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Arai H, Matsui H, Chi S, Utsu Y, Masuda S, Aotsuka N, Minami Y. Germline Variants and Characteristic Features of Hereditary Hematological Malignancy Syndrome. Int J Mol Sci 2024; 25:652. [PMID: 38203823 PMCID: PMC10779750 DOI: 10.3390/ijms25010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Due to the proliferation of genetic testing, pathogenic germline variants predisposing to hereditary hematological malignancy syndrome (HHMS) have been identified in an increasing number of genes. Consequently, the field of HHMS is gaining recognition among clinicians and scientists worldwide. Patients with germline genetic abnormalities often have poor outcomes and are candidates for allogeneic hematopoietic stem cell transplantation (HSCT). However, HSCT using blood from a related donor should be carefully considered because of the risk that the patient may inherit a pathogenic variant. At present, we now face the challenge of incorporating these advances into clinical practice for patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and optimizing the management and surveillance of patients and asymptomatic carriers, with the limitation that evidence-based guidelines are often inadequate. The 2016 revision of the WHO classification added a new section on myeloid malignant neoplasms, including MDS and AML with germline predisposition. The main syndromes can be classified into three groups. Those without pre-existing disease or organ dysfunction; DDX41, TP53, CEBPA, those with pre-existing platelet disorders; ANKRD26, ETV6, RUNX1, and those with other organ dysfunctions; SAMD9/SAMD9L, GATA2, and inherited bone marrow failure syndromes. In this review, we will outline the role of the genes involved in HHMS in order to clarify our understanding of HHMS.
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Affiliation(s)
- Hironori Arai
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Hirotaka Matsui
- Department of Laboratory Medicine, National Cancer Center Hospital, Tsukiji, Chuoku 104-0045, Japan;
- Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8665, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Shinichi Masuda
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Nobuyuki Aotsuka
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
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Larson JK, Hunter‐Schlichting DN, Crowgey EL, Mills LJ, Druley TE, Marcotte EL. KMT2A‐D
pathogenicity, prevalence, and variation according to a population database. Cancer Med 2022; 12:7234-7245. [PMID: 36479909 PMCID: PMC10067056 DOI: 10.1002/cam4.5443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The KMT2 family of genes is essential epigenetic regulators promoting gene expression. The gene family contains three subgroups, each with two paralogues: KMT2A and KMT2B; KMT2C and KMT2D; KMT2F and KMT2G. KMT2A-D are among the most frequent somatically altered genes in several different cancer types. Somatic KMT2A rearrangements are well-characterized in infant leukemia (IL), and growing evidence supports the role of additional family members (KMT2B, KMT2C, and KMT2D) in leukemogenesis. Enrichment of rare heterozygous frameshift variants in KMT2A and C has been reported in acute myeloid leukemia (AML), IL, and solid tumors. Currently, the non-synonymous variation, prevalence, and penetrance of these four genes are unknown. METHODS This study determined the prevalence of pathogenic/likely pathogenic (P/LP) germline KMT2A-D variants in a cancer-free adult population from the Genome Aggregation Database (gnomAD). Two methods of variant interpretation were utilized: a manual genomic variant interpretation and an automated ACMG pipeline. RESULTS The ACMG pipeline identified considerably fewer P/LP variants (n = 89) compared to the manual method (n = 660) in all 4 genes. Consequently, the total P/LP prevalence and allele frequency (AF) were higher in the manual method (1:112, AF = 4.46E-03) than in ACMG (1:832, AF = 6.01E-04). Multiple ancestry-exclusive P/LP variants were identified along with an increased frequency in males compared to females. Many of these variants identified in this population database are also associated with severe juvenile conditions. CONCLUSION These data demonstrate that putatively functional germline variation in these developmentally important genes is more common than previously appreciated and identification in cancer-free adults may indicate incomplete penetrance for many of these variants. Future research should examine a genetic predisposing role in IL and other pediatric cancers.
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Affiliation(s)
- Jenna K. Larson
- Deparatment of Genetic Counseling University of Minnesota Minneapolis Minnesota USA
| | - DeVon N. Hunter‐Schlichting
- Masonic Cancer Center University of Minnesota Minneapolis Minnesota USA
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics University of Minnesota Minneapolis Minnesota USA
| | | | - Lauren J. Mills
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics University of Minnesota Minneapolis Minnesota USA
| | | | - Erin L. Marcotte
- Masonic Cancer Center University of Minnesota Minneapolis Minnesota USA
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics University of Minnesota Minneapolis Minnesota USA
- Brain Tumor Program University of Minnesota Minneapolis Minnesota USA
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Qiu KY, Zhou DH, Liao XY, Huang K, Li Y, Xu HG, Weng WJ, Xu LH, Fang JP. Prognostic value and outcome for acute lymphocytic leukemia in children with MLL rearrangement: a case-control study. BMC Cancer 2022; 22:1257. [DOI: 10.1186/s12885-022-10378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Abstract
Purpose
To evaluate the prognostic factors and outcome for acute lymphoblastic leukemia (ALL) in children with MLL rearrangement (MLL-r).
Methods
A total of 124 pediatric patients who were diagnosed with ALL were classified into two groups based on the MLL-r status by using a retrospective case-control study method from June 2008 to June 2020.
