Frequency of Healthy Control Genotype of VDR Gene Polymorphisms in the Saudi Population of the Ha'il Region: A Comparative Study with Worldwide Population

Genetic polymorphisms in the vitamin D receptor (VDR) may influence the biological effects of vitamin D and increase a person's susceptibility to cancer. Previous studies have shown that different ethnic groups exhibit varying frequencies of the VDR gene variants TaqI, ApaI, FokI, and BsmI. However, the allelic distribution of these VDR polymorphisms in the Saudi population of Ha'il region is not sufficiently explored. In this study, efforts were made to ascertain the frequency of VDR polymorphisms in the Saudi population of Ha'il region, and then comparison was made for VDR polymorphism rates with other populations of the world. Allele and genotype frequencies of VDR TaqI, ApaI, BsmI and FokI gene was determined. The frequency distribution for the variant allele of VDR TaqI, ApaI, BsmI and FokI was found to be 70, 33, 50 and 25%, respectively. A significant frequency distribution was found for VDR-TaqI, ApaI and FokI variants in comparison with other populations of the world. Whereas, almost all of the studies dealing with VDR-FokI failed to show substantial difference while comparing with the data reported from the population of Ha'il region of Saudi Arabia. A significant pattern in the frequency of VDR gene variations have been found in the Saudi population of Ha'il region, which may be attributed to ethnic variance. The understanding of the worldwide distribution of VDR markers could help with high-risk screening of those who are exposed to environmental hazards and people of Ha'il region, who are predispose to cancer.

Role of available COVID-19 vaccines in reducing deaths and perspective for next generation vaccines and therapies to counter emerging viral variants: an update

The COVID-19 disease wreaked havoc all over the world causing more than 6 million deaths out of over 519 million confirmed cases. It not only disturbed the human race health-wise but also caused huge economic losses and social disturbances. The utmost urgency to counter pandemic was to develop effective vaccines as well as treatments that could reduce the incidences of infection, hospitalization and deaths. The most known vaccines that could help in managing these parameters are Oxford-AstraZeneca (AZD1222), Pfizer-BioNTech (BNT162b2), Moderna (mRNA-1273) and Johnson & Johnson (Ad26.COV2.S). The effectiveness of AZD1222 vaccine in reducing deaths is 88% in the age group 40-59 years, touching 100% in the age group 16-44 years & 65-84 years. BNT162b2 vaccine also did well in reducing deaths due to COVID-19 (95% in the age group 40-49 years and 100% in the age group 16-44 years. Similarly, mRNA-1273 vaccine showed potential in reducing COVID-19 deaths with effectiveness ranging from 80.3 to 100% depending upon age group of the vaccinated individuals. Ad26.COV2.S vaccine was also 100% effective in reducing COVID-19 deaths. The SARS-CoV-2 emerging variants have emphasized the need of booster vaccine doses to enhance protective immunity in vaccinated individuals. Additionally, therapeutic effectiveness of Molnupiravir, Paxlovid and Evusheld are also providing resistance against the spread of COVID-19 disease as well as may be effective against emerging variants. This review highlights the progress in developing COVID-19 vaccines, their protective efficacies, advances being made to design more efficacious vaccines, and presents an overview on advancements in developing potent drugs and monoclonal antibodies for countering COVID-19 and emerging variants of SARS-CoV-2 including the most recently emerged and highly mutated Omicron variant.

Diet as a modifiable factor in tumorigenesis: Focus on microbiome-derived bile acid metabolites and short-chain fatty acids

Several lines of evidences have implicated the resident microbiome as a key factor in the modulation of host physiology and pathophysiology; including the resistance to cancers. Gut microbiome heavily influences host lipid homeostasis by their modulatory effects on the metabolism of bile acids (BAs). Microbiota-derived BA metabolites such as deoxycholic acid (DCA), lithocholic acid (LCA), and ursodeoxycholic acid (UDCA) are implicated in the pathogeneses of various cancer types. The pathogenic mechanisms are multimodal in nature, with widespread influences on the host immunes system, cell survival and growth signalling and DNA damage. On the other hand, short-chain fatty acids (SCFAs) produced by the resident microbial activity on indigestible dietary fibres as well as during intermittent fasting regimens (such as the Ramazan fasting) elicit upregulation of the beneficial anti-inflammatory and anticancer pathways in the host. The present review first provides a brief overview of the molecular mechanisms of microbiota-derived lipid metabolites in promotion of tumour development. The authors then discuss the potential of diet as a therapeutic route for beneficial alteration of microbiota and the consequent changes in the production of SCFAs, particularly butyrate, in relation to the cancer prevention and treatment.

Differential differentiation of B cell lymphopoiesis in lethal and non-lethal murine malaria models

B cells in protection against malaria and need of experiencing many episodes in humans to achieve a state of immunity is largely unknown. The cellular basis of such defects in terms of B cell generation, maturation and trafficking was studied by taking Plasmodium chabaudi, a non-lethal and Plasmodium berghei, a lethal murine model. A flow cytometry (FCF) based evaluation was used to study alterations in generation and maintenance of B cells in patients with Plasmodium falciparum malaria as well as in murine malaria models. A significant accumulation of mature B cells in bone marrow and immature B cells in circulation was a feature observed only in lethal malaria. At peak parasitaemia, both the models induce a significant decrease in T2 (transitional) B cells with expansion of T1B cells. Studies in patients with acute Pf malaria showed a significant expansion of memory B cells and TB cells with a concomitant decrease in naive2 B cells as compared with healthy controls. This study clearly demonstrates that acute malarial infection induces major disturbances in B cell development in lymphoid organs and trafficking in periphery.

Combined effect of ipilimumab and nivolumab improves oncology endpoints in metastatic melanoma patients

Metastatic melanoma has less frequency, but considered as the most dreaded cancer. The combination of nivolumab & ipilimumab is proving their mettle in treating metastatic melanoma. The patients when administered with the combination of nivolumab & ipilimumab have shown improved median progression free survival, objective response rate and overall survival rate compared with nivolumab and ipilimumab monotherapy. The combination shrinks the tumor cells by attacking different checkpoints viz. CTLA-4 and PD-L1, respectively. The combination treatment reveals reduced disease progression and suggests nivolumab's non-cross resistant nature. The median progression free survival in "nivolumab plus ipilimumab" group has shown an increase of 66.7% and 296.6% in comparison to nivolumab and ipilimumab monotherapy. The other parameter viz. objective response rate improvement is equivalent to almost 14% and 38.6% when compared to nivolumab and ipilimumab monotherapy, respectively.

