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1.
Nature ; 506(7489): 451-5, 2014 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-24553141

RESUMEN

Members of the nuclear factor-κB (NF-κB) family of transcriptional regulators are central mediators of the cellular inflammatory response. Although constitutive NF-κB signalling is present in most human tumours, mutations in pathway members are rare, complicating efforts to understand and block aberrant NF-κB activity in cancer. Here we show that more than two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of canonical NF-κB signalling, and an uncharacterized gene, C11orf95. In each case, C11orf95-RELA fusions resulted from chromothripsis involving chromosome 11q13.1. C11orf95-RELA fusion proteins translocated spontaneously to the nucleus to activate NF-κB target genes, and rapidly transformed neural stem cells--the cell of origin of ependymoma--to form these tumours in mice. Our data identify a highly recurrent genetic alteration of RELA in human cancer, and the C11orf95-RELA fusion protein as a potential therapeutic target in supratentorial ependymoma.


Asunto(s)
Transformación Celular Neoplásica , Ependimoma/genética , Ependimoma/metabolismo , FN-kappa B/metabolismo , Proteínas/metabolismo , Transducción de Señal , Factor de Transcripción ReIA/metabolismo , Proteínas Adaptadoras Transductoras de Señales/genética , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Animales , Secuencia de Bases , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/patología , Línea Celular , Núcleo Celular/metabolismo , Transformación Celular Neoplásica/genética , Cromosomas Humanos Par 11/genética , Ependimoma/patología , Femenino , Humanos , Ratones , Modelos Genéticos , Datos de Secuencia Molecular , FN-kappa B/genética , Células-Madre Neurales/metabolismo , Células-Madre Neurales/patología , Proteínas de Fusión Oncogénica/genética , Proteínas de Fusión Oncogénica/metabolismo , Fosfoproteínas/genética , Fosfoproteínas/metabolismo , Proteínas/genética , Factor de Transcripción ReIA/genética , Factores de Transcripción , Translocación Genética/genética , Proteínas Señalizadoras YAP
2.
N Engl J Med ; 373(24): 2336-2346, 2015 Dec 10.
Artículo en Inglés | MEDLINE | ID: mdl-26580448

RESUMEN

BACKGROUND: The prevalence and spectrum of predisposing mutations among children and adolescents with cancer are largely unknown. Knowledge of such mutations may improve the understanding of tumorigenesis, direct patient care, and enable genetic counseling of patients and families. METHODS: In 1120 patients younger than 20 years of age, we sequenced the whole genomes (in 595 patients), whole exomes (in 456), or both (in 69). We analyzed the DNA sequences of 565 genes, including 60 that have been associated with autosomal dominant cancer-predisposition syndromes, for the presence of germline mutations. The pathogenicity of the mutations was determined by a panel of medical experts with the use of cancer-specific and locus-specific genetic databases, the medical literature, computational predictions, and second hits identified in the tumor genome. The same approach was used to analyze data from 966 persons who did not have known cancer in the 1000 Genomes Project, and a similar approach was used to analyze data from an autism study (from 515 persons with autism and 208 persons without autism). RESULTS: Mutations that were deemed to be pathogenic or probably pathogenic were identified in 95 patients with cancer (8.5%), as compared with 1.1% of the persons in the 1000 Genomes Project and 0.6% of the participants in the autism study. The most commonly mutated genes in the affected patients were TP53 (in 50 patients), APC (in 6), BRCA2 (in 6), NF1 (in 4), PMS2 (in 4), RB1 (in 3), and RUNX1 (in 3). A total of 18 additional patients had protein-truncating mutations in tumor-suppressor genes. Of the 58 patients with a predisposing mutation and available information on family history, 23 (40%) had a family history of cancer. CONCLUSIONS: Germline mutations in cancer-predisposing genes were identified in 8.5% of the children and adolescents with cancer. Family history did not predict the presence of an underlying predisposition syndrome in most patients. (Funded by the American Lebanese Syrian Associated Charities and the National Cancer Institute.).


Asunto(s)
Genes Relacionados con las Neoplasias , Predisposición Genética a la Enfermedad , Mutación de Línea Germinal , Neoplasias/genética , Adolescente , Trastorno Autístico/genética , Niño , Femenino , Genes Dominantes , Genoma Humano , Humanos , Masculino , Programa de VERF , Análisis de Secuencia de ADN/métodos , Adulto Joven
3.
Nat Methods ; 12(6): 527-30, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25938371

RESUMEN

We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), an algorithm for detecting somatic copy-number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation on the basis of changes in read depth and the detection of localized structural variations, with high accuracy and sensitivity. Analysis of 43 cancer genomes from both pediatric and adult patients revealed novel oncogenic CNAs, complex rearrangements and subclonal CNAs missed by alternative approaches.