Results
The prevalence of MLL-r positive in the whole cohort was 4.9%. The complete remission (CR) rate on Day 33 in the MLL-r positive group was not statistically different from the negative group (96.8% vs 97.8%, P = 0.736). Multivariate analysis showed that T-cell, white blood cell counts (WBC) ≥ 50 × 109/L, MLL-AF4, and D15 minimal residual disease (MRD) positive were independent risk factors affecting the prognosis of MLL-r positive children. Stem cell transplantation (SCT) was a favorable independent prognostic factor affecting event-free survival (EFS) in MLL-r positive patients (P = 0.027), and there was a trend toward an independent prognostic effect on overall survival (OS) (P = 0.065). The 10-year predicted EFS for patients with MLL-AF4, MLL-PTD, MLL-ENL, other MLL partner genes, and MLL-r negative cases were 46.67 ± 28.61%, 85.71 ± 22.37%, 75 ± 32.41%, 75 ± 32.41%, and 77.33 ± 10.81%, respectively (P = 0.048). The 10-year predicted OS were 46.67 ± 28.61%, 85.71 ± 22.37%, 75 ± 32.41%, 75 ± 32.41%, and 85.2 ± 9.77%, respectively (P = 0.049). The 124 patients with ALL were followed up and eventually 5 (4%) cases relapsed, with a median relapse time of 3.9 years.
Conclusion
Patients with MLL-r positive ALL have moderate remission rates, but are prone to relapse with low overall survival. The outcome of MLL-r positive ALL was closely related to the partner genes, and clinical attention should be paid to screening for MLL partner genes and combining them with other prognostic factors for accurate risk stratification.
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Iacobucci I, Kimura S, Mullighan CG. Biologic and Therapeutic Implications of Genomic Alterations in Acute Lymphoblastic Leukemia. J Clin Med 2021; 10:3792. [PMID: 34501239 PMCID: PMC8432032 DOI: 10.3390/jcm10173792] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most successful paradigm of how risk-adapted therapy and detailed understanding of the genetic alterations driving leukemogenesis and therapeutic response may dramatically improve treatment outcomes, with cure rates now exceeding 90% in children. However, ALL still represents a leading cause of cancer-related death in the young, and the outcome for older adolescents and young adults with ALL remains poor. In the past decade, next generation sequencing has enabled critical advances in our understanding of leukemogenesis. These include the identification of risk-associated ALL subtypes (e.g., those with rearrangements of MEF2D, DUX4, NUTM1, ZNF384 and BCL11B; the PAX5 P80R and IKZF1 N159Y mutations; and genomic phenocopies such as Ph-like ALL) and the genomic basis of disease evolution. These advances have been complemented by the development of novel therapeutic approaches, including those that are of mutation-specific, such as tyrosine kinase inhibitors, and those that are mutation-agnostic, including antibody and cellular immunotherapies, and protein degradation strategies such as proteolysis-targeting chimeras. Herein, we review the genetic taxonomy of ALL with a focus on clinical implications and the implementation of genomic diagnostic approaches.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
- Comprehensive Cancer Center, Hematological Malignancies Program, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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Maurya S, Yang W, Tamai M, Zhang Q, Erdmann-Gilmore P, Bystry A, Martins Rodrigues F, Valentine MC, Wong WH, Townsend R, Druley TE. Loss of KMT2C reprograms the epigenomic landscape in hPSCs resulting in NODAL overexpression and a failure of hemogenic endothelium specification. Epigenetics 2021; 17:220-238. [PMID: 34304711 PMCID: PMC8865227 DOI: 10.1080/15592294.2021.1954780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Germline or somatic variation in the family of KMT2 lysine methyltransferases have been associated with a variety of congenital disorders and cancers. Notably, KMT2A-fusions are prevalent in 70% of infant leukaemias but fail to phenocopy short latency leukaemogenesis in mammalian models, suggesting additional factors are necessary for transformation. Given the lack of additional somatic mutation, the role of epigenetic regulation in cell specification, and our prior results of germline KMT2C variation in infant leukaemia patients, we hypothesized that germline dysfunction of KMT2C altered haematopoietic specification. In isogenic KMT2C KO hPSCs, we found genome-wide differences in histone modifications at active and poised enhancers, leading to gene expression profiles akin to mesendoderm rather than mesoderm highlighted by a significant increase in NODAL expression and WNT inhibition, ultimately resulting in a lack of in vitro hemogenic endothelium specification. These unbiased multi-omic results provide new evidence for germline mechanisms increasing risk of early leukaemogenesis.
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Affiliation(s)
- Shailendra Maurya
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
| | - Wei Yang
- McDonnell Genome Institute, Genome Technology Access Center, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
| | - Minori Tamai
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
| | - Qiang Zhang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Petra Erdmann-Gilmore
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Amelia Bystry
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
| | | | - Mark C Valentine
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
| | - Wing H Wong
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
| | - Reid Townsend
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Todd E Druley
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Washington University in St Louis School of Medicine, St. Louis, Missouri, United States
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Liu X, Zhao Y, Luedke C, Jug R, Yang LH, Lu M, Pan Z, Wang D, Lorsbach R, Shi Y, Knez V, Rehder C, Liang X, Wang E. Infantile leukemia-What factors determine its distinct biological nature? Clinicopathological study of 78 cases. Int J Lab Hematol 2021; 43:1117-1122. [PMID: 33847065 DOI: 10.1111/ijlh.13540] [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: 12/28/2020] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Infantile leukemia encompasses a heterogeneous group which needs stratifying for treatment selection. METHODS We collected 78 cases of infantile leukemia and retrospectively analyzed their clinicopathological data. RESULTS Infantile leukemia featured a ratio of acute myeloid leukemia (AML) to B-lymphoblastic leukemia (B-ALL) of 1:2, with a better survival for AML than B-ALL (median survival 36 vs 24 months). When stratified by age, "early" infantile B-ALL (2-6 months) showed a high rate of KMT2A rearrangement (100%), similar to the rate seen in congenital B-ALL (1 month) (100%) and higher than seen in "late" infantile B-ALL (≥7 months) (68%). The three categories of infantile B-ALL exhibited an age-dependent increase in survival (median survival 8.5, 24, and >24 months, respectively). The age-dependent survival benefit remained after excluding the cases negative for KMT2A rearrangement. Conversely, infantile AML lacked an age-dependent pattern of survival. CONCLUSION The clinical outcome of infantile leukemia depends on the type of leukemia. Given the age-dependent survival, infantile B-ALL can be divided into three subcategories.
