Evidence of a synthetic lethality interaction between SETDB1 histone methyltransferase and CHD4 chromatin remodeling protein in a triple negative breast cancer cell line.

During the tumorigenic process, cancer cells may become overly dependent on the activity of backup cellular pathways for their survival, representing vulnerabilities that could be exploited as therapeutic targets. Certain molecular vulnerabilities manifest as a synthetic lethality relationship, and the identification and characterization of new synthetic lethal interactions may pave the way for the development of new therapeutic approaches for human cancer. Our goal was to investigate a possible synthetic lethal interaction between a member of the Chromodomain Helicase DNA binding proteins family (CHD4) and a member of the histone methyltransferases family (SETDB1) in the molecular context of a cell line (Hs578T) representing the triple negative breast cancer (TNBC), a subtype of breast cancer lacking validated molecular targets for treatment. Therefore, we employed the CRISPR-Cas9 gene editing tool to individually or simultaneously introduce indels in the genomic loci corresponding to the catalytic domains of SETDB1 and CHD4 in the Hs578T cell line. Our main findings included: a) introduction of indels in exon 22 of SETDB1 sensitized Hs578T to the action of the genotoxic chemotherapy doxorubicin; b) by sequentially introducing indels in exon 22 of SETDB1 and exon 23 of CHD4 and tracking the percentage of the remaining wild-type sequences in the mixed cell populations generated, we obtained evidence of the existence of a synthetic lethality interaction between these genes. Considering the lack of molecular targets in TNBC, our findings provided valuable insights for development of new therapeutic approaches not only for TNBC but also for other cancer types.

Inhibitors of Rho kinases (ROCK) induce multiple mitotic defects and synthetic lethality in BRCA2-deficient cells.

The trapping of Poly-ADP-ribose polymerase (PARP) on DNA caused by PARP inhibitors (PARPi) triggers acute DNA replication stress and synthetic lethality (SL) in BRCA2-deficient cells. Hence, DNA damage is accepted as a prerequisite for SL in BRCA2-deficient cells. In contrast, here we show that inhibiting ROCK in BRCA2-deficient cells triggers SL independently from acute replication stress. Such SL is preceded by polyploidy and binucleation resulting from cytokinesis failure. Such initial mitosis abnormalities are followed by other M phase defects, including anaphase bridges and abnormal mitotic figures associated with multipolar spindles, supernumerary centrosomes and multinucleation. SL was also triggered by inhibiting Citron Rho-interacting kinase, another enzyme that, similarly to ROCK, regulates cytokinesis. Together, these observations demonstrate that cytokinesis failure triggers mitotic abnormalities and SL in BRCA2-deficient cells. Furthermore, the prevention of mitotic entry by depletion of Early mitotic inhibitor 1 (EMI1) augmented the survival of BRCA2-deficient cells treated with ROCK inhibitors, thus reinforcing the association between M phase and cell death in BRCA2-deficient cells. This novel SL differs from the one triggered by PARPi and uncovers mitosis as an Achilles heel of BRCA2-deficient cells.

Unveiling the vulnerabilities of synthetic lethality in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is the most invasive molecular subtype of breast cancer (BC), accounting for about nearly 15% of all BC cases reported annually. The absence of the three major BC hormone receptors, Estrogen (ER), Progesterone (PR), and Human Epidermal Growth Factor 2 (HER2) receptor, accounts for the characteristic "Triple negative" phraseology. The absence of these marked receptors makes this cancer insensitive to classical endocrine therapeutic approaches. Hence, the available treatment options remain solemnly limited to only conventional realms of chemotherapy and radiation therapy. Moreover, these therapeutic regimes are often accompanied by numerous treatment side-effects that account for early distant metastasis, relapse, and shorter overall survival in TNBC patients. The rigorous ongoing research in the field of clinical oncology has identified certain gene-based selective tumor-targeting susceptibilities, which are known to account for the molecular fallacies and mutation-based genetic alterations that develop the progression of TNBC. One such promising approach is synthetic lethality, which identifies novel drug targets of cancer, from undruggable oncogenes or tumor-suppressor genes, which cannot be otherwise clasped by the conventional approaches of mutational analysis. Herein, a holistic scientific review is presented, to undermine the mechanisms of synthetic lethal (SL) interactions in TNBC, the epigenetic crosstalks encountered, the role of Poly (ADP-ribose) polymerase inhibitors (PARPi) in inducing SL interactions, and the limitations faced by the lethal interactors. Thus, the future predicament of synthetic lethal interactions in the advancement of modern translational TNBC research is assessed with specific emphasis on patient-specific personalized medicine.