Cytotoxic T-lymphocyte associated protein 4 (CTLA4) polymorphisms are linked to systemic lupus erythematosus: an updated meta-analysis

Cytotoxic T-lymphocyte associated protein 4 (CTLA-4) molecule controls T cell immune response. Functional single nucleotide polymorphisms (SNPs) in the CTLA-4 gene have been associated with several autoimmune diseases, including systemic lupus erythematosus (SLE).  However, the genetic association of the CTLA-4 variants with vulnerability to SLE remained contradictory. We have conducted a current meta-analysis by combining the findings of prior published articles in order to make a conclusive statement. Various literature databases were screened with appropriate keywords to obtain relevant articles, and eligible reports were obtained using well-defined inclusion and exclusion criteria. Meta-analysis was performed by Comprehensive Meta-analysis V 3.3, and various statistical parameters such as odds ratio, 95% confidence interval, and probability values were computed. A total of 3847 SLE patients and 5278 healthy controls were considered in the present meta-analysis from 26 individual reports. A significant association of CTLA-4 +49 A/G (G vs. A: p=0.03, OR=1.47) and -1722 T/C (p=0.02, OR=0.87) polymorphisms were observed with susceptibility and resistance against the development of SLE, respectively. However, the other two SNPs in the CTLA-4 gene (-318 C/T and -1661 A/G) failed to establish a connection. Interestingly, subgroup analysis revealed an association of CTLA-4 +49 A/G with a predisposition to SLE only in the Asian population (G vs. A: p=0.04, OR=1.26, GG vs. AA: p=0.02, OR=1.84, AG vs AA: p=0.01, OR=1.44, GG+AG vs AA: p=0.01, OR=1.52) and not in Caucasians. The current meta-analysis suggests a significant CTLA-4 +49 A/G variant association with susceptibility to SLE development in overall and Asian populations. In contrast, the other variant, -1722 T/C, is linked with protection against SLE. However, further case-control studies in diverse ethnic populations are requisite.

Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies

OBJECTIVE: The current study reviewed Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) variants for their effects on infection, transmission and neutralization by vaccine-induced antibodies. MATERIALS AND METHODS: The research articles for the current study were searched over PubMed, Google Scholar, EMBASE and Web of Science online databases. The keywords used were: (("SARS-CoV-2" OR "COVID-19") AND ("mutation" OR "variant") AND ("death" OR "hospitalization" OR "infection" OR "transmission") AND ("antibody" OR "neutralize" OR "vaccine")). A total of 333 research articles were retrieved through online-database search. These articles were further scrutinized for their relevancy. Additionally, searches were performed to find the latest relevant information over Google search engine and relevant news browsers. Finally, around 35 germane articles were considered for scripting the current report. RESULTS: The mutations have changed amino acids at key positions in spike protein viz. S477N, E484K, Q677H, E484Q, L452R, K417T, K417N and N501Y. These mutations are relevant for different characteristics and are present in newly evolved strains of SARS-CoV-2 like E484K in B.1.526, B.1.525, P.2, B.1.1.7, P.1 and B.1.351. Mutations have increased the immune escape potential leading to 3.5-6.5-folds decrease in neutralization of antibodies (Pfizer and Moderna vaccines). The variant, B.1.617 circulating in India and many other countries (double variant) having E484Q and L452R mutations, has raised the infection rate and decreased the neutralization capacity of the vaccine-induced antibodies. Deadly K417N+E484K+N501Y triplet mutations found in B.1.351 and P.1 have increased the transmission ability of these strains by 50% leading to greater COVID-19 hospitalization, ICU admissions and deaths. CONCLUSIONS: The new SARS-CoV-2 variants have compromised the neutralization potential of the currently used vaccines, but still, they have considerable efficacy to reduce infection and mortality.

Graphical Abstract

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Prioritization and characterization of validated biofilm blockers targeting glucosyltransferase C of Streptococcus mutans

To date, several Glucosyltransferase C (GtfC) inhibitors have been identified and experimentally validated. All these inhibitors have been validated at different experimental conditions like degree of purity, animal models, kinetic conditions, experimental environment etc.; and most of these inhibitors (ligands) proved to be quite effective in their respective validation environment. However, due to varied experimental validation conditions, and absence of molecular interaction data, there is no way to prioritize these validated ligands for their inhibition potential against GtfC. The present study is a novel attempt of comparative evaluation of the interaction of the validated ligands on a single platform and under similar conditions with a dual objective, i.e. ligand prioritization for their respective inhibitory potential and elucidation of the involved unknown molecular interactions. Carbohydrate derivatives (6-Deoxy sucrose and Trichloro-galactosucrose) were identified as the most promising GtfC inhibitors. In addition, Asp588, Trp517, and Asn481 amino acid residues of the domain A1 proved vital for the inhibitory effect. The study highlights the importance of the comparative analysis of the validated ligands in order to identify the most promising leads for drug discovery against dental caries.

IFN-γ +874 A>T (rs2430561) gene polymorphism and risk of pulmonary tuberculosis: a meta-analysis

INTRODUCTION

The role of interferon gamma (IFN-γ) +874 A>T (rs2430561) gene polymorphism has been evaluated in different ethnicities with pulmonary tuberculosis (PTB) infection, and inconsistent results have been reported. In this study, a meta-analysis was performed to determine the precise association between IFN-γ +874 A>T gene polymorphism and PTB susceptibility.

MATERIAL AND METHODS

A total of 21 studies comprising 4281 confirmed PTB cases and 5186 healthy controls were included in this meta-analysis by searching the PubMed (Medline), EMBASE, and Google Scholar web-databases.

RESULTS

We observed reduced risk of PTB in allelic contrast (T vs. A: p = 0.001; OR = 0.818, 95% CI: 0.723-0.926), homozygous (TT vs. AA: p = 0.017; OR = 0.715, 95% CI: 0.543-0.941), heterozygous (AT vs. AA: p = 0.002; OR = 0.782, 95% CI: 0.667-0.917), dominant (TT+AT vs. AA: p = 0.002; OR = 0.768, 95% CI: 0.652-0.906), and recessive (TT vs. AA+AT: p = 0.042; OR = 0.802, 95% CI: 0.649-0.992) genetic models. In ethnicity-wise subgroup analysis, reduced risk of PTB was found in the Caucasian population. However, we did not find an association with any of the genetic models in the Asian population.

CONCLUSIONS

In conclusion, the IFN-γ +874 A>T gene polymorphism is significantly associated with reduced risk of PTB, showing a protective effect in the overall and in the Caucasian population. However, this polymorphism is not associated with PTB risk in the Asian population.