Asunto(s)
Variaciones en el Número de Copia de ADN/genética , ADN/genética , Genómica/métodos , Neoplasias/genética , Programas Informáticos , Adulto , Algoritmos , Niño , Biología Computacional , Regulación Neoplásica de la Expresión Génica , Marcadores Genéticos , Genoma , Humanos
4.
Nature ; 481(7381): 329-34, 2012 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-22237022

RESUMEN

Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the retinoblastoma genome is stable, but that multiple cancer pathways can be epigenetically deregulated. To identify the mutations that cooperate with RB1 loss, we performed whole-genome sequencing of retinoblastomas. The overall mutational rate was very low; RB1 was the only known cancer gene mutated. We then evaluated the role of RB1 in genome stability and considered non-genetic mechanisms of cancer pathway deregulation. For example, the proto-oncogene SYK is upregulated in retinoblastoma and is required for tumour cell survival. Targeting SYK with a small-molecule inhibitor induced retinoblastoma tumour cell death in vitro and in vivo. Thus, retinoblastomas may develop quickly as a result of the epigenetic deregulation of key cancer pathways as a direct or indirect result of RB1 loss.


Asunto(s)
Epigénesis Genética/genética , Genómica , Terapia Molecular Dirigida , Inhibidores de Proteínas Quinasas/farmacología , Retinoblastoma/tratamiento farmacológico , Retinoblastoma/genética , Aneuploidia , Animales , Muerte Celular/efectos de los fármacos , Línea Celular , Supervivencia Celular/efectos de los fármacos , Inestabilidad Cromosómica/genética , Regulación Neoplásica de la Expresión Génica , Genes de Retinoblastoma/genética , Humanos , Péptidos y Proteínas de Señalización Intracelular/antagonistas & inhibidores , Péptidos y Proteínas de Señalización Intracelular/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Ratones , Mutación/genética , Inhibidores de Proteínas Quinasas/uso terapéutico , Proteínas Tirosina Quinasas/antagonistas & inhibidores , Proteínas Tirosina Quinasas/genética , Proteínas Tirosina Quinasas/metabolismo , Proto-Oncogenes Mas , Retinoblastoma/patología , Proteína de Retinoblastoma/deficiencia , Proteína de Retinoblastoma/genética , Análisis de Secuencia de ADN , Quinasa Syk , Ensayos Antitumor por Modelo de Xenoinjerto
5.
Nature ; 481(7380): 157-63, 2012 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-22237106

RESUMEN

Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.


Asunto(s)
Predisposición Genética a la Enfermedad/genética , Mutación/genética , Leucemia-Linfoma Linfoblástico de Células T Precursoras/genética , Edad de Inicio , Niño , Variaciones en el Número de Copia de ADN/genética , Genes ras/genética , Genoma Humano/genética , Genómica , Hematopoyesis/genética , Histonas/metabolismo , Humanos , Quinasas Janus/genética , Quinasas Janus/metabolismo , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/patología , Datos de Secuencia Molecular , Leucemia-Linfoma Linfoblástico de Células T Precursoras/tratamiento farmacológico , Leucemia-Linfoma Linfoblástico de Células T Precursoras/patología , Receptores de Interleucina-7/genética , Proteína Reelina , Análisis de Secuencia de ADN , Transducción de Señal/genética , Células Madre/metabolismo , Células Madre/patología , Linfocitos T/metabolismo , Linfocitos T/patología , Translocación Genética/genética
6.
Acta Neuropathol ; 131(2): 299-307, 2016 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26744350

