Polymorphisms of BCL2 and BAX Genes Associate with Outcomes in Advanced Non-small cell lung cancer Patients treated with platinum-based Chemotherapy

In silico investigation of nonsynonymous single nucleotide polymorphisms in BCL2 apoptosis regulator gene to design novel protein-based drugs against cancer

BCL2 apoptosis regulator gene encodes Bcl-2 pro-survival protein, which plays an important role to evade apoptosis in various cancers. Moreover, single nucleotide polymorphisms (SNPs) in the BCL2 gene can be nonsynonymous (nsSNPs), which might affect the protein stability and probably its function. Therefore, we implement cutting-edge computational techniques based on the Spherical Polar Fourier and Monte-Carlo algorithms to investigate the impact of these SNPs on the B cell lymphoma-2 (Bcl-2) stability and therapeutic potential of protein-based molecules to inhibit this protein. As a result, we identified two nsSNPs (Q118R and R129C) to be deleterious and highly conserved, having a negative effect on protein stability. Additionally, molecular docking and molecular dynamics simulations confirmed the decreased binding affinity of mutated Bcl-2 variants to bind three-helix bundle protein inhibitor as these mutations occurred in the protein-protein binding site. Overall, this computational approach investigating nsSNPs provides a useful basis for designing novel molecules to inhibit Bcl-2 pro-survival pathway in malignant cells.

The pro-apoptotic Bax gene modifies susceptibility to craniofacial dysmorphology following gastrulation-stage alcohol exposure

BACKGROUND

During early development, alcohol exposure causes apoptotic cell death in discrete regions of the embryo which are associated with distinctive patterns of later-life abnormalities. In gastrulation, which occurs during the third week of human pregnancy, alcohol targets the ectoderm, the precursor of the eyes, face, and brain. This midline tissue loss leads to the craniofacial dysmorphologies, such as microphthalmia and a smooth philtrum, which define fetal alcohol syndrome (FAS). An important regulator of alcohol-induced cell death is the pro-apoptotic protein Bax. The current study determines if mice lacking the Bax gene are less susceptible to the pathogenic effects of gastrulation-stage alcohol exposure.

METHODS

Male and female Bax^+/- mice mated to produce embryos with full (^-/- ) or partial (^+/- ) Bax deletions, or Bax^+/+ wild-type controls. On Gestational Day 7 (GD 7), embryos received two alcohol (2.9 g/kg, 4 hr apart), or control exposures. A subset of embryos was collected 12 hr later and examined for the presence of apoptotic cell death, while others were examined on GD 17 for the presence of FAS-like facial features.

RESULTS

Full Bax deletion reduced embryonic apoptotic cell death and the incidence of fetal eye and face malformations, indicating that Bax normally facilitates the development of alcohol-induced defects. An RNA-seq analysis of GD 7 Bax^+/+ and Bax^-/- embryos revealed 63 differentially expressed genes, some of which may interact with the Bax deletion to further protect against apoptosis.

CONCLUSIONS

Overall, these experiments identify that Bax is a primary teratogenic mechanism of gastrulation-stage alcohol exposure.

Genetic Polymorphisms and the Efficacy of Platinum-Based Chemotherapy: Review

Previous studies have indicated that genetic variations in individuals may result in changes in gene expression and amino acids. The effect of these changes may lead to different responses to platinum-based chemotherapy. A vast response rate interval and a short survival rate indicate that the efficacy and efficiency of the selection of chemotherapy have not been optimized. This article aims to illustrate the potential relationship of various genetic polymorphisms in response to platinum-based chemotherapy for several types of cancer. This review was conducted using articles from the last three- and five-year periods (2014-2019) that use gene polymorphism and its relationship to the efficacy of platinum-based chemotherapy as their theme. A total of 26 out of 488 relevant articles were included based on specific criteria. Through various mechanisms, genes, including ERCC1, ERCC2/XPD, XPC, XPA, XRCC1, APE-1, PARP1, OGG1, ABCC2, MRP, GSTP1, GSTM1, GSTT1, MATE1, and OCT2, have been associated with patient response to platinum-based chemotherapy. We conclude that genetic polymorphism analysis is recommended for the management of cancer so that each patient can be administered therapy based on his or her genetic profile to achieve an effective and efficient outcome.