A DNA Repair Inhibitor Isolated from an Ecuadorian Fungal Endophyte Exhibits Synthetic Lethality in PTEN-Deficient Glioblastoma.

Disruption of the tumor suppressor PTEN, either at the protein or genomic level, plays an important role in human cancer development. The high frequency of PTEN deficiency reported across several cancer subtypes positions therapeutic approaches that exploit PTEN loss-of-function with the ability to significantly impact the treatment strategies of a large patient population. Here, we report that an endophytic fungus isolated from a medicinal plant produces an inhibitor of DNA double-strand-break repair. Furthermore, the novel alkaloid product, which we have named irrepairzepine (1), demonstrated synthetic lethal targeting in PTEN-deficient glioblastoma cells. Our results uncover a new therapeutic lead for PTEN-deficient cancers and an important molecular tool toward enhancing the efficacy of current cancer treatments.

Can synthetic lethality approach be used with DNA repair genes for primary and secondary MDS?

Cancer-specific defects in DNA repair pathways create the opportunity to employ synthetic lethality approach. Recently, GEMA (gene expression and mutation analysis) approach detected insufficient expression of BRCA or NHEJ (non-homologous end joining) to predict PARP inhibitors response. We evaluated a possible role of DNA repair pathways using gene expression of single-strand break (XPA, XPC, XPG/ERCC5, CSA/ERCC8, and CSB/ERCC6) and double-strand break (ATM, BRCA1, BRCA2, RAD51, XRCC5, XRCC6, LIG4) in 92 patients with myelodysplastic syndrome (73 de novo, 9 therapy-related (t-MDS). Therapy-related MDS (t-MDS) demonstrated a significant downregulation of axis BRCA1-BRCA2-RAD51 comparing to normal controls (p = 0.048, p = 0.001, p = 0.001). XRCC6 showed significantly low expression in de novo MDS comparing to controls (p = 0.039) and for patients who presented chromosomal abnormalities (p = 0.047). Downregulation of LIG4 was consistently associated with poor prognostic markers in de novo MDS (hemoglobin < 8 g/dL (p = 0.040), neutrophils < 800/mm3 (p < 0.001), patients with excess of blasts (p = 0.001), very high (p = 0.002)/high IPSS-R (p = 0.043) and AML transformation (p < 0.001). We also performed an evaluation of GEPIA Database in 30 cancer types and detected a typical pattern of downregulation as here presented in primary or secondary MDS. All these results suggest synthetic lethality approach can be tested with DNA repair genes (beyond that of BRCA1/2 status) for de novo and therapy-related myelodysplastic syndrome and may encourage clinical trials evaluating the use of PARP1 inhibitors in MDS.

Polo-like Kinase 1 Inhibition as a Therapeutic Approach to Selectively Target BRCA1-Deficient Cancer Cells by Synthetic Lethality Induction.