Link between MnSOD Ala16Val (rs4880) polymorphism and asthma risk is insignificant from sequential meta-analysis

The mitochondrial manganese superoxide dismutase (MnSOD) enzyme protects lungs against oxidative stress by neutralizing the free radical superoxide produced in the respiratory function. This has relevance to asthma. Therefore, it is of interest to describe the potential effect of MnSOD Ala16Val genetic polymorphism to asthma risk. Known data in this context is inconclusive in nature. The possible link between MnSOD Ala16Val polymorphism and asthma is explored using sequence meta-analysis. Data from the pooled analysis of MnSOD Ala16Val polymorphism using five genetic models i.e., allelic (Val vs. Ala: p=0.846; OR=1.033, 95% CI=0.742 to 1.440) is discussed. Homozygous (Val Val vs. Ala Ala: p=0.517; OR=1.307, 95% CI=0.582 to 2.932) and heterozygous (Val Ala vs. Ala Ala: p=0.307; OR=1.138, 95% CI=0.888 to 1.459) data using the described models are documented. Data from the dominant model (Val Val + Val Ala vs. Ala Ala: p=0.301; OR=1.289, 95% CI=0.797 to 2.085) and the recessive model (Val Val vs. Val Ala + Ala Ala: p=0.761; OR=0.924, 95% CI=0.555 to 1.538) analyses for several ethnic subgroups in this context is reported.

Potency of inhibitors depends upon the accessibility of their aromatic rings within the hydrophobic specificity pocket: a novel avenue for future aldose reductase inhibitor design

Communicated by Ramaswamy H. Sarma.

Genistein Modulates Signaling Pathways and Targets Several Epigenetic Markers in HeLa Cells

BACKGROUND

Several epigenetic changes are responsible for transcriptional alterations of signaling pathways and tumour suppressor genes (TSGs) contributing to carcinogenesis. This study was aimed to examine the effect of the phytochemical, genistein on various molecular targets in HeLa cells.

METHODS

Quantitative PCR was used to analyze the expression of various molecular targets. Biochemical assays were employed to study the epigenetic enzymes. To correlate the transcriptional status of the selected TSGs and epigenetic modulation, their promoter 5'CpG methylation levels were evaluated by quantitative methylation array followed by methylation specific restriction digestion.

RESULTS

The expression of several genes involved in the cell cycle regulation, migration, inflammation, phosphatidylinositol 3-kinase (PI3K) and mitogen activated kinase-like protein (MAPK) pathway were found to be modulated including CCNB1, TWIST1, MMP14, TERT, AKT1, PTPRR, FOS and IL1A. Genistein modulated the expression of DNA methyltransferases (DNMTs), histone deacetylases (HDACs), histone methyltransferases (HMTs), demethylases, and histone phosphorylases. Furthermore, genistein decreased the activity of DNMTs, HDACs, and HMTs and reduced global DNA methylation levels. Promoter methylation of several TSGs, including FHIT, RUNX3, CDH1, PTEN, and SOC51, was lowered with corresponding transcriptional increase. Network analysis indicated similar effect of genistein.

CONCLUSION

This study presents a comprehensive mechanism of action of genistein showcasing effective epigenetic modulation and widespread transcriptional changes resulting in restoration of tumour suppressor gene expression. This study corroborates the development of genistein as a candidate for anti-cancer therapy.

AA genotype of cyclin D1 G870A polymorphism increases breast cancer risk: Findings of a case-control study and meta-analysis

BACKGROUND

Cyclin D1 (CCND1) polymorphisms, a regulator of the cell cycle progress from G1 to the S phase, may lead to uncontrolled cell proliferation and lack of apoptosis. G870A, a common single-nucleotide polymorphism in CCND1 influences breast cancer risk. However, the association between G870A polymorphism and breast cancer risk is ambiguous so far.

MATERIALS AND METHODS

In this case-control study, we analyzed the role of G870A polymorphism with breast cancer risk in Indian women. A meta-analysis of 18 studies was also performed to elucidate this association by increasing statistical power.

RESULTS

In our case-control study, significant risk association of the CCND1 G870A AA genotype with breast cancer in total cohort (odds ratio [OR], 2.98; 95% confidence interval [CI], 1.64-5.42; P value, 4.96e-04) and premenopausal women (OR, 3.31; 95% CI, 1.54-7.08; P value, .003) was found. The results of the meta-analysis showed that AA genotype of the CCND1 G870A polymorphism significantly increases breast cancer risk in total pooled data (AA vs GG+GA: OR = 1.20; 95% CI = 1.03 to 1.39; P value, 0.016*) and Caucasian (AA vs GG+GA: OR = 1.22; 95% CI = 0.99 to 1.51; P value, .056*) but not in Asian population. Further, a significant protective association with breast cancer was also found in the GA vs AA comparison model in pooled data (OR = 0.73; 95% CI = 0.58 to 0.92; P value, .007*) as well as in Caucasian subgroup (OR = 0.62; 95% CI = 0.49 to 0.94; P value, .022*).

CONCLUSION

CCND1 G870A AA genotype was found associated with breast cancer risk. Future association studies considering the environmental impact on gene expression are required to validate/explore this association.

A trial sequential meta-analysis of IFN-γ +874 A>T (rs2430561) gene polymorphism and extrapulmonary tuberculosis risk

Interferon-γ (IFN-γ) plays a crucial role in immunological responses against Mycobacterium tuberculosis (M.tb) infection. The polymorphism at +874 A > T (rs2430561) influences the levels of IFN-γ, which may further influence the susceptibility to extrapulmonary tuberculosis (EPTB). This polymorphism has been investigated with respect to EPTB occurrence in different populations and provided contradictory and conflicting results. This study was performed to meta-statistically analyze the data and draw a more accurate conclusion regarding the association of IFN-γ +874 A > T gene polymorphism and EPTB susceptibility. A quantitative synthesis was executed for the pertinent studies retrieved from online web-databases viz. Google Scholar, PubMed/Medline and EMBASE. The pooled odds ratios (ORs) and confidence intervals (95% CIs) were estimated for all the genetic models by meta-analysis. A total of eight studies were retrieved which included 762 confirmed EPTB cases and 1341 controls. The meta-analysis results revealed reduced association of EPTB in allelic contrast (T vs. A: p = 0.001; OR = 0.668, 95% CI = 0.524 to 0.850), homozygous (TT vs. AA: p = 0.017; OR = 0.450, 95% CI = 0.234 to 0.868), heterozygous (AT vs. AA: p = 0.004; OR = 0.574, 95% CI = 0.395 to 0.835), dominant (TT + AT vs. AA: p = 0.003; OR = 0.536, 95% CI = 0.354 to 0.810) and recessive (TT vs. AA + AT: p = 0.039; OR = 0.662, 95% CI = 0.448 to 0.980) genetic models. Furthermore, re-sampling statistics also revealed reduced risk of EPTB in overall population and Asian subgroup. This meta-analysis concluded that IFN-γ +874 A > T gene polymorphism is meaningfully related with the reduced EPTB risk in overall and Asian population, and further necessitates larger studies to be conducted on this topic in other races.