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Affiliation(s)
- Xin Liu
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Yue Zhao
- Department of Pathology, Duke University Medical Center, Durham, NC, USA.,Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Catherine Luedke
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Rachel Jug
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Lian-He Yang
- Department of Pathology, Duke University Medical Center, Durham, NC, USA.,Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Mark Lu
- Department of Laboratory Medicine, University of California and Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Zenggang Pan
- Department of Pathology, Yale University Medical Center, New Haven, CT, USA
| | - Dehua Wang
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Lorsbach
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yang Shi
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY, USA
| | - Virginia Knez
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Catherine Rehder
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Xiayuan Liang
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Endi Wang
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
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7
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Miller DB, Piccolo SR. A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects. Front Genet 2021; 12:640242. [PMID: 33828584 PMCID: PMC8019969 DOI: 10.3389/fgene.2021.640242] [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: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
Compound heterozygous (CH) variants occur when two recessive alleles are inherited and the variants are located at different loci within the same gene in a given individual. CH variants are important contributors to many different types of recessively inherited diseases. However, many studies overlook CH variants because identification of this type of variant requires knowing the parent of origin for each nucleotide. Using computational methods, haplotypes can be inferred using a process called "phasing," which estimates the chromosomal origin of most nucleotides. In this paper, we used germline, phased, whole-genome sequencing (WGS) data to identify CH variants across seven pediatric diseases (adolescent idiopathic scoliosis: n = 16, congenital heart defects: n = 709, disorders of sex development: n = 79, ewing sarcoma: n = 287, neuroblastoma: n = 259, orofacial cleft: n = 107, and syndromic cranial dysinnervation: n = 172), available as parent-child trios in the Gabriella Miller Kids First Data Resource Center. Relatively little is understood about the genetic underpinnings of these diseases. We classified CH variants as "potentially damaging" based on minor allele frequencies (MAF), Combined Annotation Dependent Depletion scores, variant impact on transcription or translation, and gene-level frequencies in the disease group compared to a healthy population. For comparison, we also identified homozygous alternate (HA) variants, which affect both gene copies at a single locus; HA variants represent an alternative mechanism of recessive disease development and do not require phasing. Across all diseases, 2.6% of the samples had a potentially damaging CH variant and 16.2% had a potentially damaging HA variant. Of these samples with potentially damaging variants, the average number of genes per sample was 1 with a CH variant and 1.25 with a HA variant. Across all samples, 5.1 genes per disease had a CH variant, while 35.6 genes per disease had a HA variant; on average, only 4.3% of these variants affected common genes. Therefore, when seeking to identify potentially damaging variants of a putatively recessive disease, CH variants should be considered as potential contributors to disease development. If CH variants are excluded from analysis, important candidate genes may be overlooked.
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Affiliation(s)
| | - Stephen R. Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States
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8
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Abstract
Neonates are at risk for 3 major forms of leukemia in the first year of life: acute leukemia, juvenile myelomonocytic leukemia, and transient abnormal myelopoiesis associated with Down syndrome. These disorders are rare but generate interest due to aggressive clinical presentation, suboptimal response to current therapies, and fascinating biology. Each can arise as a result of unique constitutional and acquired genetic events. Genetic insights are pointing the way toward novel therapeutic approaches. This article reviews key epidemiologic, clinical, and molecular features of neonatal leukemias, focusing on risk stratification, treatment, and strategies for developing novel molecularly targeted approaches to improve future outcomes.
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Affiliation(s)
- Patrick A Brown
- Department of Oncology, Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA; Department of Pediatrics, Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA.
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9
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Detection of New Translocation in Infant Twins with Concordant ALL and Discordant Outcome. Pediatr Rep 2020; 13:9-14. [PMID: 33374488 PMCID: PMC7839053 DOI: 10.3390/pediatric13010002] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/21/2020] [Indexed: 01/06/2023] Open
Abstract
About 2-5% of acute lymphoblastic leukemia (ALL) cases in pediatric patients are infants with an unfavorable prognosis because of high relapse probability. Early detection of the disease is, therefore, very important. Despite the fact that leukemia in twins occurs rarely, more attention has been paid to it in genetic studies. In the present study, through cytogenetic testing, a special case of concordant ALL in monozygotic twins was presented with different outcomes. In spite of an acceptable initial consequence to medical treatment in twins, in another brother (Twin B), early relapse was observed. In the cytogenetic study, both twins expressed t (4; 11) (q21; q23) while twin A expressed t (2; 7) (p10; q10). No cases have previously reported this mutation. Whether this translocation has a protective role for leukemia with mixed-lineage leukemia (MLL) gene rearrangement is still unclear. The difference in the translocation identified in the identical twins is also subject to further investigations.
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10
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Matsukawa T, Aplan PD. Clinical and molecular consequences of fusion genes in myeloid malignancies. Stem Cells 2020; 38:1366-1374. [PMID: 32745287 DOI: 10.1002/stem.3263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/12/2020] [Accepted: 05/17/2020] [Indexed: 11/07/2022]
Abstract
Leukemias are heterogeneous diseases characterized by aberrant hematopoietic stem and progenitor cells (HSPCs). Oncogenic fusion genes and proteins, produced via gross chromosomal rearrangements, such as chromosomal translocation, insertion, and inversion, play important roles in hematologic malignancies. These oncoproteins alter fundamental cellular properties, such as self-renewal, differentiation, and proliferation, and confer leukemogenic potential to HSPCs. In addition to providing fundamental insights into the process of leukemic transformation, these fusion genes provide targets for treatment and monitoring of myeloid leukemias. Furthermore, new technologies such as next-generation sequencing have allowed additional insights into the nature of leukemic fusion genes. In this review, we discuss the history, biologic effect, and clinical impact of fusion genes in the field of myeloid leukemias.