PURPOSE: BRCA1 and BRCA2 deficiencies are widespread drivers of human cancers that await the development of targeted therapies. We aimed to identify novel synthetic lethal relationships with therapeutic potential using BRCA-deficient isogenic backgrounds. EXPERIMENTAL DESIGN: We developed a phenotypic screening technology to simultaneously search for synthetic lethal (SL) interactions in BRCA1- and BRCA2-deficient contexts. For validation, we developed chimeric spheroids and a dual-tumor xenograft model that allowed the confirmation of SL induction with the concomitant evaluation of undesired cytotoxicity on BRCA-proficient cells. To extend our results using clinical data, we performed retrospective analysis on The Cancer Genome Atlas (TCGA) breast cancer database. RESULTS: The screening of a kinase inhibitors library revealed that Polo-like kinase 1 (PLK1) inhibition triggers strong SL induction in BRCA1-deficient cells. Mechanistically, we found no connection between the SL induced by PLK1 inhibition and PARP inhibitors. Instead, we uncovered that BRCA1 downregulation and PLK1 inhibition lead to aberrant mitotic phenotypes with altered centrosomal duplication and cytokinesis, which severely reduced the clonogenic potential of these cells. The penetrance of PLK1/BRCA1 SL interaction was validated using several isogenic and nonisogenic cellular models, chimeric spheroids, and mice xenografts. Moreover, bioinformatic analysis revealed high-PLK1 expression in BRCA1-deficient tumors, a phenotype that was consistently recapitulated by inducing BRCA1 deficiency in multiple cell lines as well as in BRCA1-mutant cells. CONCLUSIONS: We uncovered an unforeseen addiction of BRCA1-deficient cancer cells to PLK1 expression, which provides a new means to exploit the therapeutic potential of PLK1 inhibitors in clinical trials, by generating stratification schemes that consider this molecular trait in patient cohorts.

Stochastic Modeling and Simulation of Viral Evolution.

RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversity is generated and maintained is fundamental when approaching viral persistence and pathobiology in infected hosts. In this paper, we access quasispecies theory through a mathematical model based on the theory of multitype branching processes, to better understand the roles of mechanisms resulting in viral diversity, persistence and extinction. We accomplish this understanding by a combination of computational simulations and the theoretical analysis of the model. In order to perform the simulations, we have implemented the mathematical model into a computational platform capable of running simulations and presenting the results in a graphical format in real time. Among other things, we show that the establishment of virus populations may display four distinct regimes from its introduction into new hosts until achieving equilibrium or undergoing extinction. Also, we were able to simulate different fitness distributions representing distinct environments within a host which could either be favorable or hostile to the viral success. We addressed the most used mechanisms for explaining the extinction of RNA virus populations called lethal mutagenesis and mutational meltdown. We were able to demonstrate a correspondence between these two mechanisms implying the existence of a unifying principle leading to the extinction of RNA viruses.

Mecanismos moleculares do efeito citotóxico de FGF2 em células transformadas por RAS / Molecular mechanisms of the cytotoxic effect of FGF2 in rastransformed cells