RESUMEN

Gliomatosis cerebri (GC), a rare and deadly CNS neoplasm characterized by involvement of at least three cerebral lobes, predominantly affects adults. While a few small series have reported its occurrence in children, little is known about the molecular characteristics of pediatric GC. We reviewed clinical, radiological, and histological features of pediatric patients with primary GC treated at our institution over 15 years. Targeted sequencing of mutational hotspots in H3F3A, IDH1/2, and BRAF, and genome-wide analysis of DNA methylation and copy number abnormalities was performed in available tumors. Thirty-two patients [23 (72 %) with type 1 and 9 (28 %) with type 2 GC] were identified. Median age at diagnosis was 10.2 years (range 1.5-19.1). A median of 4 cerebral lobes (range 3-8) was affected at diagnosis. In addition, symmetrical bithalamic involvement was observed in 9 (28 %) patients. Twenty-two patients (69 %) had an anaplastic astrocytoma. Despite aggressive therapy, only two patients younger than 3 years at diagnosis are long-term survivors. Clustering analysis of methylation array data from 18 cases classified tumors as IDH (n = 3, 17 %), G34 (n = 4, 22 %), mesenchymal (n = 3, 17 %), and RTK I 'PDGFRA' (n = 8, 44 %). No tumors were classified as K27 subgroup. PDGFRA was the most commonly amplified oncogene in 4 of 22 tumors (18 %). H3F3A p.G34 occurred in all cases classified as G34. Two of 3 cases in the IDH subgroup had IDH1 p.R132H. No H3F3A p.K27 M, IDH2 p.R172, or BRAF p.V600E mutations were observed. There was a trend towards improved survival in the IDH subgroup (P = 0.056). Patients with bithalamic involvement had worse outcomes (P = 0.019). Despite some overlap, the molecular features of pediatric GC are distinct from its adult counterpart. Like in adults, the similarity of genetic and epigenetic characteristics with other infiltrative high-grade gliomas suggests that pediatric GC does not represent a distinct molecular entity.


Asunto(s)
Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Metilación de ADN , Neoplasias Neuroepiteliales/genética , Neoplasias Neuroepiteliales/metabolismo , Adolescente , Encéfalo/metabolismo , Neoplasias Encefálicas/clasificación , Neoplasias Encefálicas/terapia , Niño , Preescolar , Análisis por Conglomerados , Islas de CpG , Femenino , Humanos , Lactante , Masculino , Mutación , Neoplasias Neuroepiteliales/clasificación , Neoplasias Neuroepiteliales/terapia , Estudios Retrospectivos , Análisis de Supervivencia , Adulto Joven
7.
Acta Neuropathol ; 131(6): 833-45, 2016 06.
Artículo en Inglés | MEDLINE | ID: mdl-26810070

RESUMEN

Low-grade neuroepithelial tumors (LGNTs) are diverse CNS tumors presenting in children and young adults, often with a history of epilepsy. While the genetic profiles of common LGNTs, such as the pilocytic astrocytoma and 'adult-type' diffuse gliomas, are largely established, those of uncommon LGNTs remain to be defined. In this study, we have used massively parallel sequencing and various targeted molecular genetic approaches to study alterations in 91 LGNTs, mostly from children but including young adult patients. These tumors comprise dysembryoplastic neuroepithelial tumors (DNETs; n = 22), diffuse oligodendroglial tumors (d-OTs; n = 20), diffuse astrocytomas (DAs; n = 17), angiocentric gliomas (n = 15), and gangliogliomas (n = 17). Most LGNTs (84 %) analyzed by whole-genome sequencing (WGS) were characterized by a single driver genetic alteration. Alterations of FGFR1 occurred frequently in LGNTs composed of oligodendrocyte-like cells, being present in 82 % of DNETs and 40 % of d-OTs. In contrast, a MYB-QKI fusion characterized almost all angiocentric gliomas (87 %), and MYB fusion genes were the most common genetic alteration in DAs (41 %). A BRAF:p.V600E mutation was present in 35 % of gangliogliomas and 18 % of DAs. Pathogenic alterations in FGFR1/2/3, BRAF, or MYB/MYBL1 occurred in 78 % of the series. Adult-type d-OTs with an IDH1/2 mutation occurred in four adolescents, the youngest aged 15 years at biopsy. Despite a detailed analysis, novel genetic alterations were limited to two fusion genes, EWSR1-PATZ1 and SLMAP-NTRK2, both in gangliogliomas. Alterations in BRAF, FGFR1, or MYB account for most pathogenic alterations in LGNTs, including pilocytic astrocytomas, and alignment of these genetic alterations and cytologic features across LGNTs has diagnostic implications. Additionally, therapeutic options based upon targeting the effects of these alterations are already in clinical trials.