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Affiliation(s)
- Toshihiro Matsukawa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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11
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Kimura S, Mullighan CG. Molecular markers in ALL: Clinical implications. Best Pract Res Clin Haematol 2020; 33:101193. [PMID: 33038982 DOI: 10.1016/j.beha.2020.101193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/28/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and remains a main cause of death in children despite recent improvements in cure rates. In the past decade, development of massively parallel sequencing has enabled large scale genome profiling studies of ALL, which not only led to identification of new subtypes in both B-cell precursor ALL (BCP-ALL) and T-cell ALL (T-ALL), but has also identified potential new therapeutic approaches to target vulnerabilities of many subtypes. Several of these approaches have been validated in preclinical models and are now being formally evaluated in prospective clinical trials. In this review, we provide an overview of the recent advances in our knowledge of genomic bases of BCP-ALL, T-ALL, and relapsed ALL, and discuss their clinical implications.
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Affiliation(s)
- Shunsuke Kimura
- Department of Pathology, Hematological Malignancies Program, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, 38105, TN, USA
| | - Charles G Mullighan
- Department of Pathology, Hematological Malignancies Program, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, 38105, TN, USA.
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12
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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13
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Miller DB, Piccolo SR. Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review. Front Genet 2020; 11:493. [PMID: 32508881 PMCID: PMC7249936 DOI: 10.3389/fgene.2020.00493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
A compound heterozygous (CH) variant is a type of germline variant that occurs when each parent donates one alternate allele and these alleles are located at different loci within the same gene. Pathogenic germline variants have been identified for some pediatric cancer types but in most studies, CH variants are overlooked. Thus, the prevalence of pathogenic CH variants in most pediatric cancer types is unknown. We identified 26 studies (published between 1999 and 2019) that identified a CH variant in at least one pediatric cancer patient. These studies encompass 21 cancer types and have collectively identified 25 different genes in which a CH variant occurred. However, the sequencing methods used and the number of patients and genes evaluated in each study were highly variable across the studies. In addition, methods for assessing pathogenicity of CH variants varied widely and were often not reported. In this review, we discuss technologies and methods for identifying CH variants, provide an overview of studies that have identified CH variants in pediatric cancer patients, provide insights into future directions in the field, and give a summary of publicly available pediatric cancer sequencing data. Although considerable insights have been gained over the last 20 years, much has yet to be learned about the involvement of CH variants in pediatric cancers. In future studies, larger sample sizes, more pediatric cancer types, and better pathogenicity assessment and filtering methods will be needed to move this field forward.
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Affiliation(s)
- Dustin B Miller
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States
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14
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Bowler TG, Pradhan K, Kong Y, Bartenstein M, Morrone KA, Sridharan A, Kessel RM, Shastri A, Giricz O, Bhagat TD, Gordon-Mitchell S, Rohanizadegan M, Hooda L, Datt I, Przychodzen BP, Parmar S, Maqbool S, Maciejewski JP, Steidl U, Greally JM, Verma A. Misidentification of MLL3 and other mutations in cancer due to highly homologous genomic regions. Leuk Lymphoma 2019; 60:3132-3137. [PMID: 31288594 DOI: 10.1080/10428194.2019.1630620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The MLL3 gene has been shown to be recurrently mutated in many malignancies including in families with acute myeloid leukemia. We demonstrate that many MLL3 variant calls made by exome sequencing are false positives due to misalignment to homologous regions, including a region on chr21, and can only be validated by long-range PCR. Numerous other recurrently mutated genes reported in COSMIC and TCGA databases have pseudogenes and cannot also be validated by conventional short read-based sequencing approaches. Genome-wide identification of pseudogene regions demonstrates that frequency of these homologous regions is increased with sequencing read lengths below 200 bps. To enable identification of poor quality sequencing variants in prospective studies, we generated novel genome-wide maps of regions with poor mappability that can be used in variant calling algorithms. Taken together, our findings reveal that pseudogene regions are a source of false-positive mutations in cancers.
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Affiliation(s)
- Timothy G Bowler
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Kith Pradhan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Yu Kong
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | - Kerry A Morrone
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Ashwin Sridharan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Rachel M Kessel
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Aditi Shastri
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Orsi Giricz
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | | | - Lauren Hooda
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Ishan Datt
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | | | - Shahina Maqbool
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | - Ulrich Steidl
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - John M Greally
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
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15
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Panagopoulou P, Skalkidou A, Marcotte E, Erdmann F, Ma X, Heck JE, Auvinen A, Mueller BA, Spector LG, Roman E, Metayer C, Magnani C, Pombo-de-Oliveira MS, Scheurer ME, Mora AM, Dockerty JD, Hansen J, Kang AY, Wang R, Doody DR, Kane E, Schüz J, Christodoulakis C, Ntzani E, Petridou ET. Parental age and the risk of childhood acute myeloid leukemia: results from the Childhood Leukemia International Consortium. Cancer Epidemiol 2019; 59:158-165. [PMID: 30776582 PMCID: PMC7098424 DOI: 10.1016/j.canep.2019.01.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Parental age has been associated with several childhood cancers, albeit the evidence is still inconsistent. AIM To examine the associations of parental age at birth with acute myeloid leukemia (AML) among children aged 0-14 years using individual-level data from the Childhood Leukemia International Consortium (CLIC) and non-CLIC studies. MATERIAL/METHODS We analyzed data of 3182 incident AML cases and 8377 controls from 17 studies [seven registry-based case-control (RCC) studies and ten questionnaire-based case-control (QCC) studies]. AML risk in association with parental age was calculated using multiple logistic regression, meta-analyses, and pooled-effect estimates. Models were stratified by age at diagnosis (infants <1 year-old vs. children 1-14 years-old) and by study design, using five-year parental age increments and controlling for sex, ethnicity, birthweight, prematurity, multiple gestation, birth order, maternal smoking and education, age at diagnosis (cases aged 1-14 years), and recruitment time period. RESULTS Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) derived from RCC, but not from the QCC, studies showed a higher AML risk for infants of mothers ≥40-year-old (OR = 6.87; 95% CI: 2.12-22.25). There were no associations observed between any other maternal or paternal age group and AML risk for children older than one year. CONCLUSIONS An increased risk of infant AML with advanced maternal age was found using data from RCC, but not from QCC studies; no parental age-AML associations were observed for older children.
