Somatic Mutations In Key Genes Research Articles

Pan-Cancer Analysis of Potential Synthetic Lethal Drug Targets Specific to Alterations in DNA Damage Response.

Alterations in DNA damage response (DDR) is one of the several hallmarks of cancer. Genomic instability resulting from a disrupted DDR mechanism is known to contribute to cancer progression, and are subjected to radiation, cytotoxic, or more recently targeted therapies with limited success. Synthetic lethality (SL), which is a condition where simultaneous loss-of-function of the genes from complementary pathways result in loss of viability of cancer cells have been exploited to treat malignancies resulting from defects in certain DDR pathways. Albeit being a promising therapeutic strategy, number of SL based drugs currently in clinical trial is limited. In this work we performed a comprehensive pan-cancer analysis of alterations in 10 DDR pathways with different components of DNA repair. Using unsupervised clustering of single sample enrichment of these pathways in 7,272 tumor samples from 17 tumor types from TCGA, we identified three prominent clusters, each associated with specific DDR mechanisms. Somatic mutations in key DDR genes were found to be dominant in each of these three clusters with distinct DDR component. Using a machine-learning based algorithm we predicted SL partners specific to somatic mutations in key genes representing each of the three DDR clusters and identified potential druggable targets. We explored the potential FDA-approved drugs for targeting the predicted SL genes and tested the sensitivity using the drug screening data in cell lines with mutation in the primary DDR genes. We have shown clinical relevance, for selected targetable SL interactions using Kaplan-Meier analysis in terms of improved disease-free survival. Thus, our computational framework provides a basis for clinically relevant and actionable SL based drug targets specific to alterations in DDR pathways.

The cyclical hit model: how paligenosis might establish the mutational landscape in Barrett's esophagus and esophageal adenocarcinoma.

In this review, we explore a paligenosis-based model to explain Barrett's esophagus development and progression: 'the cyclical hit model.' Genomic analyses have highlighted the high mutational burden of esophageal adenocarcinoma, Barrett's esophagus, and even normal esophageal epithelium. Somatic mutations in key genes including TP53 occur early in the neoplastic progression sequence of Barrett's esophagus, whereas chromosomal amplification resulting in oncogene activation occurs as a critical late event. Paligenosis is a shared injury response mechanism characterized by activation of autophagy, expression of progenitor markers, and increased mTORC signaling-induced cell-cycle reentry. In the setting of chronic injury/inflammation, cycles of paligenosis may allow accumulation of mutations until eventually the mutational burden, in concert perhaps with mutations in key driver oncogenes, finally alters the cell's ability to redifferentiate, leading to the emergence of a potential neoplastic clone. Under conditions of chronic gastroesophageal refluxate exposure, the normal esophageal squamous epithelium might undergo multiple cycles of paligenosis, allowing initially silent mutations to accumulate until key events impart mutant clones with an oncogenic survival advantage.

Deletion of mTOR in Reactive Astrocytes Suppresses Chronic Seizures in a Mouse Model of Temporal Lobe Epilepsy.

Germline and somatic mutations in key genes of the mammalian target of rapamycin (mTOR) pathway have been identified in seizure-associated disorders. mTOR mutations lead to aberrant activation of mTOR signaling, and, although affected neurons are critical for epileptogenesis, the role of mTOR activation in glial cells remains poorly understood. We previously reported a consistent activation of the mTOR pathway in astrocytes in the epileptic foci of temporal lobe epilepsy. In this study, it was demonstrated that mTOR deletion from reactive astrocytes prevents increases in seizure frequency over the disease course. By using a tamoxifen-inducible mTOR conditional knockout system and kainic acid, a model was developed that allowed astrocyte-specific mTOR gene deletion in mice with chronic epilepsy. Animals in which mTOR was deleted from 44% of the astrocyte population exhibited a lower seizure frequency compared with controls. Down-regulation of mTOR significantly ameliorated astrogliosis in the sclerotic hippocampus but did not rescue mossy fiber sprouting. In cultured astrocytes, the mTOR pathway modulated the stability of the astroglial glutamate transporter 1 (Glt1) and influenced the ability of astrocytes to remove extracellular glutamate. Taken together, these data indicate that astrocytes with activated mTOR signaling may provide conditions that are favorable for spontaneous recurrent seizures.