Asunto(s)
Neoplasias Encefálicas/patología , Genes myb , Predisposición Genética a la Enfermedad , Glioma/genética , Mutación/genética , Proteínas Proto-Oncogénicas B-raf/genética , Receptor Tipo 1 de Factor de Crecimiento de Fibroblastos/genética , Adolescente , Adulto , Astrocitoma/genética , Astrocitoma/patología , Neoplasias Encefálicas/genética , Niño , Preescolar , Proteínas de Unión al ADN , Femenino , Ganglioglioma/genética , Ganglioglioma/patología , Glioma/patología , Humanos , Lactante , Masculino , Proteínas Nucleares/genética , Proteínas de Transporte Nucleocitoplasmático/genética , Proteínas Proto-Oncogénicas/genética , Proteínas de Unión al ARN , Transactivadores/genética , Factores de Transcripción , Adulto Joven
8.
Br J Haematol ; 168(1): 94-101, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-25164427

RESUMEN

Minimal residual disease (MRD) is a strong prognostic factor in children and adolescents with acute myeloid leukaemia (AML) but nearly one-quarter of patients who achieve MRD-negative status still relapse. The adverse prognostic factors among MRD-negative patients remain unknown. We analysed the AML02 study cohort to identify demographic and genetic prognostic factors. Among the presenting features, certain 11q23 abnormalities, such as t(6;11) and t(10;11), acute megakaryoblastic leukaemia without the t(1;22), and age ≥10 years were associated with inferior outcome in patients who had MRD-negative status after either remission induction I or II. By contrast, those with rearrangement of CBF genes had superior outcome. Our study identifies patient populations for whom close post-remission MRD monitoring to detect and treat emerging relapse and adjustment in treatment intensity might be indicated.


Asunto(s)
Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/genética , Adolescente , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Niño , Preescolar , Aberraciones Cromosómicas , Humanos , Cariotipo , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/mortalidad , Neoplasia Residual/diagnóstico , Pronóstico , Inducción de Remisión , Resultado del Tratamiento , Tirosina Quinasa 3 Similar a fms/genética
9.
Pediatr Blood Cancer ; 62(6): 1081-3, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25598012

RESUMEN

Children with diffuse intrinsic pontine glioma (DIPG) have a short onset, rapidly progressive neurologic decline before diagnosis. Therefore, incidental diagnosis of such an aggressive cancer is counterintuitive, yet our experience shows DIPG may occur as part of a spectrum of incidentally diagnosed pediatric brain cancers. Although children with incidentally diagnosed DIPG may experience a longer survival, it remains a potentially deadly cancer despite treatment with radiotherapy. Histologic confirmation is warranted when feasible in such patients to confirm diagnosis. Moreover, recent advances in genome-wide analyses may suggest incidentally diagnosed DIPGs are biologically distinct from the majority of these cancers.


Asunto(s)
Neoplasias del Tronco Encefálico/diagnóstico , Glioma/diagnóstico , Adolescente , Niño , Preescolar , Femenino , Humanos , Lactante , Masculino
10.
Cancer ; 120(10): 1514-9, 2014 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-24501014

RESUMEN

BACKGROUND: Breakpoint cluster region-Abelson murine leukemia viral oncogene homolog 1 (BCR-ABL1) tyrosine kinase inhibitors (TKIs) improve the outcome of patients with childhood Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL) when they are incorporated into postremission induction chemotherapy. To date, no data are available on the impact of TKIs on minimal residual disease (MRD) at the end of induction therapy among patients who have a poor early response to 2 weeks of induction therapy that does not include TKIs. METHODS: The authors analyzed the early response to TKIs during remission induction in children with Ph-positive ALL who were treated at St. Jude Children's Research Hospital. MRD was measured on days 15 and 42 of induction. TKIs were incorporated into induction therapy on day 22 in the post-TKI era. RESULTS: TKIs produced a marked drop in MRD levels: at the end of remission induction, 9 of 11 patients who received imatinib or dasatinib and conventional induction chemotherapy achieved MRD-negative status compared with only 2 of 16 patients who received chemotherapy alone (P < .001). The 5-year event-free survival rate (± standard deviation) was 68.6% ± 19.2% for the 11 patients who received TKIs versus 31.6% ± 9.9% for the 19 patients who did not (P = .022); notably, 2 of the former group underwent hematopoietic stem cell transplantation versus 15 of the latter group (P = .002). MRD levels and outcomes did not differ significantly among 498 patients with standard-risk/high-risk, Ph-negative ALL who were treated in the pre-TKI or post-TKI eras. CONCLUSIONS: TKIs administered in the early phases of therapy can dramatically reduce MRD and improve the outcome of childhood Ph-positive ALL.