O FGF2 (Fibroblast Growth Factor 2) é um clássico fator peptídico de crescimento que ativa vias intracelulares de sinalização molecular promovendo a transição G0 → G1 e o comprometimento com o ciclo celular. Não surpreendentemente, seus papéis pró-tumoral e angiogênico estão bem caracterizados e estabelecidos na literatura. No entanto, um crescente corpo de evidências tem indicado que o FGF2 também pode exercer efeitos anti-tumorais in vitro e in vivo, em modelos murinos e também humanos. Neste contexto, nosso grupo publicou em 2008 que o FGF2 exerce um efeito antiproliferativo seletivo em células murinas malignas dependentes de alta atividade de K-Ras e H-Ras. Os genes ras compõem a família de oncogenes mais frequentemente mutada em tumores malignos humanos, alcançando aproximadamente 30% de todos os casos. O desenvolvimento de terapias contra tumores dependentes de Ras fracassou, apesar dos intensos esforços e investimentos desde a descoberta em 1982 de suas mutações ativadoras em múltiplos cânceres. O objetivo deste trabalho foi desvendar os mecanismos moleculares pelo quais o FGF2 inibe irreversivelmente a proliferação de células malignas dependentes da atividade de Ras, empregando como modelos experimentais a linhagem murina Y1 de células adrenocorticais, e 4 linhagens humanas derivadas de sarcomas de Ewing. Identificamos que o efeito citotóxico do FGF2 não se processa por um mecanismo novo e independente das viasproliferativas classicamente ativadas por fatores peptídicos de crescimento. Ao contrário, seu efeito tóxico é resultado de sinalização mitogênica exagerada decorrente de estimulação sustentada por FGF2. A ativação da via de MAPK, principal sinalização mitogênica intracelular, a níveis elevados e sustentados provoca estresse mitogênico, que se propaga para a fase S na forma de estresse replicativo. Nesta situação, a célula passa a depender exageradamente da sinalização protetora de ATR, de modo que a combinação de estimulação com FGF2 e inibição de ATR foi altamente letal para as células malignas dependentes de Ras empregadas neste trabalho. Também analisamos as bases moleculares de resistência a FGF2 exibida por células Y1 anteriormente selecionadas para resistir ao efeito tóxico do FGF2 (Y1FRs). Descobrimos que a pressão seletiva do FGF2 não teve efeito na expressão de seus receptores, mas provocou a eliminação de um dos dois cromossomos que portam a amplificação gênica de ras nesta linhagem, enquanto o segundo cromossomo foi mantido por ser a única fonte de genes ribossomais ativos. Suas cópias de ras, no entanto, mostraram-se transcricionalmente silenciadas. Além disso, as sublinhagens Y1FRs não expressam o principal RasGEF, GRP4, encontrado nas células parentais Y1, o que pode ter influenciado o surgimento do fenótipo resistente ao FGF2. As linhagens resistentes mostraram grande redução no número de cromossomos e aumento da frequência de fusões entre cromossomos não homólogos em relação às células parentais

FGF2 (Fibroblast Growth Factor 2) is a classic peptide growth factor that activates intracellular molecular signaling pathways promoting the G0 → G1 transition and cell cycle commitment. Not surprisingly, its pro-tumor and angiogenic roles are well characterized and established in the literature. However, a growing body of evidence has indicated that FGF2 may also exert anti-tumor effects in vitro and in vivo in murine and human models. In this context, our group reported in 2008 that FGF2 exerts a selective antiproliferative effect in murine cells dependent on high activity of K-Ras and H-Ras. Ras genes make up the most frequently mutated oncogene family in human malignant tumors, reaching approximately 30% of all cases. The development of therapies against Ras-dependent tumors has failed despite intense efforts and investments since the discovery in 1982 of its activating mutations in multiple cancers. The objective of this work was to uncover the molecular mechanisms by which FGF2 irreversibly inhibits the proliferation of malignant cells dependent on Ras activity, using as experimental models the Y1 murine lineage of adrenocortical malignant cells and 4 human lineages derived from Ewing sarcomas. We showed that the cytotoxic effect of FGF2 did not involve novel cell cycle regulatory pathways; instead, this cytotoxic effect is a result of sustainedhyper mitogenic stimulation by FGF2. Activation of the KRas/MAPK pathway, the major intracellular mitogenic signaling, at high and sustained levels provokes mitogenic stress, which is propagated to S phase as replicative stress. In this situation, the cell dependence on the ATR protective signaling is enhanced, so that the combination of stimulation with FGF2 and inhibition of ATR was highly lethal for the Ras dependent malignant cells employed in this work. We also analyzed the molecular basis of FGF2 resistance exhibited by Y1 cells previously selected for resistance to FGF2. We found that the selective pressure of FGF2 had no effect on the expression of its receptors but promoted the elimination of one of the two marker chromosomes that carry the K-ras amplified copies, while the second chromosome was maintained because it is the only source of active ribosomal genes; however, its K-ras amplified copies were transcriptionally silenced. In addition, the Y1FRs sublines did not express the main RasGEF, GRP4, found in the parental Y1 cells, which might have played a role in the emergence of the FGF2-resistant phenotype. The resistant Y1FRs sublines showed a large reduction in chromosome numbers and increased frequency of fusions between non-homologous chromosomes in relation to parental cells