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1.
Mol Cell ; 63(3): 514-25, 2016 08 04.
Artículo en Inglés | MEDLINE | ID: mdl-27453043

RESUMEN

An emerging therapeutic strategy for cancer is to induce selective lethality in a tumor by exploiting interactions between its driving mutations and specific drug targets. Here we use a multi-species approach to develop a resource of synthetic lethal interactions relevant to cancer therapy. First, we screen in yeast ∼169,000 potential interactions among orthologs of human tumor suppressor genes (TSG) and genes encoding drug targets across multiple genotoxic environments. Guided by the strongest signal, we evaluate thousands of TSG-drug combinations in HeLa cells, resulting in networks of conserved synthetic lethal interactions. Analysis of these networks reveals that interaction stability across environments and shared gene function increase the likelihood of observing an interaction in human cancer cells. Using these rules, we prioritize ∼10(5) human TSG-drug combinations for future follow-up. We validate interactions based on cell and/or patient survival, including topoisomerases with RAD17 and checkpoint kinases with BLM.


Asunto(s)
Antineoplásicos/uso terapéutico , Biomarcadores de Tumor/genética , Redes Reguladoras de Genes/efectos de los fármacos , Genes Supresores de Tumor , Mutación , Medicina de Precisión/métodos , Mapas de Interacción de Proteínas/efectos de los fármacos , Saccharomyces cerevisiae/efectos de los fármacos , Neoplasias del Cuello Uterino/tratamiento farmacológico , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Proliferación Celular/efectos de los fármacos , Supervivencia Celular/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Femenino , Regulación Fúngica de la Expresión Génica/efectos de los fármacos , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Predisposición Genética a la Enfermedad , Células HeLa , Humanos , Estimación de Kaplan-Meier , Terapia Molecular Dirigida , Fenotipo , Interferencia de ARN , RecQ Helicasas/genética , RecQ Helicasas/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Transducción de Señal/efectos de los fármacos , Mutaciones Letales Sintéticas , Factores de Tiempo , Transfección , Neoplasias del Cuello Uterino/genética , Neoplasias del Cuello Uterino/metabolismo , Neoplasias del Cuello Uterino/mortalidad
2.
Nat Methods ; 14(6): 573-576, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-28319113

RESUMEN

We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.


Asunto(s)
Mapeo Cromosómico/métodos , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Técnicas Químicas Combinatorias , Epistasis Genética/genética , Proteínas de Neoplasias/genética , Células A549 , Línea Celular Tumoral , Células HeLa , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos
3.
Mol Cancer Ther ; 17(7): 1585-1594, 2018 07.
Artículo en Inglés | MEDLINE | ID: mdl-29636367

RESUMEN

Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) represents a distinct classification of cancer with worse expected outcomes. Of the 11 genes recurrently mutated in HNSCC, we identify a singular and substantial survival advantage for mutations in the gene encoding Nuclear Set Domain Containing Protein 1 (NSD1), a histone methyltransferase altered in approximately 10% of patients. This effect, a 55% decrease in risk of death in NSD1-mutated versus non-mutated patients, can be validated in an independent cohort. NSD1 alterations are strongly associated with widespread genome hypomethylation in the same tumors, to a degree not observed for any other mutated gene. To address whether NSD1 plays a causal role in these associations, we use CRISPR-Cas9 to disrupt NSD1 in HNSCC cell lines and find that this leads to substantial CpG hypomethylation and sensitivity to cisplatin, a standard chemotherapy in head and neck cancer, with a 40% to 50% decrease in the IC50 value. Such results are reinforced by a survey of 1,001 cancer cell lines, in which loss-of-function NSD1 mutations have an average 23% decrease in cisplatin IC50 value compared with cell lines with wild-type NSD1Significance: This study identifies a favorable subtype of HPV-negative HNSCC linked to NSD1 mutation, hypomethylation, and cisplatin sensitivity. Mol Cancer Ther; 17(7); 1585-94. ©2018 AACR.