Asunto(s)
Antineoplásicos/uso terapéutico , Benzamidas/uso terapéutico , Neoplasia Residual/tratamiento farmacológico , Cromosoma Filadelfia , Piperazinas/uso terapéutico , Leucemia-Linfoma Linfoblástico de Células Precursoras/tratamiento farmacológico , Inhibidores de Proteínas Quinasas/uso terapéutico , Proteínas Tirosina Quinasas/antagonistas & inhibidores , Pirimidinas/uso terapéutico , Tiazoles/uso terapéutico , Adolescente , Antineoplásicos/administración & dosificación , Benzamidas/administración & dosificación , Niño , Preescolar , Dasatinib , Esquema de Medicación , Femenino , Citometría de Flujo , Genes Codificadores de los Receptores de Linfocitos T , Humanos , Mesilato de Imatinib , Quimioterapia de Inducción , Lactante , Masculino , Neoplasia Residual/genética , Neoplasia Residual/prevención & control , Piperazinas/administración & dosificación , Reacción en Cadena de la Polimerasa , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Inhibidores de Proteínas Quinasas/administración & dosificación , Pirimidinas/administración & dosificación , Tiazoles/administración & dosificación , Resultado del Tratamiento
11.
Blood ; 119(10): e67-75, 2012 Mar 08.
Artículo en Inglés | MEDLINE | ID: mdl-22234698

RESUMEN

To identify cooperating lesions in core-binding factor acute myeloid leukemia, we performed single-nucleotide polymorphism-array analysis on 300 diagnostic and 41 relapse adult and pediatric leukemia samples. We identified a mean of 1.28 copy number alterations per case at diagnosis in both patient populations. Recurrent minimally deleted regions (MDRs) were identified at 7q36.1 (7.7%), 9q21.32 (5%), 11p13 (2.3%), and 17q11.2 (2%). Approximately one-half of the 7q deletions were detectable only by single-nucleotide polymorphism-array analysis because of their limited size. Sequence analysis of MLL3, contained within the 7q36.1 MDR, in 46 diagnostic samples revealed one truncating mutation in a leukemia lacking a 7q deletion. Recurrent focal gains were identified at 8q24.21 (4.7%) and 11q25 (1.7%), both containing a single noncoding RNA. Recurrent regions of copy-neutral loss-of-heterozygosity were identified at 1p (1%), 4q (0.7%), and 19p (0.7%), with known mutated cancer genes present in the minimally altered region of 1p (NRAS) and 4q (TET2). Analysis of relapse samples identified recurrent MDRs at 3q13.31 (12.2%), 5q (4.9%), and 17p (4.9%), with the 3q13.31 region containing only LSAMP, a putative tumor suppressor. Determining the role of these lesions in leukemogenesis and drug resistance should provide important insights into core-binding factor acute myeloid leukemia.


Asunto(s)
Aberraciones Cromosómicas , Factores de Unión al Sitio Principal/genética , Perfilación de la Expresión Génica/métodos , Regulación Leucémica de la Expresión Génica , Leucemia Mieloide/genética , Enfermedad Aguda , Adulto , Niño , Deleción Cromosómica , Variaciones en el Número de Copia de ADN , Humanos , Leucemia Mieloide/patología , Pérdida de Heterocigocidad , Mutación , Análisis de Secuencia por Matrices de Oligonucleótidos , Proteínas de Fusión Oncogénica/genética , Polimorfismo de Nucleótido Simple , Recurrencia
13.
Nature ; 453(7191): 110-4, 2008 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-18408710

RESUMEN

The Philadelphia chromosome, a chromosomal abnormality that encodes BCR-ABL1, is the defining lesion of chronic myelogenous leukaemia (CML) and a subset of acute lymphoblastic leukaemia (ALL). To define oncogenic lesions that cooperate with BCR-ABL1 to induce ALL, we performed a genome-wide analysis of diagnostic leukaemia samples from 304 individuals with ALL, including 43 BCR-ABL1 B-progenitor ALLs and 23 CML cases. IKZF1 (encoding the transcription factor Ikaros) was deleted in 83.7% of BCR-ABL1 ALL, but not in chronic-phase CML. Deletion of IKZF1 was also identified as an acquired lesion at the time of transformation of CML to ALL (lymphoid blast crisis). The IKZF1 deletions resulted in haploinsufficiency, expression of a dominant-negative Ikaros isoform, or the complete loss of Ikaros expression. Sequencing of IKZF1 deletion breakpoints suggested that aberrant RAG-mediated recombination is responsible for the deletions. These findings suggest that genetic lesions resulting in the loss of Ikaros function are an important event in the development of BCR-ABL1 ALL.