Association of MBL2 gene polymorphisms with pulmonary tuberculosis susceptibility: trial sequence meta-analysis as evidence

Background

Mannose-binding lectin (MBL) or mannose-binding protein (MBP), encoded by MBL2 gene and secreted by the liver, activates complement system through lectin pathway in innate immunity against the host’s infection. Conflictingly, a number of MBL2 variants, rs1800450 (A>B), rs1800451 (A>C), rs5030737 (A>D), rs7096206 (Y>X), rs11003125 (H>L), and rs7095891 (P>Q) allele, have been found to be associated with compromised serum levels and pulmonary tuberculosis (PTB) susceptibility. The present meta-analysis study was performed to evaluate the potential association of these MBL2 gene variants with PTB susceptibility.

Materials and methods

A quantitative synthesis was performed on PubMed (Medline), EMBASE, and Google Scholar web database searches. A meta-analysis was performed to calculate the pooled odds ratios and 95% CIs for all the genetic models.

Results

A total of 14 eligible studies were included to analyze their pooled data for associations between alleles, genotypes, and minor allele carriers. The statistical analysis revealed the significant reduced PTB risk with homozygous variant genotype of rs1800451 polymorphism (CC vs AA: P=0.043; OR =0.828, 95% CI =0.689–0.994). Contrary to this, the variant allele of rs5030737 polymorphism showed association with increased PTB risk (D vs A: P=0.026; OR =1.563, 95% CI =1.054–2.317). However, the other genetic models of rs1800450 (A>B), rs7096206 (Y>X), and rs11003125 (H>L) MBL2 gene polymorphisms did not divulge any association with PTB susceptibility.

Conclusion

The current meta-analysis concludes that rs1800451 (A>C) and rs5030737 (A>D) polymorphisms of MBL2 gene play a significant role in PTB susceptibility. Further, well-designed epidemiological studies with larger sample size including consideration of environmental factors are warranted for the future.

Angiotensin-Converting Enzyme Gene I/D Polymorphism Is Associated With Systemic Lupus Erythematosus Susceptibility: An Updated Meta-Analysis and Trial Sequential Analysis

Angiotensin-converting enzyme (ACE) gene is indispensable for endothelial control and vascular tone regulatory systems, usually affected in Systemic Lupus Erythematosus (SLE). ACE insertion/deletion (I/D) polymorphism may influence the progress of SLE. Earlier studies have investigated this association without any consistency in results. We performed this meta-analysis to evaluate the precise association between ACE I/D polymorphism and SLE susceptibility. The relevant studies were searched until December, 2017 using Medline (PubMed), Google-Scholar and EMBASE search engines. Twenty-five published studies involving 3,308 cases and 4,235 controls were included in this meta-analysis. Statistically significant increased risk was found for allelic (D vs. I: p = 0.007; OR = 1.202, 95% CI = 1.052–1.374), homozygous (DD vs. II: p = 0.025; OR = 1.347, 95% CI = 1.038–1.748), dominant (DD+ID vs. II: p = 0.002; OR = 1.195, 95% CI = 1.070–1.334), and recessive (DD vs. ID+II: p = 0.023; OR = 1.338, 95% CI = 1.042–1.718) genetic models. Subgroup analysis stratified by Asian ethnicity revealed significant risk of SLE in allelic (D vs. I: p = 0.045; OR = 1.238, 95% CI = 1.005–1.525) and marginal risk in dominant (DD+ID vs. II: p = 0.056; OR = 1.192, 95% CI = 0.995–1.428) models; whereas, no association was observed for Caucasian and African population. Publication bias was absent. In conclusion, ACE I/D polymorphism has significant role in overall SLE risk and it can be exploited as a prognostic marker for early SLE predisposition.

Glutathione S-Transferase P1 313 (A > G) Ile105Val Polymorphism Contributes to Cancer Susceptibility in Indian Population: A Meta-analysis of 39 Case-Control Studies

GSTP1 involved in the metabolism of carcinogens and toxins, reduces damage of DNA and act as a suppressor of carcinogenesis. Many studies have reported that 313 A > G polymorphism is associated with different cancer in Indian population, but the results remain conflicting rather than conclusive. Therefore, we have performed meta-analysis to clarify the more precise association of GSPT1 313 A > G polymorphism with cancer risk in Indian population. We retrieved all relevant published literature from PubMed (Medline) and Google scholar web database and included those study only based on the established inclusion criteria. Pooled ORs and 95% CIs were used to appraise the strength of association. Publication bias and sensitivity analysis was also evaluated. A total of 6581 confirmed cancer cases and 8218 controls were included from eligible thirty nine case-controls studies. Pooled analysis suggested that the variant genotypes significantly increased the risk of cancer in allele (G vs. A: OR 1.266, 95% CI 1.129-1.418, p = 0.001), heterozygous (AG vs. AA: OR 1.191, 95% CI 1.047-1.355, p = 0.008), homozygous (GG vs. AA: OR 1.811, 95% CI 1.428-2.297, p = 0.001), dominant (GG + AG vs. AA: OR 1.276, 95% CI 1.110-1.466, p = 0.001) and recessive (GG vs. AG + AA: OR 1.638, 95% CI 1.340-2.002, p = 0.001) genetic models. The stability of these observations was confirmed by a sensitivity analysis. Begger's funnel plot and Egger's test did not reveal any publication bias. This meta-analysis suggests that the GSTP1 313 A > G polymorphism may contribute to genetic susceptibility to cancer in Indian population. However, larger studies and randomized clinical trial will be required to elucidate the biological and molecular mechanism of GSTP1 gene in cancer.

Niacin deficiency modulates genes involved in cancer: Are smokers at higher risk?