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Affiliation(s)
- Paraskevi Panagopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Alkistis Skalkidou
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Erin Marcotte
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, U
| | - Friederike Erdmann
- International Agency for Research on Cancer, Section of Environment and Radiation, Lyon, France; Danish Cancer Society Research Center, Childhood Cancer Research Group, Copenhagen, Denmark
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Cancer Prevention and Control, Yale Comprehensive Cancer Center, Yale School of Medicine, CT, USA
| | - Julia E Heck
- Department of Epidemiology, School of Public Health, University of California, Los Angeles, CA, USA
| | - Anssi Auvinen
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | - Beth A Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Logan G Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, U
| | - Eve Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, Heslington, York, United Kingdom
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, CA, USA
| | - Corrado Magnani
- Cancer Epidemiology Unit, Department of Translational Medicine, CPO Piedmont and University of Eastern Piedmont, Novara, Italy
| | - Maria S Pombo-de-Oliveira
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, Heslington, York, United Kingdom; Pediatric Hematology-Oncology Program, Instituto Nacional de Cancer, Rio de Janeiro, Brazil
| | - Michael E Scheurer
- Baylor College of Medicine, Department of Pediatrics Texas Children's Cancer Center, TX, USA
| | - Ana-Maria Mora
- Central American Institute for Studies on Toxic Substances (IRET), Universidad Nacional, Heredia, Costa Rica
| | - John D Dockerty
- School of Public Health, University of California, Berkeley, CA, USA; Department of Preventative and Social Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Johnni Hansen
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Alice Y Kang
- School of Public Health, University of California, Berkeley, CA, USA
| | - Rong Wang
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Cancer Prevention and Control, Yale Comprehensive Cancer Center, Yale School of Medicine, CT, USA
| | - David R Doody
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eleanor Kane
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, Heslington, York, United Kingdom
| | - Joachim Schüz
- International Agency for Research on Cancer, Section of Environment and Radiation, Lyon, France
| | - Christos Christodoulakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Ntzani
- Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Greece; Center for Evidence Synthesis in Health, Brown University School of Public Health, Providence, RI, USA
| | - Eleni Th Petridou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Clinical Epidemiology Unit, Department of Medicine, Karolinska Institute, Stockholm, Sweden.
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16
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Abstract
Leukemia in infants is rare but generates tremendous interest due to its aggressive clinical presentation in a uniquely vulnerable host, its poor response to current therapies, and its fascinating biology. Increasingly, these biological insights are pointing the way toward novel therapeutic approaches. Using representative clinical case presentations, we review the key clinical, pathologic, and epidemiologic features of infant leukemia, including the high frequency of KMT2A gene rearrangements. We describe the current approach to risk-stratified treatment of infant leukemia in the major international cooperative groups. We highlight recent discoveries that elucidate the molecular biology of infant leukemia and suggest novel targeted therapeutic strategies, including modulation of aberrant epigenetic programs, inhibition of signaling pathways, and immunotherapeutics. Finally, we underscore the need for increased global collaboration to translate these discoveries into improved outcomes.
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17
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Diagnostic and Prognostic Utility of Fluorescence In situ Hybridization (FISH) Analysis in Acute Myeloid Leukemia. Curr Hematol Malig Rep 2018; 12:568-573. [PMID: 29064023 DOI: 10.1007/s11899-017-0426-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Acute myeloid leukemia (AML) is a hematologic neoplasia consisting of incompletely differentiated hematopoietic cells of the myeloid lineage that proliferate in the bone marrow, blood, and/or other tissues. Clinical implementation of fluorescence in situ hybridization (FISH) in cytogenetic laboratories allows for high-resolution analysis of recurrent structural chromosomal rearrangements specific to AML, especially in AML with normal karyotypes, which comprises approximately 33-50% of AML-positive specimens. Here, we review the use of several FISH probe strategies in the diagnosis of AML. We also review the standards and guidelines currently in place for use by clinical cytogenetic laboratories in the evaluation of AML. RECENT FINDINGS Updated standards and guidelines from the WHO, ACMG, and NCCN have further defined clinically significant, recurring cytogenetic anomalies in AML that are detectable by FISH. FISH continues to be a powerful technique in the diagnosis of AML, with higher resolution than conventional cytogenetic analysis, rapid turnaround time, and a considerable diagnostic and prognostic utility.
