RESUMEN
Synthetic lethal interactions can assist in characterizing protein functions and cellular processes, but they can also be used to identify novel drug targets for the development of innovative cancer therapeutic strategies. Despite recent technological advancements including CRISPR/Cas9 approaches, the systematic assessment of all pairwise gene interactions in humans (~ 200 million pairs) remains an unmet goal. Thus, hypothesis-driven approaches, which prioritize subsets of promising candidate SL interactions for experimental assessment, are critical to expedite the identification of novel SL interactions. Here, we provide a guide to screen and validate focused libraries of promising candidate SL interactions, typically consisting of 50-500 targets. First, we describe two siRNA and image-based screening protocols to rapidly assess candidate SL interactions. Subsequently, we provide methods to validate a subset of the most promising interactions uncovered in the screens. These approaches employ commercially available reagents and standard laboratory equipment to facilitate and expedite the identification of bona fide human SL interactions.
Asunto(s)
ARN Interferente Pequeño/genética , Humanos , NeoplasiasRESUMEN
Mutations in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis (ALS). Both toxic gain of function and loss of function pathogenic mechanisms have been proposed. Accruing evidence from mouse knockout studies point to a role for C9ORF72 as a regulator of immune function. To provide further insight into its cellular function, we performed a genome-wide synthetic lethal CRISPR screen in human myeloid cells lacking C9ORF72. We discovered a strong synthetic lethal genetic interaction between C9ORF72 and FIS1, which encodes a mitochondrial membrane protein involved in mitochondrial fission and mitophagy. Mass spectrometry experiments revealed that in C9ORF72 knockout cells, FIS1 strongly bound to a class of immune regulators that activate the receptor for advanced glycation end (RAGE) products and trigger inflammatory cascades. These findings present a novel genetic interactor for C9ORF72 and suggest a compensatory role for FIS1 in suppressing inflammatory signaling in the absence of C9ORF72.
Asunto(s)
Esclerosis Amiotrófica Lateral/genética , Proteína C9orf72/genética , Proteínas de la Membrana/genética , Proteínas Mitocondriales/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Técnicas de Inactivación de Genes/métodos , Pruebas Genéticas , Humanos , RNA-Seq , Mutaciones Letales Sintéticas/genética , Células U937RESUMEN
BACKGROUND: Aurora B kinase plays an essential role in chromosome segregation and cytokinesis, and is dysregulated in many cancer types, making it an attractive therapeutic target. TAK-901 is a potent aurora B inhibitor that showed efficacy in both in vitro and in vivo oncology models. MATERIALS AND METHODS: We conducted a synthetic lethal siRNA screening to identify the genes that, when silenced, can potentiate the cell growth-inhibitory effect of TAK-901. RESULTS: B-cell lymphoma-extra large (BCL-xL) depletion by siRNA or chemical inhibition synergized with TAK-901 in cancer cell lines. As a mechanism of synthetic lethality, active BCL2 associated X, apoptosis regulator (BAX) was induced by TAK-901. BCL-xL protected cells from BAX-dependent apoptosis induction. Therefore, TAK-901 sensitizes cancer cells to BCL-xL inhibition. CONCLUSION: Polyploid cells induced by TAK-901 are vulnerable to BCL-xL inhibition. Our findings may have an impact on combination strategies with aurora B inhibitors in clinical studies.
Asunto(s)
Aurora Quinasa B/antagonistas & inhibidores , Carbolinas/farmacología , Neoplasias/terapia , Inhibidores de Proteínas Quinasas/farmacología , Sulfonas/farmacología , Proteína X Asociada a bcl-2/biosíntesis , Proteína bcl-X/antagonistas & inhibidores , Línea Celular Tumoral , Sinergismo Farmacológico , Técnicas de Silenciamiento del Gen , Células HCT116 , Células HT29 , Humanos , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Neoplasias/metabolismo , ARN Interferente Pequeño/genética , Transfección , Proteína bcl-X/genéticaRESUMEN
Synthetic lethal screens are used to discover new combination treatments for cancer. In traditional high-throughput synthetic lethal screens, compounds are tested at a single dose, and hit selection is based on threshold activity values from the variance of the efficacy of the compounds tested. The limitation of the single-dose screening for synthetic lethal screens is that it does not allow for the robust detection of differential activities from compound collections with a broad range of potencies and efficacies. There is therefore a need to develop screening approaches that enable the identification of compounds with synthetic lethal effects based on changes in both potency and efficacy. Here we describe the implementation of a dose response-based synthetic lethal screen to find drugs that enhance or mitigate the cytotoxic effect of an immunotoxin protein (HA22). We developed a data analysis framework for the selection of compounds with enhancing or mitigating cytotoxic activities based on the use of dose-response parameters. The data analysis framework includes an ensemble ranking approach that allows the use of multiple dose-response parameters in a nonparametric fashion. Quantitative high-throughput screening (HTS) enables the identification of compounds with synthetic lethal activity not identified by single-dose HTS.