The role of niacin's metabolite, nicotinamide adenine dinucleotide (NAD), in DNA repair via base-excision repair pathway is well documented. We evaluated if niacin deficiency results in genetic instability in normal human fetal lung fibroblasts (MRC-5), and further, does it leads to enhanced accumulation of cigarette smoke-induced genetic damage? MRC-5 cells were grown discretely in niacin-proficient/deficient media, and exposed to nicotine-derived nitrosamine ketone (NNK, a cigarette smoke carcinogen). Niacin deficiency abated the NAD polymerization, augmented the spontaneous induction of micronuclei (MN) and chromosomal aberrations (CA) and raised the expression of 10 genes and suppressed 12 genes involved in different biological functions. NNK exposure resulted in genetic damage as measured by the induction of MN and CA in cells grown in niacin-proficient medium, but the damage became practically marked when niacin-deficient cells were exposed to NNK. NNK exposure raised the expression of 16 genes and suppressed the expression of 56 genes in cells grown in niacin-proficient medium. NNK exposure to niacin-deficient cells raised the expression of eight genes including genes crucial in promoting cancer such as FGFR3 and DUSP1 and suppressed the expression of 33 genes, including genes crucial in preventing the onset and progression of cancer like RASSF2, JUP, and IL24, in comparison with the cells grown in niacin-proficient medium. Overall, niacin deficiency interferes with the DNA damage repair process induced by chemical carcinogens like NNK, and niacin-deficient population are at the higher risk of genetic instability caused by cigarette smoke carcinogen NNK.

In silico CD4+, CD8+ & humoral immunity associated antigenic epitope prediction and HLA distribution analysis of HTLV-I

PURPOSE

The linkage of human T-cell leukemia virus type 1 (HTLV-1) to fatal diseases is a well known fact for many years. However, there has been no significant progress in the field of the treatment that can lead to the development of a successful vaccine. Furthermore, there are no means of assessing the risk of disease and its prognosis in the infected people.

METHODS

The current study has taken the cognizance of the importance of host's immune response in reducing the risk of infectious diseases to carry out immunoinformatics driven epitope screening strategy of vaccine candidates against HTLV-1. In this study, a genetic variability and HLA distribution analysis among the documented HTLV-1 genotypes I, II, III, IV, V & VI was performed to ensure the coverage of the vast majority of population, where vaccine would be employed. The meticulous screening of effective dominant immunogens was done with the help of ABCPred and Immune Epitope Database.

RESULTS

The results showed that the identified epitopes might be protective immunogens with high conservancy and potential of inducing both protective neutralizing antibodies and T-cell responses. The peptides "PSQLPPTAPPLLPHSNLDHI", "PCPNLVAYSSYHATY", and "YHATYSLYLF", were 100% conserved among different isolates from far and wide separated countries, suggesting negligible antigenic drift in HTLV-1.

CONCLUSIONS

Overall, the mentioned epitopes are soluble, non-toxic suitable candidates for the development of vaccine against HTLV-1 and warrant further investigation and experimental validation.

Impact of p53 arg72pro SNP on Breast Cancer Risk in North Indian Population

Background:

Genetic changes in p53 gene contribute to breast cancer susceptibility.

Objective and Methods:

A case-control study and a meta-analysis were performed to investigate the role of p53 codon72 SNP with breast cancer susceptibility in Indian women.

Results:

p53 heterozygous arginine variant was associated with decreased risk of breast cancer in total cohort. In meta-analysis, Allelic and GG vs. CC genetic comparison model were found to be associated with breast cancer risk. Moreover, recessive comparison model indicated a protective correlation with breast cancer occurrence.

Conclusion:

The findings of our case-control study and meta-analysis suggest a significant association between p53 Arg72Pro polymorphism and an increased risk of breast cancer in Indian population.

Developments in strategies for Quorum Sensing virulence factor inhibition to combat bacterial drug resistance

Quorum sensing (QS) is a complex bacterial intercellular communication system. It is mediated by molecules called auto-inducers (AIs) and allows coordinated responses to a variety of environmental signals by inducing alterations in gene expression. Communication through QS can tremendously stimulate the pathogenicity and virulence via multiple mechanisms in pathogenic bacteria. The present review explores the major types of multitudinous QS systems known in Gram-positive and Gram-negative bacteria and their roles in bacterial pathogenesis and drug resistance. Because bacterial resistance to antibiotics is increasingly becoming a significant clinical challenge to human health; alternate strategies to combat drug resistance are warranted. Targeting bacterial pathogenicity by interruptions in QS using natural QS inhibitors and synthetic quorum-quenching analogs are being increasingly considered for development of next generation antimicrobials. The review highlights the recent advancements in discovery of promising new QS modulators and their efficiency in controlling infections caused by multidrug-resistant bacterial pathogens.

Inhibition of C298S mutant of human aldose reductase for antidiabetic applications: Evidence from in silico elementary mode analysis of biological network model

Human aldose reductase (hAR) is the key enzyme in sorbitol pathway of glucose utilization and is implicated in the etiology of secondary complications of diabetes, such as, cardiovascular complications, neuropathy, nephropathy, retinopathy, and cataract genesis. It reduces glucose to sorbitol in the presence of NADPH and the major cause of diabetes complications could be the change in the osmotic pressure due to the accumulation of sorbitol. An activated form of hAR (activated hAR or ahAR) poses a potential obstacle in the development of diabetes drugs as hAR-inhibitors are ineffective against ahAR. The therapeutic efficacy of such drugs is compromised when a large fraction of the enzyme (hAR) undergoes conversion to the activated ahAR form as has been observed in the diabetic tissues. In the present study, attempts have been made to employ systems biology strategies to identify the elementary nodes of human polyol metabolic pathway, responsible for normal metabolic states, followed by the identification of natural potent inhibitors of the activated form of hAR represented by the mutant C298S for possible antidiabetic applications. Quantum Mechanical Molecular Mechanical docking strategy was used to determine the probable inhibitors of ahAR. Rosmarinic acid was found as the most potent natural ahAR inhibitor and warrants for experimental validation in the near future.

Meta-analysis reveals no correlation of caveolin-1 G14713A (G>A) gene polymorphism with increased cancer risk in Taiwanese population

OBJECTIVES

The role of caveolin-1 (CAV1)(G>A, rs3807987) polymorphism is still dubious in cancer causation in Taiwanese population. The present study is an effort to assess the above relation for precise conclusion.

METHODS

EMBASE and PubMed (MEDLINE) databases were explored for the pertinent case-control studies reporting the connection of CAV1 G14713A polymorphism to the vulnerability to cancer. A cumulative analysis using meta-analytic approach was accomplished and pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were estimated for all the polymorphs.

