PMID: 32384149 DOI: 10.1182/blood.2019004684] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in the FMS-like tyrosine kinase 3 (FLT3) gene in 13q12.2 are among the most common driver events in acute leukemia, leading to increased cell proliferation and survival through activation of the phosphatidylinositol 3-kinase/AKT-, RAS/MAPK-, and STAT5-signaling pathways. In this study, we examine the pathogenetic impact of somatic hemizygous 13q12.2 microdeletions in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) using 5 different patient cohorts (in total including 1418 cases). The 13q12.2 deletions occur immediately 5' of FLT3 and involve the PAN3 locus. By detailed analysis of the 13q12.2 segment, we show that the deletions lead to loss of a topologically associating domain border and an enhancer of FLT3. This results in increased cis interactions between the FLT3 promoter and another enhancer located distally to the deletion breakpoints, with subsequent allele-specific upregulation of FLT3 expression, expected to lead to ligand-independent activation of the receptor and downstream signaling. The 13q12.2 deletions are highly enriched in the high-hyperdiploid BCP ALL subtype (frequency 3.9% vs 0.5% in other BCP ALL) and in cases that subsequently relapsed. Taken together, our study describes a novel mechanism of FLT3 involvement in leukemogenesis by upregulation via chromatin remodeling and enhancer hijacking. These data further emphasize the role of FLT3 as a driver gene in BCP ALL.
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11
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Mroczek A, Zawitkowska J, Kowalczyk J, Lejman M. Comprehensive Overview of Gene Rearrangements in Childhood T-Cell Acute Lymphoblastic Leukaemia. Int J Mol Sci 2021; 22:E808. [PMID: 33467425 PMCID: PMC7829804 DOI: 10.3390/ijms22020808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Acute lymphoblastic leukaemia (ALL) is a relevant form of childhood neoplasm, as it accounts for over 80% of all leukaemia cases. T-cell ALL constitutes a genetically heterogeneous cancer derived from T-lymphoid progenitors. The diagnosis of T-ALL is based on morphologic, immunophenotypic, cytogenetic, and molecular features, thus the results are used for patient stratification. Due to the expression of surface and intracellular antigens, several subtypes of T-ALL can be distinguished. Although the aetiology of T-ALL remains unclear, a wide spectrum of rearrangements and mutations affecting crucial signalling pathways has been described so far. Due to intensive chemotherapy regimens and supportive care, overall cure rates of more than 80% in paediatric T-ALL patients have been accomplished. However, improved knowledge of the mechanisms of relapse, drug resistance, and determination of risk factors are crucial for patients in the high-risk group. Even though some residual disease studies have allowed the optimization of therapy, the identification of novel diagnostic and prognostic markers is required to individualize therapy. The following review summarizes our current knowledge about genetic abnormalities in paediatric patients with T-ALL. As molecular biology techniques provide insights into the biology of cancer, our study focuses on new potential therapeutic targets and predictive factors which may improve the outcome of young patients with T-ALL.
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Affiliation(s)
- Anna Mroczek
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Joanna Zawitkowska
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Jerzy Kowalczyk
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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12
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Smith SC, Farooqi MS, Gener MA, Ginn K, Joyce JM, Bendorf TM, Cooley LD. Clinical Validation of Somatic Mutation Detection by the OncoScan CNV Plus Assay. J Mol Diagn 2020; 23:29-37. [PMID: 33080408 DOI: 10.1016/j.jmoldx.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/02/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
The OncoScan CNV Plus Assay (OS+) is a single-nucleotide polymorphism microarray platform that can detect 74 hotspot somatic mutations (SMs) in nine genes via molecular inversion probes. We report validation of the SM component of OS+ using a cohort of pediatric high-grade brain tumor specimens. SM calls were generated from 46 brain tumor cases, most tested orthogonally via bidirectional Sanger sequencing. The initial calling algorithm result showed that 31 tumors were positive and 15 were negative for SM, with a total of 71 OS+ SM calls [28 high-confidence (HC) and 43 low-confidence (LC)]. Sanger sequencing was performed for 54 of the 71 calls (27 HC and 27 LC), as well as for 21 randomly selected hotspots across the 15 OS+ negative cases. HC calls (except EGFR) Sanger sequencing confirmed positive, negative calls confirmed negative, but none of the LC calls were Sanger-confirmed positive. An update of the OS+ algorithm resolved the LC calls, but of the 11 HC SM EGFR calls, Sanger sequencing confirmed only one. Two PTEN SM calls by OS+ in two separate cases were also negative per Sanger sequencing. We conclude that a majority of HC OS+ SM calls were accurate, except calls identified in EGFR and PTEN. Clinically, we report SMs identified by OS+ only after Sanger sequencing verification.
