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  • 1
    In: Nature, Springer Science and Business Media LLC, Vol. 534, No. 7607 ( 2016-6), p. 402-406
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
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  • 2
    In: The American Journal of Human Genetics, Elsevier BV, Vol. 103, No. 3 ( 2018-09), p. 440-447
    Type of Medium: Online Resource
    ISSN: 0002-9297
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2018
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 19 ( 2021-10-01), p. 4926-4938
    Abstract: Esophageal squamous cell carcinoma (ESCC) often recurs after chemoradiotherapy, and the prognosis of ESCC after chemoradiotherapy has not improved over the past few decades. The mutation process in chemoradiotherapy-resistant clones and the functional relevance of genetic alterations remain unclear. To address these problems, we performed whole-exome sequencing of 52 tumor samples from 33 patients with ESCC who received radiotherapy combined with 5-fluorouracil/platinum. In multiregion analyses of pretreatment and locally recurrent lesions from five cases, most driver gene-altered clones remained under chemoradiotherapy selection pressure, while few driver gene alterations were acquired at recurrence. The mutation signatures of recurrent ESCC, including increased deletion frequency and platinum dose-dependent base substitution signatures, were substantially different from those of primary ESCC and reflected the iatrogenic impacts of chemoradiotherapy. Single-region analysis of 28 pretreatment tumors indicated that focal copy-number gain at the MYC locus was significantly associated with poor progression-free survival and overall survival after chemoradiotherapy. MYC gain remained throughout the chemoradiotherapy course and potentially contributes to intrinsic resistance to chemoradiotherapy. Consistent with these findings, MYC copy number and mRNA and protein levels in ESCC cell lines correlated positively with resistance to radiotherapy, and MYC knockdown improved sensitivity to radiotherapy. Overall, these data characterize the clonal evolution process induced by chemoradiotherapy and clinically relevant associations for genetic alterations in ESCC. These findings increase our understanding of therapeutic resistance and support the rationale for precision chemoradiotherapy. Significance: Whole-exome sequencing reveals the genetic evolution of ESCC during chemoradiotherapy, highlighting MYC gain in pretreatment tumors as a potential marker of therapy resistance.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 4
    In: Cancer Science, Wiley, Vol. 110, No. 10 ( 2019-10), p. 3358-3367
    Abstract: Children with Down syndrome ( DS ) are at a 20‐fold increased risk for acute lymphoblastic leukemia ( ALL ). Compared to children with ALL and no DS (non‐ DS ‐ ALL ), those with DS and ALL ( DS ‐ ALL ) harbor uncommon genetic alterations, suggesting DS ‐ ALL could have distinct biological features. Recent studies have implicated several genes on chromosome 21 in DS ‐ ALL , but the precise mechanisms predisposing children with DS to ALL remain unknown. Our integrated genetic/epigenetic analysis revealed that DS ‐ ALL was highly heterogeneous with many subtypes. Although each subtype had genetic/epigenetic profiles similar to those found in non‐ DS ‐ ALL , the subtype distribution differed significantly between groups. The Philadelphia chromosome‐like subtype, a high‐risk B‐cell lineage variant relatively rare among the entire pediatric ALL population, was the most common form in DS ‐ ALL . Hypermethylation of RUNX 1 on chromosome 21 was also found in DS ‐ ALL , but not non‐ DS ‐ ALL . RUNX 1 is essential for differentiation of blood cells, especially B cells; thus, hypermethylation of the RUNX 1 promoter in B‐cell precursors might be associated with increased incidence of B‐cell precursor ALL in DS patients.