RESULTS

Overall, 2549 subjects and 3161 controls were analyzed from six selected studies. Our study showed no confirmation of noteworthy risk between CAV1 G14713A polymorphism and susceptibility to cancer in any of the polymorph, for instance, allele (A vs. G: P = 0.165; OR = 1.252, 95% CI = 0.911-1.721), homozygous (AA vs. GG: P = 0.252; OR = 1.328, 95% CI = 0.817-2.157), heterozygous (AG vs. GG: P = 0.091; OR = 1.356, 95% CI = 0.952-1.930), dominant (AA vs. GG + AG: P = 0.345; OR = 1.191, 95% CI = 0.829-1.709), and recessive (AA + AG vs. GG: P = 0.125; OR = 1.344, 95% CI = 0.921-1.961).

CONCLUSIONS

We conclude that CAV1 G14713A polymorphism does not contribute as an independent predisposing risk factor for developing cancer in Taiwanese population.

Impact of LMP7 (rs2071543) gene polymorphism in increasing cancer risk: evidence from a meta-analysis and trial sequential analysis

Genetic variant LMP7 (low molecular weight polypeptide 7) –145 C > A may influence the function of immune surveillance of an individual and lead to cancer development. Various studies have investigated the relevance of LMP7 –145 C > A gene polymorphism with cancer risk; but, their results are conflicting and inconsistent. To obtain a comprehensive conclusion, a meta-analysis was performed by including eight eligible published studies retrieved from PubMed (Medline), EMBASE and Google Scholar web search until December 2016. Individuals with AA genotype (AA vs CC: p = 0.001; OR = 2.602, 95% CI = 1.780 to 3.803) of LMP7 -145 C > A were found to have 2 folds higher risk of cancer than those with CC genotype. The recessive genetic model (AA vs AC + CC) also indicated that individuals with AA genotype have 2 folds higher cancer risk than AC and CC genotypes (p = 0.001; OR = 2.216, 95% CI = 1.525 to 3.221). Also, significant increased cancer risk was observed in Asians but not in Caucasians. No publication bias was observed during the analysis. Trial sequential analysis also strengthened our current findings. These results suggest that genetic variant LMP7–145 C > A has significant role in increasing cancer risk in overall and Asian population, and could be useful as a prognostic marker for early cancer predisposition.

MIF -173 G > C (rs755622) Gene Polymorphism Modulates Tuberculosis Risk: Evidence from a Meta-analysis and Trial Sequential Analysis

The macrophage migration inhibitory factor (MIF) is a cytokine that plays an important role in inhibiting the growth of pathogenic Mycobacterium tuberculosis (M.tb) and regulates immune responses against M.tb pathogen. MIF -173 G > C gene polymorphism may affect immunity in an individual and leads to susceptibility to tuberculosis (TB). A large number of studies have investigated the relevance of this polymorphism with TB risk, but their results were inconclusive. To obtain a precise conclusion, a meta-analysis was performed by retrieving six eligible studies from Google Scholar, PubMed (Medline), and EMBASE online databases. Overall combined analysis suggested increased TB risk between MIF -173 G > C polymorphism and overall risk in four genetic models, i.e., allelic (C vs. G: p = 0.001; OR = 1.517, 95% CI = 1.312 to 1.753), homozygous (CC vs. GG: p = 0.026; OR = 1.874, 95% CI = 1.079 to 3.257), heterozygous (GC vs. GG: p = 0.001; OR = 1.542, 95% CI = 1.273 to 1.868) and dominant model (CC + GC vs. GG: p = 0.001; OR = 1.631, 95% CI = 1.362 to 1.955). Similarly, increased TB risk was observed in subgroup analysis of Asian ethnicity. No publication bias was observed. These results suggested that MIF -173 G > C variant is a significant risk factor for TB in overall and in Asian populations, and can be used as prognostic marker for TB susceptibility.

Vitamin D Receptor ApaI (rs7975232) Polymorphism Confers Decreased Risk of Pulmonary Tuberculosis in Overall and African Population, but not in Asians: Evidence from a Meta-analysis

GOALS

The involvement of the VDR ApaI gene polymorphism in the development of pulmonary tuberculosis (PTB) has been reported by numerous published studies and yielded inconsistent results. The present meta-analysis evaluated the association of VDR ApaI polymorphism and risk of PTB occurrence.

PROCEDURES

PubMed (Medline), EMBASE and Google Scholar web-databases were searched and a meta-analysis was performed by calculating the pooled odds ratios (ORs) and 95% confidence intervals (95% CIs).

RESULTS

This meta-analysis included a total of 14 eligible studies comprising of 1958 confirmed PTB cases and 2938 controls. We observed decreased risk of PTB in allelic (a vs. A: p=0.003; OR=0.873, 95% CI=0.798 to 0.955), homozygous (aa vs. AA: p=0.006; OR=0.761, 95% CI=0.626 to 0.924), dominant (aa+Aa vs. AA: p=0.039; OR=0.874, 95% CI=0.769 to 0.993) and recessive (aa vs. AA+Aa: p=0.025; OR=0.819, 95% CI=0.688 to 0.975) genetic models. During subgroup analysis, allele (a vs. A: p=0.005; OR=0.846, 95% CI=0.753 to 0.951), homozygous (aa vs. AA: p=0.002; OR=0.662, 95% CI=0.513 to 0.854) and recessive genetic models (aa vs. AA+Aa: p=0.003; OR=0.709, 95% CI=0.566 to 0.889) demonstrated decreased PTB risk in African population. However, no significant association was observed in Asian population.

CONCLUSION

In conclusion, VDR ApaI polymorphism is significantly associated with decreased risk of PTB for in overall and African population, but not in Asians.

Fullerenes May Cause eIF Mediated Perturbation in Translational Machinery: Evidence from in-silico Analysis

GOALS

Fullerenes have tremendous potential for human biological studies which may further lead to their therapeutic applications. Hence, it has become necessary to explore the possibility of their interference with various important cellular processes. The current study was designed to explore how the presence of fullerenes can affect the binding of DNA with different enzymes and factors involved in transcription and translation process.

METHODS

Various bioinformatics approaches and software programs were used to study the effect of fullerenes on the binding pattern of DNA with different enzymes and factors involved in transcription and translation process.

RESULTS

Fullerenes of different molecular weights were interacted with various transcription enzymes and factors and no significant effects were observed on transcription machinery. On the contrary, the factors involved in translation process when docked with their functional partners in the presence/absence of fullerenes display reduced activity of eIF2, eIF4A, eIF4H, eIF4G, eIF4B, eIF5B, and eEF1 with fullerenes of different molecular weights.