A genome-scale CRISPR knock-out screen in chronic myeloid leukemia identifies novel drug resistance mechanisms along with intrinsic apoptosis and MAPK signaling

Understanding resistance mechanisms in cancer is of utmost importance for the discovery of novel "druggable" targets. Efficient genetic screening, now even more possible with CRISPR-Cas9 gene-editing technology, next-generation sequencing and bioinformatics, is an important tool for deciphering novel cellular processes, such as resistance to treatment in cancer. Imatinib specifically eliminates chronic myeloid leukemia (CML) cells by targeting and blocking the kinase activity of BCR-ABL1; however, resistance to treatment exists. In order to discover BCR-ABL1 independent mechanisms of imatinib resistance, we utilized the genome-scale CRISPR knock-out library to screen for imatinib-sensitizing genes in vitro on K562 cells. We revealed genes that seem essential for imatinib-induced cell death, such as proapoptotic genes (BIM, BAX) or MAPK inhibitor SPRED2. Specifically, reestablishing apoptosis in BIM knock-out (KO) cells with BH3 mimetics, or inhibiting MAPK signaling in SPRED2 KO cells with MEK inhibitors restores sensitivity to imatinib. In this work, we discovered previously identified pathways and novel pathways that modulate response to imatinib in CML cell lines, such as the implication of the Mediator complex, mRNA processing and protein ubiquitinylation. Targeting these specific genetic lesions with combinational therapy can overcome resistance phenotypes and paves the road for the use of precision oncology.

Genetic Polymorphisms and Platinum-Based Chemotherapy-Induced Toxicities in Patients With Lung Cancer: A Systematic Review and Meta-Analysis

Background: Platinum-based agents, including cisplatin, carboplatin, and oxaliplatin, are indispensable for the treatment of lung cancer. The development of toxicity frequently necessitates dose reduction or discontinuation of therapy, despite the clinical response. Pharmacogenomics studies were reviewed to identify the possible genetic variants that underlie individual susceptibility to platinum-related toxicities. Method: We conducted a systematic search in PubMed and Embase for pharmacogenomics reports that focused on commonly reported platinum-induced toxicities, such as gastrointestinal (GI), hematological, neurological, and other toxicities, in patients diagnosed with lung cancer. Meta-analyses were conducted to determine the association between genetic polymorphisms and platinum-induced toxicity by checking the odds ratio (OR) and 95% confidence interval (CI) using random or fixed-effects models as appropriate. Results: Twenty eligible studies that met the inclusion criteria with sufficient data were extracted and presented comprehensively. A total of 16 polymorphisms from 11 genes were included in the meta-analysis. MTHFR rs1801131 and MDM2 rs1690924 were significantly correlated with platinum-induced GI toxicity (P = 0.04 and P = 0.02, respectively). Patients with the MTHFR rs1801131AA and MDM2 rs1690924TC/CC genotype tended to have a higher risk of GI toxicity than patients with other genotypes did (OR = 1.73, 95% CI = 0.86-2.18; and OR = 0.51, 95% CI = 0.29-0.88, respectively). Compared to carriers of the MTHFR rs1801133CC genotype, carriers of the CT/TT genotype had a significantly increased risk of hematological toxicity (P = 0.01, OR = 1.68, 95% CI = 1.12-2.52). Conclusion: In the future, physicians should pay careful attention to MTHFR and MDM2 for personalized chemotherapy treatment among patients with lung cancer.

Prognostic value and susceptibility of BAX rs4645878 polymorphism in cancer: A systematic review and meta-analysis

BACKGROUND

BCL-2 Associated X (BAX) is an important modulator of apoptosis. The associations between BAX gene polymorphism and cancer susceptibility and prognosis in different ethnic groups and types of cancer have yielded controversial results. To reconcile the results, a systematic review followed by meta-analysis was performed to assess the associations.

METHODS

A systematic search of Medline database (PubMed), EMBASE, China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang databases for publications on BAX polymorphisms, and susceptibility and prognosis was carried out until July 2017. Retrieved 14 articles met the inclusions. Summary odds ratios (ORs) and hazard ratios (HRs) with their 95% confidence intervals (CIs) were harnessed to determine the strength of correlation between BAX polymorphisms and cancer susceptibility and prognosis, which were combined using fixed- or random-effects models as appropriate.

RESULTS

A total of 12 trials involving 3321 cases and 3209 controls were included in our pooled analysis regarding the polymorphisms and the susceptibility of cancers. Overall, results of the present meta-analysis demonstrated that there was no significant association between BAX polymorphisms and susceptibility of cancers (OR = 1.052, 95% CI: 0.827-1.339, P = .679, A vs G). Even in a stratified analysis by ethnicity and the sources of control groups, the results were consistent. Four retrospective studies of 549 cases qualified for meta-analysis were identified to set forth the associations of the polymorphisms with cancer prognosis. Our results suggested that BAX gene polymorphisms were significantly associated with unfavorable prognosis (HR = 1.735, 95% CI: 1.368-2.202, P = .000, GG vs GA/AA).