    Type of Medium: Online Resource
    ISSN: 1347-9032 , 1349-7006
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
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  • 5
    In: Blood, American Society of Hematology, Vol. 128, No. 22 ( 2016-12-02), p. 4084-4084
    Abstract: Background Children with Down syndrome (DS), which caused by an extra copy of chromosome 21, are predisposed to develop acute lymphoblastic leukemia (ALL). On the other hand, in non-DS children, acquisition of chromosome 21 gain is observed in 95% of hyperdiploid (HD) ALL, which is the most common cytogenetic abnormality pattern in childhood ALL. These may suggest that gain of chromosome 21 relates molecular pathogenesis of ALL. Genetic aberrations of RUNX1 locus on chromosome 21 including iAMP21 or t(12; 21)(p13; q22)/ETV6-RUNX1 were often found in pediatric ALL. While recent studies implicated that HMGN1 or DYRK1A on chromosome 21 were associated with molecular pathogenesis of DS-ALL, it remains to be elucidated what predispose DS children to develop ALL. Compared with ALL of non-DS children, DS-ALL have uncommon genetic alterations such as mutations in JAK2 and RAS, mutations or overexpression of CRLF2. These suggest that DS-ALL may have unique biological features compared with ALL of non-DS children. Difference of biological basis between them may correlate to worse prognosis of DS-ALL. Although microarray transcript profiling provided some characteristic gene expression in DS-ALL, no study showed comprehensive transcriptome analysis in DS-ALL. Purpose This study was conducted to elucidate comprehensive transcriptomic landscape in DS-ALL and to reveal biological features through clustering by gene expression profiling. Methods Our cohort includes 72 pediatric B-cell precursor ALL samples (48 DS-ALL, 13 HD-ALL, and 11 euploid (EP) ALL). All HD-ALL samples gained chromosome 21. Three cases of DS-ALL and one case of EP-ALL had ETV6-RUNX1 rearrangement. We applied genome-wide analysis using whole-transcriptome sequencing (WTS) to 55 samples, Illumina 450k methylation array to 12 samples, and Illumina EPIC methylation array to 26 samples. For gene expression profiling, we conducted consensus clustering algorithms. Data from methylation arrays were normalized by beta-mixture quantile normalization and merged by common probes. Results Our consensus clustering analysis of gene expression stratified samples into three groups such as DS-ALL (cluster 1), DS-ALL and HD-ALL (cluster 2), and EP-ALL (cluster 3). Eight cases with DS-ALL having RAS mutations were classified into cluster 1. DYRK1A, HMGN1, ETS2 on chromosome 21 were highly expressed in cluster 1 and cluster 2 compared with cluster 3. Expression of RUNX1 was lower in cluster 1 and cluster 2 although it was not significant. In addition, FLT3, ELK1, and ETV6 were more highly expressed in cluster 1 and cluster 2 compared with cluster 3. Comparing cluster 1 with cluster 2, NRAS, MAP2K1, JUN, FOS, WT1, EPOR, and PDGFRB were highly expressed in cluster 1. Methylation analysis indicated that methylation pattern of DS-ALL was distinct from that of HD-ALL. Using methylation analysis, we detected differentially methylated regions (DMRs) between DS-ALL and HD-ALL. In DMRs of promoter-associated regions, RUNX1, IGF2BP1, and ETV6 were included. These genes were significantly hypermethylated in DS-ALL. Next, we elucidated methylation profiling of DS-ALL compared with HD-ALL and found hypermethylated genes in DS-ALL. Although these genes may participate pathogenesis of DS-ALL, we could not find any association of gene expression pattern. Conclusion We identified specific gene expression profiling of DS-ALL and significantly upregulated genes in DS-ALL compared with HD-ALL and EP-ALL. Overexpression of these genes was characteristic gene profiling common to ALL with gaining extra chromosome 21. While ETS2, FLT3, ELK1, NRAS, MAP2K, JUN, FOS, and WT1 were highly expressed in AML, overexpression of these genes may also be related to pathogenesis of DS-ALL. In addition, DS-ALL highly expressed PDGFRB and EPOR, to which these genes are targetable by TKIs and may improve prognosis of DS-ALL. Intriguingly, RUNX1 was hypermethylated in DS-ALL compared with HD-ALL and EP-ALL, indicating that underexpression of RUNX1 was a unique gene profiling of DS-ALL and was due to hypermethylation of RUNX1. In DS patient, hyprmethylation of RUNX1 in their normal blood cells has been reported. This aberrant hypermethylation may be related to pathogenesis of DS-ALL. In this study, we unveiled gene expression profiling and methylation pattern of DS-ALL. However, to elucidate the whole picture of molecular pathogenesis of DS-ALL, we may need further analysis. Disclosures Kataoka: Yakult: Honoraria; Boehringer Ingelheim: Honoraria; Kyowa Hakko Kirin: Honoraria. Ogawa:Kan research institute: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding; Takeda Pharmaceuticals: Consultancy, Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