CONCLUSIONS

We conclude that these molecules mostly control the translation of a number of genes. The reduced expression of these factors may cause a number of clinical pathological conditions including neurodegenerative disorders like Alzheimer's, Parkinson's, and Huntington's diseases.

Pembrolizumab's non-cross resistance mechanism of action successfully overthrown ipilimumab

The incidences of melanomas are increasing by leaps and bounds across the globe despite early detection and intervention. The numbers of patients dying from metastatic melanoma have been continually increased over the past thirty years. It has been considered as one of the most therapy-resistant malignancies due to the cross-resistant mechanism developed by the metastatic cells. With time, many new therapies came and they failed miserably. Ipilimumab, a monoclonal antibody that works to activate the immune system by targeting CTLA-4 proved to be a boon for advance melanoma very recently. But it could not stand firmly against the resistant metastatic skin cancer cells. Now, the new skin cancer drug named pembrolizumab proved as a new miraculous molecule. It's a humanized monoclonal antibody that blocks a biological pathway called programmed cell death-1 (PD-1), which melanoma cells activate to suppress the immune system. This antibody has surpassed ipilimumab at all the stages of clinical trials because of its non-cross resistant mechanism to malignant cells. The present review critically analyses the reasons of efficacy success of pembrolizumab over ipilizumab shown at various stages of clinical trials.

Proteome mining for the identification and in-silico characterization of putative drug targets of multi-drug resistant Clostridium difficile strain 630

Clostridium difficile is an enteric pathogen that causes approximately 20% to 30% of antibiotic-associated diarrhea. In recent years, there has been a substantial rise in the rate of C. difficile infections as well as the emergence of virulent and antibiotic resistant C. difficile strains. So, there is an urgent need for the identification of therapeutic potential targets and development of new drugs for the treatment and prevention of C. difficile infections. In the current study, we used a hybrid approach by combining sequence similarity-based approach and protein-protein interaction network topology-based approach to identify and characterize the potential drug targets of C. difficile. A total of 155 putative drug targets of C. difficile were identified and the metabolic pathway analysis of these putative drug targets using DAVID revealed that 46 of them are involved in 9 metabolic pathways. In-silico characterization of these proteins identified seven proteins involved in pathogen-specific peptidoglycan biosynthesis pathway. Three promising targets viz. homoserine dehydrogenase, aspartate-semialdehyde dehydrogenase and aspartokinase etc. were found to be involved in multiple enzymatic pathways of the pathogen. These 3 drug targets are of particular interest as they can be used for developing effective drugs against multi-drug resistant C. difficile strain 630 in the near future.

Differential pharmacology and clinical utility of sonidegib in advanced basal cell carcinoma

Patients suffering from advanced basal cell carcinoma (BCC) have very limited treatment options. Sonidegib selectively inhibits the growth of Hedgehog pathway-dependent tumors and can treat locally advanced BCC patients who are not candidates for surgery or radiation therapy. The BOLT clinical trials were conducted to evaluate the efficacy/potency of sonidegib in the treatment of advanced BCC or metastatic BCC. The patients were randomized in 1:2 ratios to receive 200 or 800 mg oral sonidegib daily, stratified by disease, histological subtype and geographical region. The primary efficacy analyses showed that 18 patients in the 200 mg group and 35 patients in the 800 mg group show an objective response (Central Review Committee) that corresponds to 43% (95% confidence interval [CI]: 28–59) and 38% (95% CI: 28–48) in their respective categories. Disease control was found in 93% (39 patients) and 80% (74 patients) of the patients administered 200 and 800 mg sonidegib, respectively. The adverse events were assessed by the Central Review Committee as well as the investigator review team as per the guidelines of National Cancer Institute Common Terminology Criteria for Adverse Events version 4.03. The most frequently found adverse events reported in BOLT trials were muscle spasms, alopecia, dysgeusia (taste disturbance), nausea, elevated blood creatine kinase and fatigue. Comparatively, the patients administered 200 mg sonidegib showed fewer adverse events than those in the 800 mg sonidegib category. Thus, the benefit of using the 200 mg dose of sonidegib outweighs the associated risks and it can be inferred that it would be judicious to choose doses of lesser strength.

A Meta-analysis of MBL2 Polymorphisms and Tuberculosis Risk

MBL2 gene encodes mannose-binding lectin, is a member of innate immune system. Earlier studies revealed that MBL2 gene variants, rs1800451, rs1800450, rs5030737, rs7096206, rs11003125 and rs7095891 are associated with impaired serum level and susceptibility to TB, but their results are inconsistent. A meta-analysis was performed by including 22 studies (7095 TB-patients and 7662 controls) and data were analyzed with respect to associations between alleles, genotypes and minor allele carriers to evaluate the potential association between MBL2 polymorphisms and TB risk. Statistically significant results were found only for the homozygous variant genotype (CC vs. AA: p = 0.045; OR = 0.834, 95% CI = 0.699 to 0.996) of rs1800451 and showed reduced risk of TB in overall population. However, other genetic models of rs1800450, rs5030737, rs7096206, rs11003125, rs7095891 and combined rs1800450, rs1800451, rs5030737 polymorphisms of MBL2 gene did not reveal any association with TB risk. Stratified analysis by ethnicity showed decreased risk of TB in African population for rs1800450 and rs1800451. Whereas, no association was observed between other MBL2 polymorphisms and TB risk in all the evaluated ethnic populations. In conclusion, MBL2 rs1800450 and rs1800451 polymorphisms play a protective role in TB infection and reinforce their critical significance as a potential genetic marker for TB resistance.

Artificial Intelligence vs. Statistical Modeling and Optimization of Continuous Bead Milling Process for Bacterial Cell Lysis

For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery. RSM predicted an optimum of feed rate of 310.73 mL/h, bead loading of 79.9% (v/v), cell loading OD600nm of 74, and run time of 29.9 min with a recovery of ~3.2 g/L. ANN-GA predicted a maximum COD recovery of ~3.5 g/L at an optimum feed rate (mL/h): 258.08, bead loading (%, v/v): 80%, cell loading (OD600nm): 73.99, and run time of 32 min. An overall 3.7-fold increase in productivity is obtained when compared to a batch process. Optimization and comparison of statistical vs. artificial intelligence techniques in continuous bead milling process has been attempted for the very first time in our study. We were able to successfully represent the complex non-linear multivariable dependence of enzyme recovery on bead milling parameters. The quadratic second order response functions are not flexible enough to represent such complex non-linear dependence. ANN being a summation function of multiple layers are capable to represent complex non-linear dependence of variables in this case; enzyme recovery as a function of bead milling parameters. Since GA can even optimize discontinuous functions present study cites a perfect example of using machine learning (ANN) in combination with evolutionary optimization (GA) for representing undefined biological functions which is the case for common industrial processes involving biological moieties.