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18
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Marcotte EL, Druley TE, Johnson KJ, Richardson M, von Behren J, Mueller BA, Carozza S, McLaughlin C, Chow EJ, Reynolds P, Spector LG. Parental Age and Risk of Infant Leukaemia: A Pooled Analysis. Paediatr Perinat Epidemiol 2017; 31:563-572. [PMID: 28940632 PMCID: PMC5901723 DOI: 10.1111/ppe.12412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Infant leukaemia (IL) is extremely rare with fewer than 150 cases occurring each year in the United States. Little is known about its causes. However, recent evidence supports a role of de novo mutations in IL aetiology. Parental age has been associated with several adverse outcomes in offspring, including childhood cancers. Given the role of older parental age in de novo mutations in offspring, we carried out an analysis of parental age and IL. METHODS We evaluated the relationship between parental age and IL in a case-control study using registry data from New York, Minnesota, California, Texas, and Washington. Records from 402 cases [219 acute lymphoblastic leukaemia (ALL), 131 acute myeloid leukaemia (AML), and 52 other] and 45 392 controls born during 1981-2004 were analysed. Odds ratios (OR) and 95% confidence intervals (CI) were calculated by logistic regression. Estimates were adjusted for infant sex, birth year category, maternal race, state, and mutually adjusted for paternal or maternal age, respectively. RESULTS Infants with mothers' age ≥40 years had an increased risk of developing AML (OR 4.80, 95% CI 1.80, 12.76). In contrast, paternal age <20 was associated with increased risk of ALL (OR 3.69, 95% CI 1.62, 8.41). CONCLUSION This study demonstrates increased risk of infant ALL in relation to young paternal age. Given record linkage, there is little concern with recall or selection bias, although data are lacking on MLL gene status and other potentially important variables. Parent of origin effects, de novo mutations, and/or carcinogenic exposures may be involved in IL aetiology.
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Affiliation(s)
- Erin L Marcotte
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN,Masonic Cancer Center, Minneapolis, MN,Corresponding author: Erin L Marcotte, PhD, Department of Pediatrics, Division of Epidemiology & Clinical Research, MMC 715, 420 Delaware St. S.E., Minneapolis, MN 55455; phone: 612-626-3281, fax: 612-624-7147,
| | - Todd E Druley
- Departments of Pediatrics and Genetics, Washington University, St Louis, MO
| | - Kimberly J Johnson
- Brown School and Department of Pediatrics, Washington University, St Louis, MO
| | - Michaela Richardson
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | | | - Beth A Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Susan Carozza
- Epidemiology Program, College of Public Health & Human Sciences, Oregon State University, Corvallis, OR
| | - Colleen McLaughlin
- Department of Population Health Sciences, Albany College of Pharmacy and Health Sciences, Albany, NY
| | - Eric J Chow
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Logan G Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN,Masonic Cancer Center, Minneapolis, MN
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19
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Pombo-de-Oliveira MS, Andrade FG. Early-age Acute Leukemia: Revisiting Two Decades of the Brazilian Collaborative Study Group. Arch Med Res 2017; 47:593-606. [PMID: 28476187 DOI: 10.1016/j.arcmed.2016.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022]
Abstract
The understanding of leukemogenesis in early-age acute leukemia (EAL) has improved remarkably. Initiating somatic mutations detected in dried neonatal blood spots (DNBS) and in cord blood samples of affected children with leukemia have been proven to be acquired prenatally. However, to date, few epidemiological studies have been carried out exploring EAL that include infants and children 13-24 months of age at the diagnosis. Maternal exposure to transplacental DNA-damaging substances during pregnancy has been suggested to be a risk factor for EAL. Most cases of infants with acute lymphoblastic (i-ALL) or myeloid leukemia (i-AML) have KMT2A gene rearrangements (KMT2A-r), which disturb its essential role as an epigenetic regulator of hematopoiesis. Due to the short latency period for EAL and the fact that KMT2A-r resembles those found in secondary AML, exposure to topoisomerase II inhibitors has been associated with transplacental risk as proxi for causality. EAL studies have been conducted in Brazil for over two decades, combining observational epidemiology, leukemia biology, and clinical data. EAL was investigated considering (i) age strata (infants vs. 13-24 months-old); (ii) somatic mutations associated with i-ALL and i-AML; (iii) ethnic-geographic variations; (iv) contribution of maternal genotypes; and (v) time latency of exposures and mutations in DNBS. Interactions of acquired and constitutive gene mutations are challenging tools to test risk factor associations for EAL. In this review we summarize the EAL scenario (including B-cell precursor-ALL, T-ALL, and AML) results combining environmental and genetic susceptibility risk factors and we raise questions that should be considered for further action.
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Affiliation(s)
- Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Research Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| | - Francianne Gomes Andrade
- Pediatric Hematology-Oncology Research Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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- Pediatric Hematology-Oncology Research Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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20
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Abstract
PURPOSE OF REVIEW The prognosis for infants less than 12 months of age who are diagnosed with acute lymphoblastic leukemia (ALL) remains poor despite overall advances in the treatment of childhood ALL. In this review, we highlight the recent advances in the understanding of the pathogenesis of infant ALL and discuss opportunities for translating these findings into clinical trials. RECENT FINDINGS Infant ALL can be divided into two major disease types, defined by the presence or absence of KMT2A (MLL) rearrangement (KMT2A-R). Recent molecular profiling studies have found that infant ALL with KMT2A-R is an epigenomic disease that lacks other somatic driver mutations. Strategies to intensify therapy have not improved survival for infants with KMT2A-R ALL. In contrast, infant ALL without KMT2A-R is more similar to ALL of older children and survival has improved modestly with intensification of chemotherapy. Discovery of clonal molecular markers that predict chemoresistance will allow further risk classification and development of novel treatment strategies. Modern clinical trials are integrating molecularly targeted therapies into the treatment of infant ALL. SUMMARY Advances in molecular profiling and integration of targeted therapy have the potential to reduce toxicity and improve survival for infants with ALL.