Asunto(s)
Carcinoma de Células Escamosas/tratamiento farmacológico , Metilación de ADN/genética , Neoplasias de Cabeza y Cuello/tratamiento farmacológico , Péptidos y Proteínas de Señalización Intracelular/genética , Proteínas Nucleares/genética , Sistemas CRISPR-Cas/genética , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/patología , Línea Celular Tumoral , Cisplatino/farmacología , Islas de CpG/efectos de los fármacos , Metilación de ADN/efectos de los fármacos , Resistencia a Antineoplásicos/genética , Femenino , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Neoplasias de Cabeza y Cuello/genética , Neoplasias de Cabeza y Cuello/patología , Histona Metiltransferasas , N-Metiltransferasa de Histona-Lisina , Humanos , Masculino , Mutación/efectos de los fármacos , Papillomaviridae
4.
Nat Genet ; 50(4): 613-620, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29610481

RESUMEN

Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer.


Asunto(s)
Genes Relacionados con las Neoplasias , Mutación , Neoplasias/genética , Proteínas Adaptadoras Transductoras de Señales/genética , Isomerasas Aldosa-Cetosa/genética , Línea Celular Tumoral , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Humanos , Proteínas de Microfilamentos , Proteínas de Unión al GTP Monoméricas/genética , Invasividad Neoplásica/genética , Neoplasias/metabolismo , Sitios de Carácter Cuantitativo , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN Neoplásico/genética , ARN Neoplásico/metabolismo , ARN no Traducido/genética , ARN no Traducido/metabolismo , Secuenciación Completa del Genoma , Proteínas de Unión al GTP rho
5.
Oncotarget ; 6(34): 35755-69, 2015 Nov 03.
Artículo en Inglés | MEDLINE | ID: mdl-26437225

RESUMEN

Chemical inhibitors of the checkpoint kinases have shown promise in the treatment of cancer, yet their clinical utility may be limited by a lack of molecular biomarkers to identify specific patients most likely to respond to therapy. To this end, we screened 112 known tumor suppressor genes for synthetic lethal interactions with inhibitors of the CHEK1 and CHEK2 checkpoint kinases. We identified eight interactions, including the Replication Factor C (RFC)-related protein RAD17. Clonogenic assays in RAD17 knockdown cell lines identified a substantial shift in sensitivity to checkpoint kinase inhibition (3.5-fold) as compared to RAD17 wild-type. Additional evidence for this interaction was found in a large-scale functional shRNA screen of over 100 genotyped cancer cell lines, in which CHEK1/2 mutant cell lines were unexpectedly sensitive to RAD17 knockdown. This interaction was widely conserved, as we found that RAD17 interacts strongly with checkpoint kinases in the budding yeast Saccharomyces cerevisiae. In the setting of RAD17 knockdown, CHEK1/2 inhibition was found to be synergistic with inhibition of WEE1, another pharmacologically relevant checkpoint kinase. Accumulation of the DNA damage marker γH2AX following chemical inhibition or transient knockdown of CHEK1, CHEK2 or WEE1 was magnified by knockdown of RAD17. Taken together, our data suggest that CHEK1 or WEE1 inhibitors are likely to have greater clinical efficacy in tumors with RAD17 loss-of-function.


Asunto(s)
Antineoplásicos/farmacología , Proteínas de Ciclo Celular/metabolismo , Proteínas de Unión al ADN/metabolismo , Neoplasias/tratamiento farmacológico , Proteínas Nucleares/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/fisiología , Saccharomyces cerevisiae/patogenicidad , Tiofenos/farmacología , Urea/análogos & derivados , Biomarcadores Farmacológicos/metabolismo , Ciclo Celular/efectos de los fármacos , Ciclo Celular/genética , Proteínas de Ciclo Celular/genética , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1) , Quinasa de Punto de Control 2/genética , Quinasa de Punto de Control 2/metabolismo , Daño del ADN/efectos de los fármacos , Daño del ADN/genética , Proteínas de Unión al ADN/genética , Descubrimiento de Drogas , Células HeLa , Humanos , Terapia Molecular Dirigida , Mutación/genética , Neoplasias/diagnóstico , Proteínas Nucleares/genética , Proteínas Quinasas/genética , Proteínas Quinasas/metabolismo , Proteínas Tirosina Quinasas/genética , Proteínas Tirosina Quinasas/metabolismo , ARN Interferente Pequeño/genética , Proteínas de Saccharomyces cerevisiae/genética , Urea/farmacología
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