CONCLUSION

There is no significant association between BAX gene polymorphism and cancer susceptibility, but it probably contributes to increased adverse prognosis to cancer.

MicroRNA-137-regulated AKT serine/threonine kinase 2 inhibits tumor growth and sensitizes cisplatin in patients with non-small cell lung cancer

The present study investigated the role of microRNA-137-regulated AKT serine/threonine kinase 2 (AKT2) on tumor growth and cisplatin sensitivity in patients with non-small cell lung cancer (NSCLC). The results demonstrated that the expression of microRNA-137 in cisplatin-treated NSCLC patient tissue samples was markedly lower than that in healthy tissue samples. The disease-free survival and overall survival rates of patients with NSCLC exhibiting a high microRNA-137 expression were higher than the survival rates of patients with NSCLC exhibiting a low expression of microRNA-137. Overexpression of microRNA-137 inhibited the proliferation of A549 and H520 cells treated with cisplatin. Overexpression of miR-137 suppressed the protein expression of AKT2, increased caspase-3 activity, increased Bax protein expression and suppressed Cyclin D1 protein expression in A549 and H520 cells treated with cisplatin. MK2206, an AKT2 inhibitor, inhibited AKT2 protein expression and suppressed the proliferation of A549 and H520 cells treated with cisplatin following overexpression of miR-137. The inhibition of AKT2 also increased caspase-3 activity and Bax protein expression, and suppressed Cyclin D1 protein expression in A549 and H520 cells treated with cisplatin following overexpression of miR-137. Taken together, the results of the present study suggested that microRNA-137-regulated AKT2 inhibits tumor growth and sensitizes cisplatin in patients with NSCLC.

Expression of Bcl-2 is a favorable prognostic biomarker in lung squamous cell carcinoma

Lung squamous cell carcinoma (LUSC) is the second major type of lung cancer globally. The majority of patients with LUSC are clinically diagnosed at the advanced stages, thus it is urgent to identify suitable prognostic markers for LUSC. B-cell lymphoma 2 (Bcl-2) has been widely studied in non-small cell lung cancer (NSCLC). However, the prognostic role of Bcl-2 in NSCLC remains conflicting and controversial, particularly for LUSC. Although certain studies have been performed to identify the prognostic value of Bcl-2, to the best of our knowledge, no study has investigated the prognostic role of Bcl-2 in LUSC specifically. The present study aimed to comprehensively evaluate the prognostic value of Bcl-2 in LUSC. Microarray data for LUSC were downloaded from public databases, including the Gene Expression Omnibus and The Cancer Genome Atlas. Microarray data of 901 patients with LUSC from 16 data sets were retrieved. The meta-z algorithm was applied and the combined z score was identified as -2.43, suggesting Bcl-2 is a favorable prognostic biomarker. Furthermore, immunohistochemical staining of Bcl-2 expression was performed in a tissue microarray of 72 patients with LUSC and survival analysis demonstrated that patients with high expression Bcl-2 exhibited significantly more improved overall survival rates compared with those with low Bcl-2 expression. Multivariate Cox regression revealed that high expression of Bcl-2 is an independent favorable prognostic factor (hazard ratio, 0.295; confidence interval, 0.097-0.904; P<0.05). Therefore, the results of the present study demonstrated that Bcl-2 is a favorable prognostic biomarker in LUSC.

Understanding the Role of Intrinsic Disorder of Viral Proteins in the Oncogenicity of Different Types of HPV

Intrinsic disorder is very important in the biological function of several proteins, and is directly linked to their foldability during interaction with their targets. There is a close relationship between the intrinsically disordered proteins and the process of carcinogenesis involving viral pathogens. Among these pathogens, we have highlighted the human papillomavirus (HPV) in this study. HPV is currently among the most common sexually transmitted infections, besides being the cause of several types of cancer. HPVs are divided into two groups, called high- and low-risk, based on their oncogenic potential. The high-risk HPV E6 protein has been the target of much research, in seeking treatments against HPV, due to its direct involvement in the process of cell cycle control. To understand the role of intrinsic disorder of the viral proteins in the oncogenic potential of different HPV types, the structural characteristics of intrinsically disordered regions of high and low-risk HPV E6 proteins were analyzed. In silico analyses of primary sequences, prediction of tertiary structures, and analyses of molecular dynamics allowed the observation of the behavior of such disordered regions in these proteins, thereby proving a direct relationship of structural variation with the degree of oncogenicity of HPVs. The results obtained may contribute to the development of new therapies, targeting the E6 oncoprotein, for the treatment of HPV-associated diseases.