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Affiliation(s)
- Scott C Smith
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, SUNY Upstate Medical University, Syracuse, New York
| | - Midhat S Farooqi
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Melissa A Gener
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Kevin Ginn
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Julie M Joyce
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Tara M Bendorf
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Linda D Cooley
- Department of Pathology & Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; Department of Pathology & Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri.
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13
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IKZF1 rs4132601 and rs11978267 Gene Polymorphisms and Acute Lymphoblastic Leukemia: Relation to Disease Susceptibility and Outcome. J Pediatr Hematol Oncol 2020; 42:420-428. [PMID: 32769565 DOI: 10.1097/mph.0000000000001874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
(IKZF1) rs4132601 and rs11978267 are common gene polymorphisms and have been associated with the risk of acute lymphoblastic leukemia. However, these associations are less evident in races and/or ethnicities other than European and Hispanic. Therefore, we investigated the association between these single-nucleotide polymorphisms and acute lymphoblastic leukemia susceptibility and disease outcome. Real-time polymerase chain reaction typing was performed for IKZF1 rs4132601 and rs11978267 for 128 pediatric acute lymphoblastic leukemia (pALL), 45 adult acute lymphoblastic leukemia (aALL), and 436 healthy controls. The G allele-containing and G-containing genotypes (GG+GT) of rs4132601 were significantly higher in pALL (P=0.003, odds ratio [OR]=1.65, 0.009, OR=1.42, respectively) and aALL (P=0.016, OR=1.81 and 0.011, OR=1.61, respectively). However, the GG haplotype was associated with the risk of pALL (P=0.044), the GA haplotype was associated with the risk of aALL (P=0.007). In aALL, the GG genotype of rs4132601 was associated with absence of remission and poor overall survival (P=0.003 and 0.041, respectively). The IKZF1 rs4132601 single-nucleotide polymorphism can be considered a susceptibility risk factor for the development of pALL and aALL in the studied cohort of Egyptian patients. The GG genotype of IKZF1 rs4132601 may be a risk factor for poor outcome in aALL patients.