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21
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Winters AC, Bernt KM. MLL-Rearranged Leukemias-An Update on Science and Clinical Approaches. Front Pediatr 2017; 5:4. [PMID: 28232907 PMCID: PMC5299633 DOI: 10.3389/fped.2017.00004] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/09/2017] [Indexed: 12/18/2022] Open
Abstract
The mixed-lineage leukemia 1 (MLL1) gene (now renamed Lysine [K]-specific MethylTransferase 2A or KMT2A) on chromosome 11q23 is disrupted in a unique group of acute leukemias. More than 80 different partner genes in these fusions have been described, although the majority of leukemias result from MLL1 fusions with one of about six common partner genes. Approximately 10% of all leukemias harbor MLL1 translocations. Of these, two patient populations comprise the majority of cases: patients younger than 1 year of age at diagnosis (primarily acute lymphoblastic leukemias) and young- to-middle-aged adults (primarily acute myeloid leukemias). A much rarer subgroup of patients with MLL1 rearrangements develop leukemia that is attributable to prior treatment with certain chemotherapeutic agents-so-called therapy-related leukemias. In general, outcomes for all of these patients remain poor when compared to patients with non-MLL1 rearranged leukemias. In this review, we will discuss the normal biological roles of MLL1 and its fusion partners, how these roles are hypothesized to be dysregulated in the context of MLL1 rearrangements, and the clinical manifestations of this group of leukemias. We will go on to discuss the progress in clinical management and promising new avenues of research, which may lead to more effective targeted therapies for affected patients.
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Affiliation(s)
- Amanda C Winters
- Division of Pediatric Hematology/Oncology/BMT, University of Colorado School of Medicine and Children's Hospital Colorado , Aurora, CO , USA
| | - Kathrin M Bernt
- Division of Pediatric Hematology/Oncology/BMT, University of Colorado School of Medicine and Children's Hospital Colorado , Aurora, CO , USA
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22
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Urtishak KA, Robinson BW, Rappaport EF, Sarezky MD, Biegel JA, Nichols KE, Wilmoth DM, Wang LS, Stern JW, Felix CA. Unique Familial MLL(KMT2A)-Rearranged Precursor B-Cell Infant Acute Lymphoblastic Leukemia in Non-twin Siblings. Pediatr Blood Cancer 2016; 63:1175-80. [PMID: 26999444 DOI: 10.1002/pbc.25957] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Infant acute lymphoblastic leukemia (ALL) has never occurred in families except for the ∼100% concordant cases in monozygous twins attributed to twin-to-twin metastases. We report the first kindred with infant ALL in non-twin siblings. The siblings were diagnosed with MLL-rearranged (MLL-R) ALL 26 months apart. The second affected sibling had an unaffected dichorionic monozygous co-twin. Both had fatal outcomes. PROCEDURES Translocations were characterized by karyotype, FISH, multiplex FISH, and MLL breakpoint cluster region (bcr) Southern blot analysis. Breakpoint junctions and fusion transcripts were cloned by PCR. TP53 mutation and NADPH quinone oxidorecuctase 1 (NQO1) C609T analyses were performed, and pedigree history and parental occupations were ascertained. The likelihood of chance occurrence of infant ALL in non-twin siblings was computed based on a binomial distribution. Zygosity was determined by single nucleotide polymorphism (SNP) array. RESULTS The translocations were not related or vertically transmitted. The complex karyotype of the proband's ALL had chromosome 2, 3, 4, and 11 abnormalities causing a 5'-MLL-AFF1-3' fusion and a non-productive rearrangement of 3'MLL with a chromosome 3q intergenic region. The affected twin's ALL exhibited a simple t(4;11). The complex karyotype of the proband's ALL suggested a genotoxic insult, but no exposure was identified. There was no germline TP53 mutation. The NQO1 C609T risk allele was absent. The likelihood of infant ALL occurring in non-twin siblings by chance alone is one in 1.198 × 10(9) families. CONCLUSIONS Whether because of a deleterious transplacental exposure, novel predisposition syndrome, or exceedingly rare chance occurrence, MLL-R infant ALL can occur in non-twin siblings. The discordant occurrence of infant ALL in the monozygous twins was likely because they were dichorionic.
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Affiliation(s)
- Karen A Urtishak
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Blaine W Robinson
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eric F Rappaport
- Nucleic Acids & Protein Core Facility, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Margaret D Sarezky
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jaclyn A Biegel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kim E Nichols
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Donna M Wilmoth
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Julie W Stern
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carolyn A Felix
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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23
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Characterization of two de novoKCNT1 mutations in children with malignant migrating partial seizures in infancy. Mol Cell Neurosci 2016; 72:54-63. [PMID: 26784557 DOI: 10.1016/j.mcn.2016.01.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/06/2015] [Accepted: 01/15/2016] [Indexed: 01/08/2023] Open
Abstract
The KCNT1 gene encodes for subunits contributing to the Na(+)-activated K(+) current (KNa), expressed in many cell types. Mutations in KCNT1 have been found in patients affected with a wide spectrum of early-onset epilepsies, including Malignant Migrating Partial Seizures in Infancy (MMPSI), a severe early-onset epileptic encephalopathy characterized by pharmacoresistant focal seizures migrating from one brain region or hemisphere to another and neurodevelopment arrest or regression, resulting in profound disability. In the present study we report identification by whole exome sequencing (WES) of two de novo, heterozygous KCNT1 mutations (G288S and, not previously reported, M516V) in two unrelated MMPSI probands. Functional studies in a heterologous expression system revealed that channels formed by mutant KCNT1 subunits carried larger currents when compared to wild-type KCNT1 channels, both as homo- and heteromers with these last. Both mutations induced a marked leftward shift in homomeric channel activation gating. Interestingly, the KCNT1 blockers quinidine (3-1000μM) and bepridil (0.03-10μM) inhibited both wild-type and mutant KCNT1 currents in a concentration-dependent manner, with mutant channels showing higher sensitivity to blockade. This latter result suggests two genotype-tailored pharmacological strategies to specifically counteract the dysfunction of KCNT1 activating mutations in MMPSI patients.