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  • 6
    In: HemaSphere, Ovid Technologies (Wolters Kluwer Health), Vol. 7, No. S3 ( 2023-08), p. e51775a7-
    Type of Medium: Online Resource
    ISSN: 2572-9241
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2023
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  • 7
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 2817-2817
    Abstract: Background Acute lymphoblastic leukemia (ALL) in Down syndrome (DS) have uncommon genetic alterations such as mutations of JAK2, RAS, and overexpressions of CRLF2. These findings suggest DS-ALL may have unique biological features compared with non-DS-ALL. While recent studies implicated HMGN1 or DYRK1A in chromosome 21 were associated with molecular pathogenesis of DS-ALL, it remains to be elucidated what predispose DS children to develop ALL. Materials and Methods We performed whole transcriptome sequencing, targeted deep sequencing, and SNP array analysis in 25 DS-ALL samples, which included four ETV6-RUNX1 fusions and one high hyperdiploid. To compare with DS-ALL, we also performed whole transcriptome sequencing and whole exome sequencing to 118 non-DS-ALL samples, which included several subtypes such as ETV6-RUNX1 or BCR-ABL1. To cluster gene expression profiling, we applied the hierarchical clustering method. The detection of Ph-like signatures was performed by the hierarchical clustering by the gene set reported by Harvey. Results In expression analysis, we identified 19 fusions in 25 DS-ALL samples. These fusions included 15 recurrent fusions in pediatric BCP-ALL and 4 novel fusions, which including SSBP3-DHCR24, PDGFA-TTYH3, and NIN-NDUFA6. In novel fusions, PDGFA-TTYH3 fusions were detected in two DS-ALL samples. The hierarchical clustering analysis (Figure 1) combining 25 DS-ALL with 123 non-DS ALL samples. In our cohort, we defined samples with PAX5 alteration only such as a mutation or fusion as PAX5-altered. This clustering revealed ALL samples were divided into six clusters (cluster E1 to E6). Among six clusters, DS-ALL samples were divided into four clusters. In these four clusters, chi-square test revealed the significant enrichment of DS-ALL in E6 cluster. Importantly, our expression analysis revealed DS-ALL samples were highly heterogeneous and had the same expression pattern corresponding to each subtype same as non-DS-ALL. Cluster E3 included most samples with PAX5 fusions. All samples with ETV6-RUNX1 fusions were classified into cluster E4. Most samples of high hyperdiploid were classified into cluster E5. Cluster E6 was characterized by BCR-ABL1 fusions and Ph-like signatures. We detected 21 samples had Ph-like signatures, which included seven DS-ALL samples and 14 non-DS-ALL samples. Though we also analyzed differentially expressed genes between DS-ALL and non-DS-ALL, no genes on chromosome 21 such as HNGN1 or DYRK1A was significantly expressed. To investigate a relation between expression and genomic status, we further searched mutational analysis and copy number analysis (Figure 2). In 25 DS-ALL samples, six samples revealed JAK2 mutations and CRLF2 fusions. Interestingly, all of these six samples had Ph-like signatures. In cluster E5, one non-DS-ALL sample revealed JAK2 mutation and CRLF2 fusion and this particular sample was expected to have the Ph-like signature. To detect other Ph-like samples, we performed hierarchical clustering of 143 ALL samples based on the genes with a significantly (adjusted P value 〈 0.0001) high expression in already detected 21 Ph-like samples. This analysis revealed three additional samples (two DS-ALL and one non-DS-ALL) had Ph-like signatures. Intriguingly, Ph-like samples accounted for 36% in 25 DS-ALL samples. In contrast, because several subtypes in non-DS-ALL showed mutations of RAS pathway genes, mutations of RAS pathway genes are common drivers in pediatric BCP-ALL. Copy number analysis elucidated one DS-ALL sample in cluster E3 had a known focal amplification of chromosome 9 involving exon 2 to 5 of PAX5, which may result