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14
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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: 0.8] [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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15
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Berry NK, Scott RJ, Sutton R, Law T, Trahair TN, Dalla-Pozza L, Ritchie P, Barbaric D, Enjeti AK. Enrichment of atypical hyperdiploidy and IKZF1 deletions detected by SNP-microarray in high-risk Australian AIEOP-BFM B-cell acute lymphoblastic leukaemia cohort. Cancer Genet 2020; 242:8-14. [PMID: 32058318 DOI: 10.1016/j.cancergen.2020.01.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/11/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) is the most common childhood malignancy with the majority of patients being classified as B-cell lineage (B-ALL). The sub-classification of B-ALL is based on genomic architecture. Recent studies have demonstrated the capability of SNP-microarrays to detect genomic changes in B-ALL which cannot be observed by conventional cytogenetic methods. In current clinical trials, B-ALL patients at high risk of relapse are mainly identified by adverse cancer genomics and/or poor response to early therapy. To test the hypothesis that inclusion of SNP-microarrays in frontline diagnostics could more efficiently and accurately identify adverse genomic factors than conventional techniques, we evaluated the Australian high-risk B-ALL cohort enrolled on AIEOP-BFM ALL 2009 study (n = 33). SNP-microarray analysis identified additional aberrations in 97% of patients (32/33) compared to conventional techniques. This changed the genomic risk category of 24% (8/33) of patients. Additionally, 27% (9/33) of patients exhibited a 'hyperdiploid' genome, which is generally associated with a good genomic risk and favourable outcomes. An enrichment of IKZF1 deletions was observed with one third of the cohort affected. Our findings suggest the current classification system could be improved and highlights the need to use more sensitive techniques such as SNP-microarray for cytogenomic risk stratification in B-ALL.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, Australia; School of Women's and Children's Health, UNSW Medicine, Randwick, Australia
| | - Tamara Law
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, Australia
| | - Toby N Trahair
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, Australia; School of Women's and Children's Health, UNSW Medicine, Randwick, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick Australia
| | - Luce Dalla-Pozza
- Cancer Centre for Children, The Children's Hospital at Westmead, Australia
| | - Petra Ritchie
- Women's and Children's Hospital, SA Pathology, University of Adelaide, Adelaide, Australia
| | - Draga Barbaric
- School of Women's and Children's Health, UNSW Medicine, Randwick, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia; Department of Haematology, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia
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16
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Deak D, Pop C, Zimta AA, Jurj A, Ghiaur A, Pasca S, Teodorescu P, Dascalescu A, Antohe I, Ionescu B, Constantinescu C, Onaciu A, Munteanu R, Berindan-Neagoe I, Petrushev B, Turcas C, Iluta S, Selicean C, Zdrenghea M, Tanase A, Danaila C, Colita A, Colita A, Dima D, Coriu D, Einsele H, Tomuleasa C. Let's Talk About BiTEs and Other Drugs in the Real-Life Setting for B-Cell Acute Lymphoblastic Leukemia. Front Immunol 2020; 10:2856. [PMID: 31921126 PMCID: PMC6934055 DOI: 10.3389/fimmu.2019.02856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/20/2019] [Indexed: 01/07/2023] Open
Abstract
Background: Therapy for acute lymphoblastic leukemia (ALL) are currently initially efficient, but even if a high percentage of patients have an initial complete remission (CR), most of them relapse. Recent data shows that immunotherapy with either bispecific T-cell engagers (BiTEs) of chimeric antigen receptor (CAR) T cells can eliminate residual chemotherapy-resistant B-ALL cells. Objective: The objective of the manuscript is to present improvements in the clinical outcome for chemotherapy-resistant ALL in the real-life setting, by describing Romania's experience with bispecific antibodies for B-cell ALL. Methods: We present the role of novel therapies for relapsed B-cell ALL, including the drugs under investigation in phase I-III clinical trials, as a potential bridge to transplant. Blinatumomab is presented in a critical review, presenting both the advantages of this drug, as well as its limitations. Results: Bispecific antibodies are discussed, describing the clinical trials that resulted in its approval by the FDA and EMA. The real-life setting for relapsed B-cell ALL is described and we present the patients treated with blinatumomab in Romania. Conclusion: In the current manuscript, we present blinatumomab as a therapeutic alternative in the bridge-to-transplant setting for refractory or relapsed ALL, to gain a better understanding of the available therapies and evidence-based data for these patients in 2019.