The Mutational Landscape of CTCL and Sezary Syndrome

Mycosis fungoides and Sézary syndrome (SS) are cutaneous T-cell lymphomas (CTCL) derived from mature CD4-positive skin-homing T cells with Sézary representing the most aggressive leukemic form of the disease. To investigate the pathogenic mechanisms of Sézary syndrome and aggressive CTCLs, we performed whole exome sequencing of matched tumor and normal DNA samples from 42 CTCL cases, including 26 Sézary syndrome. Copy number analysis revealed a distinctive pattern of somatic copy number alterations in Sézary syndrome including highly prevalent recurrent chromosomal deletions involving the TP53, RB1, PTEN, DNMT3A and CDKN1B tumor suppressor genes. Moreover, exome-wide somatic mutation analysis identified a broad spectrum of somatic mutations in key genes involved in epigenetic regulation (TET2, CREBBP, MLL2, MLL3, BRD9, SMARCA4 and CHD3) and signaling, including mutations in MAPK1, BRAF, CARD11 and PRKG1.In this context, we identified three mutations involving position E322 in MAPK1 (p.Glu322Ala and p.Glu322Lys). Functional characterization of these recurrent alleles showed increased ERK1/2 activation upon expression of both MAPK1 E322K and E322A. In addition we identified two mutations (p.Ser615Phe and p.Ser626Lys) in CARD11, an important mediator of NFκB activation. Notably, and in contrast with diffuse B-cell lymphomas where CARD11 mutations are primarily located in the coiled-coil domain, CARD11 alleles present in CTCL cases are located in the linker domain region of the protein. Functional characterization of CTCL associated CARD11 S615F and CARD11 E626K linker mutations revealed markedly increased NFκΒ activity in reporter assays, which was further enhanced upon TCR activation. Finally, we also noted the presence of two closely located mutations (p.Glu17Lys and p.Arg21Gln) in the N-terminal dimerization domain of the cGKIβ protein, in Sézary syndrome samples. cGKIβ, PRKG1 gene, is a cGMP-binding protein implicated in nitric oxide signaling. cGKIβ signaling in T-cells antagonizes TCR activation-induced interleukin 2 release and proliferation. Structural and functional characterization of the two PRKG1 mutations found in Sézary syndrome revealed impaired dimerization and decreased cGKIβ-mediated activation after stimulation with the cGMP analog 8-CPT-cGMP. Moreover, analysis of the effects of cGKIβ E17K and cGKIβ R21Q expression in JURKAT T cells revealed increased NFAT activity after PMA plus ionomycin stimulation, supporting a positive role for these mutations in enhancing the TCR signaling response. In all, these results mechanistically involve increased MAPK-ERK, NFκB and NFAT signaling in the pathogenesis of CTCLs.To analyze the therapeutic potential of targeting these oncogenic signaling pathways in CTCL we performed analysis of MAPK, JNK and NFκB signaling in CTCL cell lines. Therapeutically, inhibition of NFκB signaling with Mi-2 and bortezomib was broadly and highly active across all cell lines tested, while MEK1/2 inhibition with U0126 and inhibition of NFAT with FK506 showed more modest antitumor effects. Collectively, our findings provide new insights into the genetics of Sézary syndrome and CTCL and support the development of personalized therapies targeting key oncogenically activated signaling pathways for the treatment of these diseases. DisclosuresNo relevant conflicts of interest to declare.