in dysfunction of PAX5. Though no report analyzed PAX5 status except for deletion in DS-ALL, DS-ALL had not only deletion of PAX5, but also miscellaneous aberrations such as amplification or fusion. One DS-ALL sample without ETV6-RUNX1 in cluster E4 had homozygous deletions of ETV6, implicating ETV6-RUNX1-like signature. Conclusion Our result suggested DS-ALL were highly heterogeneous. Though expression profiles of DS-ALL had similar to non-DS-ALL, frequencies of subtypes in DS-ALL were quite different from non-DS-ALL, that is, low incidence of ETV6-RUNX1 or HeH, and high incidence of Ph-like signatures. Because molecular targeting agents such as imatinib or ruxolitinib improve the prognosis of Ph-like ALL, these agents may be also promising for treatment of DS-ALL. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
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  • 8
    In: Blood, American Society of Hematology, Vol. 121, No. 21 ( 2013-05-23), p. 4377-4387
    Abstract: Genetically heterogeneous subclones with varying leukemia-initiating potential exist in neonatal transient abnormal myelopoiesis. This novel xenograft model of transient abnormal myelopoiesis may provide unique insight into the evolutionary process of leukemia.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
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  • 9
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 711-711
    Abstract: Background: Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative therapy for patients with myelodysplastic syndromes (MDS), whose benefit, however, is frequently offset by accompanying mortality and morbidity, underscoring the importance of accurate prognostication before the therapeutic choice. For this purpose, several systems, such as the International Prognostic Scoring System (IPSS), are being successfully applied to clinics, and recent genome profiling studies indicate that molecular diagnostics can further improve the prediction. Nevertheless, existing systems are based on the observation from those patients who were untreated or only supportively treated and therefore, may not successfully be applied to the prognostication of the patients who are actually treated by HSCT. Methods: We analyzed patients with MDS (N = 719) from a cohort of Japan Marrow Donor Program (JMDP) who were treated by unrelated HSCT between 2006 and 2013. Peripheral blood DNA was subjected to targeted deep sequencing in 68 major driver genes for the detection of both somatic mutations and copy number variations (CNVs) with accurate determination of their allelic burdens. Results: The median age at HSCT and observation period were 53 years old (20-66) and 372 days (2-3001), respectively. At the diagnosis, 63, 203, 163 and 65 patients have low, intermediate-1, intermediate-2 and high risk classified on the basis of IPSS, respectively (IPSS data was not available for 250 patients). The median time from diagnosis to HSCT was 274 (9-10900) days. Mutations were observed in 75% of the patients, of which TP53 was most frequently mutated (14.3%), followed by U2AF1 (13.2%), RUNX1 (12.2%), ASXL1 (11.0%) and DNMT3A (9.3%). The mean number of mutations was 2.1 per patient and the mean allelic burden was 23.4%. To evaluate karyotyping we combined metaphase cytogenetics and copy number variations using targeted sequencing data. Complex karyotype, chromosome 7 anomaly, deletion 5q, and deletion 20q were observed in 174 (24.4%), 173 (24.3%), 91 (12.8%), and 50 (7.0%) of the patients, respectively. Combined, 86.6% of the patients had one or more genetic lesions. Patients with one or more mutations or CNVs showed unfavorable overall survival (Hazard Ratio (HR) 2.46, P = 2.12 x 10-5). Univariate analysis for each gene identified mutations in TP53 (HR 2.85, P 〈 2.0 x 10-16), NRAS (HR 1.90, P = 5.4 x 10-4), ETV6 (HR 1.54, P = 0.029), CBL (HR 2.25, P = 5.3 x10-5), EZH2 (HR 1.74, P = 0.014), KRAS (HR 2.01, P = 2.0 x 10-3), U2AF2 (HR 1.97, P = 0.027), JARID2 (HR 2.09, P = 0.039), and RIT1 (HR 2.16, P = 0.023) as the unfavorable factors for the overall survival. Besides, mutations in PRPF8 had a favorable effect on overall survival (HR 0.50, P = 0.029). Then, we performed multivariate analysis with stepwise model selection of these significant mutations and clinical parameters. Mutations in TP53 (HR 2.31, P=0.015), and ETV6 (HR 2.57, P=0.015) remained significant together with complex karyotype (HR 2.15, P = 0.0063), grade of acute graft versus host disease (GVHD) (Grade I or II: HR 