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Affiliation(s)
- Dalma Deak
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Cristina Pop
- Department of Pharmacology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina-Andreea Zimta
- Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandra Ghiaur
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Angela Dascalescu
- Department of Hematology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, Regional Institute of Oncology, Iasi, Romania
| | - Ion Antohe
- Department of Hematology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, Regional Institute of Oncology, Iasi, Romania
| | - Bogdan Ionescu
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Catalin Constantinescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Onaciu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Raluca Munteanu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bobe Petrushev
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Turcas
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Sabina Iluta
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Selicean
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Alina Tanase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Catalin Danaila
- Department of Hematology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, Regional Institute of Oncology, Iasi, Romania
| | - Anca Colita
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Department of Pediatrics, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Andrei Colita
- Department of Hematology, Coltea Hospital, Bucharest, Romania.,Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Delia Dima
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Daniel Coriu
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania.,Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Wurzburg, Würzburg, Germany
| | - Ciprian Tomuleasa
- Department of Hematology/Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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17
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Eckert C, Groeneveld-Krentz S, Kirschner-Schwabe R, Hagedorn N, Chen-Santel C, Bader P, Borkhardt A, Cario G, Escherich G, Panzer-Grümayer R, Astrahantseff K, Eggert A, Sramkova L, Attarbaschi A, Bourquin JP, Peters C, Henze G, von Stackelberg A. Improving Stratification for Children With Late Bone Marrow B-Cell Acute Lymphoblastic Leukemia Relapses With Refined Response Classification and Integration of Genetics. J Clin Oncol 2019; 37:3493-3506. [DOI: 10.1200/jco.19.01694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Minimal residual disease (MRD) helps to accurately assess when children with late bone marrow relapses of B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) will benefit from allogeneic hematopoietic stem-cell transplantation (allo-HSCT). More detailed dissection of MRD response heterogeneity and the specific genetic aberrations could improve current practice. PATIENTS AND METHODS MRD was assessed after induction treatment and at different times during relapse treatment until allo-HSCT (indicated in poor responders to induction; MRD ≥ 10−3) for patients being treated for late BCP-ALL bone marrow relapses (n = 413; median follow-up, 9.4 years) in the ALL-REZ BFM 2002 trial/registry (ClinicalTrials.gov identifier: NCT00114348 ). RESULTS Patients with both good (MRD < 10−3) and poor responses to induction treatment reached excellent event-free survival (EFS; 72% v 65%) and overall survival (OS; 82% v 74%). Patients with MRD of 10−2 or greater after induction had reduced EFS (56%), and their MRD persisted until allo-HSCT more frequently than it did in patients with MRD of 10−3 or greater to less than 10−2 ( P = .037). Patients with 25% or more leukemic blasts after induction (early nonresponders) had the poorest prognosis (EFS, 22%). Interestingly, patients with MRD of 10−3 or greater before allo-HSCT (late nonresponders) still had an EFS of 50% and OS of 63%, which in principle justifies allo-HSCT in these patients. From a panel of selected candidate genes, TP53 alterations (frequency, 8%) were the only genetic alteration with independent prognostic value in any MRD-based response subgroup. CONCLUSION After induction treatment, MRD-based treatment stratification resulted in excellent survival in patients with late relapsed BCP-ALL. Prognosis could be further improved in very poor responders by intensifying treatment directly after induction. TP53 alterations can be defined as a novel genetic high-risk marker in all MRD response groups in late relapsed BCP-ALL. Here we identified early and late nonresponders to be considered as events in future trials.