Asunto(s)
Proteínas de Fusión bcr-abl/genética , Eliminación de Gen , Factor de Transcripción Ikaros/deficiencia , Factor de Transcripción Ikaros/genética , Leucemia Mielógena Crónica BCR-ABL Positiva/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Adulto , Niño , Humanos , Factor de Transcripción Ikaros/química , Factor de Transcripción Ikaros/metabolismo , Leucemia Mielógena Crónica BCR-ABL Positiva/patología , Polimorfismo de Nucleótido Simple/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/patología , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Estructura Terciaria de Proteína
14.
NPJ Precis Oncol ; 8(1): 218, 2024 Oct 02.
Artículo en Inglés | MEDLINE | ID: mdl-39358389

RESUMEN

As part of the advancement in therapeutic decision-making for brain tumor patients at St. Jude Children's Research Hospital (SJCRH), we developed three robust classifiers, a deep learning neural network (NN), k-nearest neighbor (kNN), and random forest (RF), trained on a reference series DNA-methylation profiles to classify central nervous system (CNS) tumor types. The models' performance was rigorously validated against 2054 samples from two independent cohorts. In addition to classic metrics of model performance, we compared the robustness of the three models to reduced tumor purity, a critical consideration in the clinical utility of such classifiers. Our findings revealed that the NN model exhibited the highest accuracy and maintained a balance between precision and recall. The NN model was the most resistant to drops in performance associated with a reduction in tumor purity, showing good performance until the purity fell below 50%. Through rigorous validation, our study emphasizes the potential of DNA-methylation-based deep learning methods to improve precision medicine for brain tumor classification in the clinical setting.

15.
Blood ; 117(23): 6267-76, 2011 Jun 09.
Artículo en Inglés | MEDLINE | ID: mdl-21487112

RESUMEN

To identify new markers for minimal residual disease (MRD) detection in acute lymphoblastic leukemia (ALL), we compared genome-wide gene expression of lymphoblasts from 270 patients with newly diagnosed childhood ALL to that of normal CD19⁺CD10⁺ B-cell progenitors (n = 4). Expression of 30 genes differentially expressed by ≥ 3-fold in at least 25% of cases of ALL (or 40% of ALL subtypes) was tested by flow cytometry in 200 B-lineage ALL and 61 nonleukemic BM samples, including samples containing hematogones. Of the 30 markers, 22 (CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, CD49f) were differentially expressed in up to 81.4% of ALL cases; expression of some markers was associated with the presence of genetic abnormalities. Results of MRD detection by flow cytometry with these markers correlated well with those of molecular testing (52 follow-up samples from 18 patients); sequential studies during treatment and diagnosis-relapse comparisons documented their stability. When incorporated in 6-marker combinations, the new markers afforded the detection of 1 leukemic cell among 10(5) BM cells. These new markers should allow MRD studies in all B-lineage ALL patients, and substantially improve their sensitivity.


Asunto(s)
Biomarcadores de Tumor/biosíntesis , Citometría de Flujo/métodos , Regulación Neoplásica de la Expresión Génica , Leucemia-Linfoma Linfoblástico de Células Precursoras/metabolismo , Adolescente , Niño , Preescolar , Femenino , Estudio de Asociación del Genoma Completo , Humanos , Lactante , Masculino , Neoplasia Residual , Leucemia-Linfoma Linfoblástico de Células Precursoras/terapia , Sensibilidad y Especificidad
16.
Nature ; 446(7137): 758-64, 2007 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-17344859

RESUMEN

Chromosomal aberrations are a hallmark of acute lymphoblastic leukaemia (ALL) but alone fail to induce leukaemia. To identify cooperating oncogenic lesions, we performed a genome-wide analysis of leukaemic cells from 242 paediatric ALL patients using high-resolution, single-nucleotide polymorphism arrays and genomic DNA sequencing. Our analyses revealed deletion, amplification, point mutation and structural rearrangement in genes encoding principal regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL cases. The PAX5 gene was the most frequent target of somatic mutation, being altered in 31.7% of cases. The identified PAX5 mutations resulted in reduced levels of PAX5 protein or the generation of hypomorphic alleles. Deletions were also detected in TCF3 (also known as E2A), EBF1, LEF1, IKZF1 (IKAROS) and IKZF3 (AIOLOS). These findings suggest that direct disruption of pathways controlling B-cell development and differentiation contributes to B-progenitor ALL pathogenesis. Moreover, these data demonstrate the power of high-resolution, genome-wide approaches to identify new molecular lesions in cancer.