Genetic determinants for chemo- and radiotherapy resistance in bladder cancer

Bladder cancer (BCa) is burdened by high rates of chemo- and radio-resistance. We reviewed and summarized the current evidence regarding the genetic determinants of resistance in patients treated with chemotherapy and/or radiotherapy (RT) for BCa. Genetic heterogeneity may preexist to treatment arising with tumorigenesis or increasing progressively during the treatment. Several biological pathways seem to be involved in the cellular response to treatment. These pathways comprehend mechanisms leading to modify the intracellular concentration of the drug, mechanisms leading to increase the repair of DNA damage caused by the treatment, mechanisms leading to increase cell survival, despite DNA damage, acting on the signaling pathways affecting apoptosis, mechanisms promoting autophagy. In the present review, we focused on the genetic determinants of resistance affecting the aforementioned mechanisms.

Mutations in apoptotic genes and micronucleus occurrence in vinyl chloride-exposed workers in China

BACKGROUND

Vinyl chloride is an occupational carcinogen which caused micronuclei in human directly. It has recently been demonstrated that micronuclei formation could generate a spectrum of genomic rearrangements and play a key role in the early tumorigenesis process. We aimed to investigate the association between polymorphisms in the apoptosis process related genes and micronuclei rate in vinyl chloride-exposed workers in China.

MATERIALS AND METHODS

Cytokinesis block micronucleus test was performed on 342 vinyl chloride-exposed workers and 107 nonexposed workers to determine chromosomal damage. The polymerase chain reaction and restriction fragment length polymorphism technique were used to detect nine Single Nucleotide Polymorphisms in the apoptosis process related genes.

RESULTS

There was a highly significant dose-response relationship between vinyl chloride exposure and chromosomal damage. Individuals carrying the variant heterozygote MDM2 -309T > G (rs2279744) and variant homozygote BCL2 -938C > A (rs2279115) were at higher risk for chromosomal damage compared with their wild-type genotype, respectively. Although individuals possessing the variant genotype of BAX -248G > A (rs4645878) had decreased risk compared with the corresponding wild type, this did not reach statistical significant.

CONCLUSION

Genetic polymorphisms in genes related to apoptosis process may have an impact on chromosomal damage induced by vinyl chloride. Environ. Mol. Mutagen. 58:39-45, 2017. © 2016 Wiley Periodicals, Inc.

Genetic variants of BCL2 gene predict clinical outcomes of non-small-cell lung cancer patients treated with platinum-based chemotherapy in a Chinese population

Platinum agents induce cancer cell death through BCL2-dependent intrinsic apoptotic pathway and are commonly used as anti-tumor drug. In this study, we evaluated whether single nucleotide polymorphism (SNPs) of BCL2 can affect the overall survival (OS) and progression-free survival (PFS) in non-small-cell lung cancer (NSCLC) patients treated with platinum-based chemotherapy. We genotyped 48 SNPs of BCL2 gene by Illumina Custom Designed Chip in 972 advanced NSCLC patients treated with platinum-based chemotherapy. We evaluated the relationship between genotype/haplotype/diplotype and OS/PFS by COX regression analysis. As a result, five SNPs, rs949037, rs3810027, rs4987739, rs4987726 and rs7226979, were significantly associated with overall survival time in 972 NSCLC patients after platinum-based chemotherapy. rs1381547 and rs8083946 were associated with progression-free survival. As representative, the G allele of rs949037 was associated with longer OS in NSCLC patients with platinum-based chemotherapy. Patients with GG or AG genotype showed a 19.9 months mOS vs AA genotype 14.2 months mOS (HR: 1.38, 95% CI: 1.11-1.72, p=0.004). In further analysis, rs949037 was found to predominantly contribute to the OS of patients with platinum-tubulin-targeting drugs, moreover, the GG genotype of rs949037 showed an 8.5 months longer OS compared with the unfavorable AA genotype (mOS: 21.36 vs 12.83, HR=0.70, 95% CI: 0.52-0.94, p=0.000). To conclude, polymorphisms of BCL2 gene may have an impact on the OS of platinum-based chemotherapy in NSCLC patients, which may be prognostic biomarkers of chemotherapy if validated in larger studies.

Pharmacogenomics of platinum-based chemotherapy sensitivity in NSCLC: toward precision medicine

Lung cancer is one of the leading causes of cancer-related death in the world. Platinum-based chemotherapy is the first-line treatment for non-small-cell lung cancer (NSCLC), however, the therapeutic efficiency varies remarkably among individuals. A large number of pharmacogenomics studies aimed to identify genetic variations which can be used to predict platinum response. Those studies are leading NSCLC treatment to the new era of precision medicine. In the current review, we provided a comprehensive update on the main recent findings of genetic variations which can be used to predict platinum sensitivity in the NSCLC patients.