1.95, P = 0.011, Grade III or IV: HR 4.18, P = 7.94 x 10-5), and the number of red blood cell transfusion received before HSCT ( 〉 =10 times: HR 2.64, P = 0.027). Next, we analyzed the impact of mutations on relapse in cases who achieved complete response after HSCT (N = 423 (58.8%)). Patients with mutations in one or more genetic lesions showed unfavorable relapse free survival (HR 2.27, P = 1.65 x 10-4). Univariate analysis for each gene revealed mutations in TP53 (HR 3.09, P = 9.5 x 10-16), NRAS (HR 2.21, P = 0.0019), ETV6 (HR 1.90, P = 0.012), PRPF8 (HR 0.40, P = 0.046), and WT1 (HR 2.24, P = 0.013) were significant for the relapse free survival. Multivariate analysis and stepwise model selection identified ETV6 (HR 2.98, P = 0.011), WT1 (HR 4.01, P = 0.014), complex karyotype (HR 2.39, P = 0.0083), IPSS High (HR 6.22, P = 0.0053), and Grade III or IV acute GVHD (HR 2.91, P = 0.0071) as unfavorable factors. Conclusions: This large study of MDS cases treated by unrelated HSCT demonstrated that somatic mutations of several driver genes were novel prognostic factors for overall and relapse free survival. These genetic factors were independent of well-known prognostic makers, and therefore could be used to better guide therapy for MDS patients. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 10
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 1410-1410
    Abstract: Pediatric acute myeloid leukemia (AML) comprises ∼20% of pediatric leukemia, representing one of the major therapeutic challenges in pediatric oncology. Nearly 40% of patients still relapse after present first-line therapies and once the relapse occurs, the long-term survival rates decrease, ranging from 21% to 34%. As for the pathogenesis of AML relapse, the recent development of massively parallel sequencing technologies has provided a new opportunity to investigate comprehensive genetic alterations that are involved in tumor recurrence of adult AML. However, little is known about the molecular details of relapsed pediatric AML. Methods In order to reveal the clonal origin and the major mutational events in relapsed pediatric AML, we performed whole exome sequencing of 4 trio samples from diagnostic, relapsed and complete remission phases using Illumina HiSeq 2000. Copy number abnormalities were also detected using whole exome sequencing. Subsequently, deep sequencing of identified mutations was performed to evaluate intra-tumor heterogeneity and the clonolocal history of relapsed clones. Results Whole-exome sequencing of 12 samples from 4 patients were analyzed with a mean coverage of more than x100, and 95 % of the targeted sequences were analyzed at more than x20 depth on average. A total of 98 somatic mutations were identified, where mean number of non-silent mutations was higher at relapsed phase than at the time of diagnosis (14.0/case vs 10.5/case) (p=0.270). Assessment of clonality using variant allele frequencies of individual mutations suggested that some mutations were subclonal mutations, consisting of intra-tumor heterogeneity both at the time of diagnosis and at relapse. In all 4 patients, relapsed AML evolved from one of the subclones at the initial phase, which was accompanied by many additional mutations including common driver mutations that were absent or existed only with lower allele frequency in the diagnostic samples, indicating a multistep process of leukemia recurrence. Forty-six out of the 98 mutations were specific either at the time of diagnosis (n = 16) or at relapse (n = 30). Relapse-specific mutations and copy number changes were found in several genes including known drivers such as NRAS and CREBBP. These mutations were further investigated in an extended cohort of relapsed pediatric AML samples using targeted sequencing to evaluate their prevalence. In some cases, AML relapse may accompany a dynamic clonal change. For example, some bona fide driver mutations, such as KRAS mutations, that were predominant at the time of diagnosis disappeared in relapsed samples. Discussion Whole exome sequencing unmasked clonal structure of primary and relapsed pediatric AML, which helped to understand the underlying mechanism of relapse in pediatric AML. Our results suggested that pediatric AML has intra-tumor heterogeneity and subclonal mutations such as NRAS and CREBBP occurring in one of the subclones could drive the AML relapse. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
    detail.hit.zdb_id: 1468538-3
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