Asunto(s)
Genoma Humano/genética , Mutación/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Alelos , Linfocitos B/metabolismo , Linfocitos B/patología , Niño , Proteínas de Unión al ADN/genética , Amplificación de Genes/genética , Genómica , Humanos , Datos de Secuencia Molecular , Factor de Transcripción PAX5/genética , Mutación Puntual/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/patología , Eliminación de Secuencia/genética , Transactivadores/genética , Translocación Genética/genética
17.
N Engl J Med ; 360(5): 470-80, 2009 Jan 29.
Artículo en Inglés | MEDLINE | ID: mdl-19129520

RESUMEN

BACKGROUND: Despite best current therapy, up to 20% of pediatric patients with acute lymphoblastic leukemia (ALL) have a relapse. Recent genomewide analyses have identified a high frequency of DNA copy-number abnormalities in ALL, but the prognostic implications of these abnormalities have not been defined. METHODS: We studied a cohort of 221 children with high-risk B-cell-progenitor ALL with the use of single-nucleotide-polymorphism microarrays, transcriptional profiling, and resequencing of samples obtained at diagnosis. Children with known very-high-risk ALL subtypes (i.e., BCR-ABL1-positive ALL, hypodiploid ALL, and ALL in infants) were excluded from this cohort. A copy-number abnormality was identified as a predictor of poor outcome, and it was then tested in an independent validation cohort of 258 patients with B-cell-progenitor ALL. RESULTS: More than 50 recurring copy-number abnormalities were identified, most commonly involving genes that encode regulators of B-cell development (in 66.8% of patients in the original cohort); PAX5 was involved in 31.7% and IKZF1 in 28.6% of patients. Using copy-number abnormalities, we identified a predictor of poor outcome that was validated in the independent validation cohort. This predictor was strongly associated with alteration of IKZF1, a gene that encodes the lymphoid transcription factor IKAROS. The gene-expression signature of the group of patients with a poor outcome revealed increased expression of hematopoietic stem-cell genes and reduced expression of B-cell-lineage genes, and it was similar to the signature of BCR-ABL1-positive ALL, another high-risk subtype of ALL with a high frequency of IKZF1 deletion. CONCLUSIONS: Genetic alteration of IKZF1 is associated with a very poor outcome in B-cell-progenitor ALL.


Asunto(s)
Resistencia a Antineoplásicos/genética , Eliminación de Gen , Factor de Transcripción Ikaros/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras B/genética , Linfocitos B/metabolismo , Niño , Estudios de Cohortes , Análisis Mutacional de ADN , Expresión Génica , Perfilación de la Expresión Génica , Genotipo , Células Madre Hematopoyéticas/metabolismo , Humanos , Mutación Missense , Factor de Transcripción PAX5/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras B/tratamiento farmacológico , Pronóstico , Recurrencia , Transactivadores/genética , Resultado del Tratamiento
18.
Cancer Cell ; 1(2): 133-43, 2002 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-12086872

RESUMEN

Treatment of pediatric acute lymphoblastic leukemia (ALL) is based on the concept of tailoring the intensity of therapy to a patient's risk of relapse. To determine whether gene expression profiling could enhance risk assignment, we used oligonucleotide microarrays to analyze the pattern of genes expressed in leukemic blasts from 360 pediatric ALL patients. Distinct expression profiles identified each of the prognostically important leukemia subtypes, including T-ALL, E2A-PBX1, BCR-ABL, TEL-AML1, MLL rearrangement, and hyperdiploid >50 chromosomes. In addition, another ALL subgroup was identified based on its unique expression profile. Examination of the genes comprising the expression signatures provided important insights into the biology of these leukemia subgroups. Further, within some genetic subgroups, expression profiles identified those patients that would eventually fail therapy. Thus, the single platform of expression profiling should enhance the accurate risk stratification of pediatric ALL patients.


Asunto(s)
Perfilación de la Expresión Génica , Leucemia-Linfoma Linfoblástico de Células Precursoras/diagnóstico , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Algoritmos , Niño , Biología Computacional , Humanos , Inmunofenotipificación , Leucemia Mieloide Aguda/clasificación , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/patología , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Leucemia-Linfoma Linfoblástico de Células Precursoras/clasificación , Leucemia-Linfoma Linfoblástico de Células Precursoras/patología , Pronóstico , Recurrencia , Factores de Riesgo , Insuficiencia del Tratamiento
19.
Proc Natl Acad Sci U S A ; 106(31): 12944-9, 2009 Aug 04.
Artículo en Inglés | MEDLINE | ID: mdl-19651601