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24
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Zimmerman R, Schimmenti L, Spector L. A Catalog of Genetic Syndromes in Childhood Cancer. Pediatr Blood Cancer 2015; 62:2071-5. [PMID: 26312571 DOI: 10.1002/pbc.25726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/06/2015] [Indexed: 12/13/2022]
Abstract
Genetic syndromes and pediatric cancers are rare, so instances of co-occurrence raise the question of whether the two conditions may be etiologically linked. Clear examples of causal association can be found in the cancer predisposition syndromes. This report contains the results of a systematic literature search using Ovid Medline for co-occurrence of genetic syndromes with 23 types of pediatric cancer. The results reflect known associations as well as many reports of infrequently observed co-occurrences. This compilation may suggest previously overlooked patterns, and the information could be used to identify gene pathways critical in the development of childhood cancers.
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25
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Mansur MB, van Delft FW, Colman SM, Furness CL, Gibson J, Emerenciano M, Kempski H, Clappier E, Cave H, Soulier J, Pombo-de-Oliveira MS, Greaves M, Ford AM. Distinctive genotypes in infants with T-cell acute lymphoblastic leukaemia. Br J Haematol 2015. [PMID: 26205622 PMCID: PMC4737125 DOI: 10.1111/bjh.13613] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Infant T‐cell acute lymphoblastic leukaemia (iT‐ALL) is a very rare and poorly defined entity with a poor prognosis. We assembled a unique series of 13 infants with T‐ALL, which allowed us to identify genotypic abnormalities and to investigate prenatal origins. Matched samples (diagnosis/remission) were analysed by single nucleotide polymorphism‐array to identify genomic losses and gains. In three cases, we identified a recurrent somatic deletion on chromosome 3. These losses result in the complete deletion of MLF1 and have not previously been described in T‐ALL. We observed two cases with an 11p13 deletion (LMO2‐related), one of which also harboured a deletion of RB1. Another case presented a large 11q14·1‐11q23·2 deletion that included ATM and only five patients (38%) showed deletions of CDKN2A/B. Four cases showed NOTCH1 mutations; in one case FBXW7 was the sole mutation and three cases showed alterations in PTEN. KMT2A rearrangements (KMT2A‐r) were detected in three out of 13 cases. For three patients, mutations and copy number alterations (including deletion of PTEN) could be backtracked to birth using neonatal blood spot DNA, demonstrating an in utero origin. Overall, our data indicates that iT‐ALL has a diverse but distinctive profile of genotypic abnormalities when compared to T‐ALL in older children and adults.
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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
| | | | - Susan M Colman
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Jane Gibson
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Mariana Emerenciano
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Helena Kempski
- Paediatric Malignancy Cytogenetics Unit, Institute of Child Health & Great Ormond Street Hospital, London, UK
| | | | - Hélène Cave
- Department of Genetics, Robert Debré Hospital, APHP, Paris, France
| | - Jean Soulier
- Haematology Laboratory, Saint-Louis Louis Hospital, APHP, Paris, France
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Anthony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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Recent Advances in the 5q- Syndrome. Mediterr J Hematol Infect Dis 2015; 7:e2015037. [PMID: 26075044 PMCID: PMC4450650 DOI: 10.4084/mjhid.2015.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/28/2015] [Indexed: 12/12/2022] Open
Abstract
The 5q- syndrome is the most distinct of the myelodysplastic syndromes (MDS) and patients with this disorder have a deletion of chromosome 5q [del(5q)] as the sole karyotypic abnormality. Several genes mapping to the commonly deleted region of the 5q- syndrome have been implicated in disease pathogenesis in recent years. Haploinsufficiency of the ribosomal gene RPS14 has been shown to cause the erythroid defect in the 5q- syndrome. Loss of the microRNA genes miR-145 and miR-146a has been associated with the thrombocytosis observed in 5q- syndrome patients. Haploinsufficiency of CSNK1A1 leads to hematopoietic stem cell expansion in mice and may play a role in the initial clonal expansion in patients with 5q- syndrome. Moreover, a subset of patients harbor mutation of the remaining CSNK1A1 allele. Mouse models of the 5q- syndrome, which recapitulate the key features of the human disease, indicate that a p53-dependent mechanism underlies the pathophysiology of this disorder. Importantly, activation of p53 has been demonstrated in the human 5q- syndrome. Recurrent TP53 mutations have been associated with an increased risk of disease evolution and with decreased response to the drug lenalidomide in del(5q) MDS patients. Potential new therapeutic agents for del(5q) MDS include the translation enhancer L-leucine.
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Abstract
The causes of childhood cancer have been systematically studied for decades, but apart from high-dose radiation and prior chemotherapy there are few strong external risk factors. However, inherent risk factors including birth weight, parental age, and congenital anomalies are consistently associated with most types of pediatric cancer. Recently the contribution of common genetic variation to etiology has come into focus through genome-wide association studies. These have highlighted genes not previously implicated in childhood cancers and have suggested that common variation explains a larger proportion of childhood cancers than adult. Rare variation and nonmendelian inheritance may also contribute to childhood cancer risk but have not been widely examined.
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Affiliation(s)
- Logan G. Spector
- Division of Epidemiology/Clinical Research Department of Pediatrics University of Minnesota 420 Delaware Street, SE, MMC 715 Minneapolis, MN 55455
| | - Nathan Pankratz
- Department of Lab Medicine and Pathology University of Minnesota
| | - Erin L. Marcotte
- Division of Epidemiology/Clinical Research Department of Pediatrics University of Minnesota
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