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Affiliation(s)
- Cornelia Eckert
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | - Renate Kirschner-Schwabe
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | | | - Peter Bader
- University Hospital Frankfurt, Frankfurt, Germany
| | | | - Gunnar Cario
- University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Angelika Eggert
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | - Günter Henze
- Charité - Universitätsmedizin Berlin, Berlin, Germany
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18
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Sun Y, Zhang Q, Feng G, Chen Z, Gao C, Liu S, Zhang R, Zhang H, Zheng X, Gong W, Wang Y, Wu Y, Li J, Zheng H. An improved advanced fragment analysis-based classification and risk stratification of pediatric acute lymphoblastic leukemia. Cancer Cell Int 2019; 19:110. [PMID: 31049032 PMCID: PMC6482565 DOI: 10.1186/s12935-019-0825-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) contains cytogenetically distinct subtypes that respond differently to cytotoxic drugs. Therefore, subtype classification is important and indispensable in ALL diagnosis. In our previous study, we identified some marker genes in childhood ALL by means of microarray technology and, furthermore, detected the relative expression levels of 57 marker genes and built a comparatively convenient and cost-effective classifier with a prediction accuracy as high as 94% based on the advanced fragment analysis (AFA) technique. METHODS A more convenient improved AFA (iAFA) technique with one-step multiplex RT-PCR and an anti-contamination system was developed to detect 57 marker genes for ALL. RESULTS The iAFA assay is much easier and more convenient to perform than the previous AFA assay and has a prediction accuracy of 95.29% in ALL subtypes. The anti-contamination system could effectively prevent the occurrence of lab DNA contamination. We also showed that marker gene expression profiles in pediatric ALL revealed 2 subgroups with different outcomes. Most ALL patients (95.8%) had a good-risk genetic profile, and only 4.2% of ALL patients had a poor-risk genetic profile, which predicted an event-free survival (EFS) of 93.6 ± 1.3% vs 18.8 ± 9.8% at 5 years, respectively (P < 0.001). CONCLUSIONS Compared to the previous AFA assay, the iAFA technique is more functional, time-saving and labor-saving. It could be a valuable clinical tool for the classification and risk stratification of pediatric ALL patients.
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Affiliation(s)
- Yanran Sun
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Qiaosheng Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, 150001 Heilongjiang China
| | - Guoshuang Feng
- Center for Clinical Epidemiology & Evidence-based Medicine, Beijing Children’s Hospital Medical, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Zhen Chen
- Ningbo Health Gene Technologies Ltd., Ningbo, 315800 Zhejiang China
| | - Chao Gao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Shuguang Liu
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Ruidong Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Han Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
- Present Address: Institute of Medical Biology, Chinese Academy of Medicine Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650031 Yunnan China
| | - Xueling Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Wenyu Gong
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, 150001 Heilongjiang China
| | - Yong Wu
- Ningbo Health Gene Technologies Ltd., Ningbo, 315800 Zhejiang China
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin, 150001 Heilongjiang China
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics (Capital Medical University), Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, 56 Nanlishi Road, Beijing, 100045 China
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19
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Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K. Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia. Nat Commun 2019; 10:1519. [PMID: 30944321 PMCID: PMC6447538 DOI: 10.1038/s41467-019-09469-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/11/2019] [Indexed: 12/21/2022] Open
Abstract
Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic analysis on matched datasets from genomic profiling, RNA-sequencing, and mass spectrometry-based analysis of >8,000 genes and proteins as well as Hi-C of primary patient samples from hyperdiploid and ETV6/RUNX1-positive pediatric ALL. We show that CTCF and cohesin, which are master regulators of chromatin architecture, display low expression in hyperdiploid ALL. In line with this, a general genome-wide dysregulation of gene expression in relation to topologically associating domain (TAD) borders were seen in the hyperdiploid group. Furthermore, Hi-C of a limited number of hyperdiploid childhood ALL cases revealed that 2/4 cases displayed a clear loss of TAD boundary strength and 3/4 showed reduced insulation at TAD borders, with putative leukemogenic effects.
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Affiliation(s)
- Minjun Yang
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Mattias Vesterlund
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, SE-171 21, Stockholm, Sweden
| | - Ioannis Siavelis
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, SE-171 21, Stockholm, Sweden
| | - Larissa H Moura-Castro
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, SE-221 85, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Rozbeh Jafari
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, SE-171 21, Stockholm, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics, 69120, Heidelberg, Germany
| | - Linda Olsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, SE-221 85, Lund, Sweden
| | - Naveen Ravi
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Eleanor L Woodward
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Louise Harewood
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
- Precision Medicine Centre of Excellence, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Janne Lehtiö
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, SE-171 21, Stockholm, Sweden.
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.
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