RESUMEN

Pediatric de novo acute myeloid leukemia (AML) is an aggressive malignancy with current therapy resulting in cure rates of only 60%. To better understand the cause of the marked heterogeneity in therapeutic response and to identify new prognostic markers and therapeutic targets a comprehensive list of the genetic mutations that underlie the pathogenesis of AML is needed. To approach this goal, we examined diagnostic leukemic samples from a cohort of 111 children with de novo AML using single-nucleotide-polymorphism microarrays and candidate gene resequencing. Our data demonstrate that, in contrast to pediatric acute lymphoblastic leukemia (ALL), de novo AML is characterized by a very low burden of genomic alterations, with a mean of only 2.38 somatic copy-number alterations per leukemia, and less than 1 nonsynonymous point mutation per leukemia in the 25 genes analyzed. Even more surprising was the observation that 34% of the leukemias lacked any identifiable copy-number alterations, and 28% of the leukemias with recurrent translocations lacked any identifiable sequence or numerical abnormalities. The only exception to the presence of few mutations was acute megakaryocytic leukemias, with the majority of these leukemias being characterized by a high number of copy-number alterations but rare point mutations. Despite the low overall number of lesions across the patient cohort, novel recurring regions of genetic alteration were identified that harbor known, and potential new cancer genes. These data reflect a remarkably low burden of genomic alterations within pediatric de novo AML, which is in stark contrast to most other human malignancies.


Asunto(s)
Dosificación de Gen , Leucemia Mieloide Aguda/genética , Mutación , Polimorfismo de Nucleótido Simple , Niño , Femenino , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Cinesinas/genética , Pérdida de Heterocigocidad , Masculino , Miosinas/genética , Proteínas Proto-Oncogénicas/genética , ARN Largo no Codificante , Proteína 1 Compañera de Translocación de RUNX1 , Factores de Transcripción/genética , Translocación Genética
20.
Clin Cancer Res ; 28(12): 2536-2546, 2022 06 13.
Artículo en Inglés | MEDLINE | ID: mdl-35344039

RESUMEN

PURPOSE: To evaluate the safety, activity, and emergence of FLT3-kinase domain (KD) mutations with combination therapy of crenolanib and sorafenib in acute myeloid leukemia (AML) with FLT3-internal tandem duplication (ITD). PATIENTS AND METHODS: After in vitro and xenograft efficacy studies using AML cell lines that have FLT3-ITD with or without FLT3-KD mutation, a pilot study was performed with crenolanib (67 mg/m2/dose, three times per day on days 1-28) and two dose levels of sorafenib (150 and 200 mg/m2/day on days 8-28) in 9 pediatric patients with refractory/relapsed FLT3-ITD-positive AML. Pharmacokinetic, pharmacodynamic, and FLT3-KD mutation analysis were done in both preclinical and clinical studies. RESULTS: The combination of crenolanib and sorafenib in preclinical models showed synergy without affecting pharmacokinetics of each agent, inhibited p-STAT5 and p-ERK for up to 8 hours, and led to significantly better leukemia response (P < 0.005) and survival (P < 0.05) compared with single agents. Fewer FLT3-KD mutations emerged with dose-intensive crenolanib (twice daily) and low-intensity sorafenib (three times/week) compared with daily crenolanib or sorafenib (P < 0.05). The crenolanib and sorafenib combination was tolerable without dose-limiting toxicities, and three complete remissions (one with incomplete count recovery) and one partial remission were observed in 8 evaluable patients. Median crenolanib apparent clearance showed a nonsignificant decrease during treatment (45.0, 40.5, and 20.3 L/hour/m2 on days 1, 7, and 14, respectively) without drug-drug interaction. Only 1 patient developed a FLT3-KD mutation (FLT3 F691L). CONCLUSIONS: The combination of crenolanib and sorafenib was tolerable with antileukemic activities and rare emergence of FLT3-TKD mutations, which warrants further investigation.


Asunto(s)
Antineoplásicos , Bencimidazoles , Leucemia Mieloide Aguda , Piperidinas , Antineoplásicos/uso terapéutico , Bencimidazoles/uso terapéutico , Niño , Humanos , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/genética , Mutación , Compuestos de Fenilurea , Proyectos Piloto , Piperidinas/uso terapéutico , Inhibidores de Proteínas Quinasas/farmacología , Sorafenib/uso terapéutico , Tirosina Quinasa 3 Similar a fms/antagonistas & inhibidores
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