Association of Single Nucleotide Polymorphisms in Wnt Signaling Pathway Genes with Breast Cancer in Saudi Patients

Breast cancer is a complex heterogeneous disease involving genetic and epigenetic alterations in genes encoding proteins that are components of various signaling pathways. Candidate gene approach have identified association of genetic variants in the Wnt signaling pathway genes and increased susceptibility to several diseases including breast cancer. Due to the rarity of somatic mutations in key genes of Wnt pathway, we investigated the association of genetic variants in these genes with predisposition to breast cancers. We performed a case-control study to identify risk variants by examining 15 SNPs located in 8 genes associated with Wnt signaling. Genotypic analysis of individual locus showed statistically significant association of five SNPs located in β-catenin, AXIN2, DKK3, SFRP3 and TCF7L2 with breast cancers. Increased risk was observed only with the SNP in β-catenin while the other four SNPs conferred protection against breast cancers. Majority of these associations persisted after stratification of the cases based on estrogen receptor status and age of on-set of breast cancer. The rs7775 SNP in exon 6 of SFRP3 gene that codes for either arginine or glycine exhibited very strong association with breast cancer, even after Bonferroni's correction. Apart from these five variants, rs3923086 in AXIN2 and rs3763511 in DKK4 that did not show any association in the overall population were significantly associated with early on-set and estrogen receptor negative breast cancers, respectively. This is the first study to utilize pathway based approach to identify association of risk variants in the Wnt signaling pathway genes with breast cancers. Confirmation of our findings in larger populations of different ethnicities would provide evidence for the role of Wnt pathway as well as screening markers for early detection of breast carcinomas.

Analysis of biomarkers during early phase clinical development of AMG 479, an investigational fully human monoclonal antibody antagonist of type 1 insulin-like growth factor receptor (IGF-1R)

3545 Background: AMG 479 showed anti-tumor activity in a phase 1 (P1) and phase 1b (P1b) trial (Tolcher, J Clin Oncol. 2007;25:3002; Sarantopoulos, J Clin Oncol. 2008;26:3583). We sought to identify predictive markers of response to AMG 479 in these trials by analyzing pharmacodynamic (PD) markers in serum, and expression and mutations of regulators of the IGF-1R pathway in tumors. Methods: Patients (pts) had advanced solid tumors and received AMG 479 (1–20 mg/kg Q2W) in the P1 trial or AMG 479 (6 or 12 mg/kg Q2W) + panitumumab (6 mg/kg Q2W) or gemcitabine (1,000 mg/m2 QW) in the P1b trial. Serum levels of IGF-1 and IGFBP-3 were measured pre dose on Day -1 and post dose at various time points. In the P1 trial, we examined relationships between tumor response (by RECIST) and: 1) levels of IGF-1 and IGFBP-3 (at baseline or PD change from baseline); 2) somatic mutations in key genes (including K-ras, and PTEN) of the IGF-1R pathway (in archival tumors); and 3) expression of PTEN (measured by immunohistochemistry in archival tumors). Results: Serum IGF-1 and IGFBP-3 increased in a concentration-dependent manner between 1 and 12 mg/kg AMG 479, with an apparent plateau between 12 and 20 mg/kg AMG 479. Baseline and PD changes in IGF-1 and IGFBP-3 were not substantially different in pts with a tumor response compared with those without a tumor response. A partial response to AMG 479 was observed in a pt with an activating K-ras mutation. No responses have been observed in tumors that lack expression of PTEN. Conclusions: The PD results suggest near complete biochemical coverage at 12-mg/kg AMG 479. Our hypothesis-generating analyses suggest that: 1) pre and postdose levels of IGF-1 and IGFBP-3 do not predict response to single-agent AMG 479; 2) activating K-ras mutations do not appear to preclude responsiveness to single-agent AMG 479 (in contrast to EGFR inhibitors); 3) expression and mutations of regulators of the PI3K/Akt pathway downstream of IGF-1R activation may be useful in predicting response to AMG 479. [Table: see text]