P2X71513 A>C Polymorphism Confers Increased Risk of Extrapulmonary Tuberculosis: A Meta-analysis of Case-Control Studies

The association of A1513C (rs3751143) polymorphism of P2X7 gene with the risk of extrapulmonary tuberculosis (EPTB) has been extensively analyzed, but no consensus has been achieved. In this study, a meta-analysis was done to assess this precise association. Online web databases, like PubMed (MEDLINE) and EMBASE were searched for pertinent reports showing association of P2X7 A1513C polymorphism with EPTB risk. To assess the strength of this association, we calculated pooled odds ratios (ORs) and 95% confidence intervals (95% CIs). A total of eight reports involving 2237controls and 594 EPTB cases were included in this study. Four genetic models, viz. allele (C vs. A: p=0.011; OR= 1.677, 95% CI = 1.125–2.501), homozygous (CC vs. AA: p = 0.053; OR= 2.362, 95% CI = 0.991–5.632), heterozygous (AC vs. AA: p = 0.003; OR= 1.775, 95% CI = 1.209–2.607) and dominant (CC + AC vs. AA: p = 0.005; OR= 1.890, 95% CI = 1.207–2.962) showed significant associations compared with wild type genotypes. Subgroup analysis stratified by ethnicity was also performed and the results suggested that homozygous and heterozygous genotypes were associated significantly with increased susceptibility of EPTB in Asian population. Similarly, heterozygous and dominant models showed increased EPTB risk in Caucasian population. The present meta-analysis suggests that P2X7 A1513C polymorphism may be an important risk factor for EPTB. Also, our sub-group analysis indicates that P2X7 A1513C polymorphism confers increased EPTB risk among Asians and Caucasians. However, future larger studies are needed to provide more precise conclusion and endorse the present results.

Therapeutic potential and critical analysis of trastuzumab and bevacizumab in combination with different chemotherapeutic agents against metastatic breast/colorectal cancer affecting various endpoints

Researchers are working day and night across the globe to eradicate or at least lessen the menace of cancer faced by the mankind. The two very frequently occurring cancers faced by the human beings are metastatic breast cancer and metastatic colorectal cancer. The various chemotherapeutic agents like anthracycline, cyclophosphamide, paclitaxel, irinotecan, fluorouracil and leucovorin etc., have been used impressively for long. But the obstinate character of metastatic breast cancer and metastatic colorectal cancer needs more to tackle the threat. So, the scientists found the use of monoclonal antibodies trastuzumab (Herceptin(®)) and bevacizumab (Avastin(®)) for the same. The current study critically investigates the therapeutic potential of trastuzumab and bevacizumab in combination with various chemotherapeutic agents against metastatic breast cancer and metastatic colorectal cancer. To the best of our knowledge, this is the very first critical analysis showing percent wise increase in various positive endpoints like median time to disease progression, median survival, and progression free survival etc. for the treatment of metastatic breast/colorectal cancer using trastuzumab and bevacizumab in combination with different chemotherapeutic agents and provides the rational for the success and failure of the selected monoclonal antibodies.

Modeling and optimization of a continuous bead milling process for bacterial cell lysis using response surface methodology

Schematic representation of the modeling and optimization of continuous bead milling process for efficient bacterial cell lysis.

G894T and 4a/b polymorphisms of NOS3 gene are not associated with cancer risk: a meta-analysis

Endothelial nitric oxide synthase (eNOS or NOS3) produces nitric oxide and genetic polymorphisms of NOS3 gene play significant roles in various processes of carcinogenesis. The results from published studies on the association between NOS3 G894T and NOS3 intron 4 (4a/b) polymorphisms and cancer risk are conflicting and inconclusive. However, i n order to assess this relationship more precisely, a meta-analysis was performed with PubMed (Medline), EMBASE and Google web searches until February 2014 to select all published case- control and cohort studies. Genotype distribution data were collected to calculate the pooled odd ratios (ORs) and 95% confidence intervals (CIs) to evaluate the strength of association. A total of 10,546 cancer cases and 10,550 controls were included from twenty four case-control studies for the NOS3 G894T polymorphism. The results indicated no significant association with cancer risk as observed in allelic (T vs G: OR=1.024, 95%CI=0.954 to 1.099, p=0.508), homozygous (TT vs GG: OR=1.137, 95%CI=0.944 to 1.370, p=0.176), heterozygous (GT vs GG: OR=0.993, 95%CI=0.932 to 1.059, p=0.835), recessive (TT vs GG+GT: OR=1.100, 95%CI=0.936 to 1.293, p=0.249) and dominant (TT+GT vs GG: OR=1.012, 95%CI=0.927 to 1.105, p=0.789) genetic models. Similarly, a total of 3,449 cancer cases and 3,691 controls were recruited from fourteen case-control studies for NOS3 4a/b polymorphism. Pooled results indicated no significant association under allelic (A vs B: OR=0.981, 95%CI=0.725 to 1.329, p=0.902), homozygous (AA vs BB: OR=1.166, 95%CI=0.524 to 2.593, p=0.707), heterozygous (BA vs BB: OR=1.129, 95%CI=0.896 to 1.422, p=0.305), dominant (AA+BA vs BB: OR=1.046, 95%CI=0.779 to 1.405, p=0.763) and recessive (AA vs BB+BA: OR=1.196, 95%CI=0.587 to 2.439, p=0.622) genetic contrast models. This meta-analysis suggests that G894T and 4a/b polymorphisms of NOS3 gene are not associated with increased or decreased risk of overall cancer.

Matrix metalloproteinase-2 -1306 C>T gene polymorphism is associated with reduced risk of cancer: a meta-analysis

Matrix metalloproteinase-2 (MMP2) is an endopeptidase, mainly responsible for degradation of extracellular matrix components, which plays an important role in cancer disease. A single nucleotide polymorphism (SNP) at -1306 disrupts a Sp1-type promoter site. The results from the published studies on the association between MMP2 -1306 C>T polymorphism and cancer risk are contradictory and inconclusive. In the present study, a meta-analysis was therefore performed to evaluate the strength of any association between the MMP2 -1306 C>T polymorphism and risk of cancer. We searched all eligible studies published on association between MMP2 -1306 C>T polymorphism and cancer risk in PubMed (Medline), EMBASE and Google Scholar online web databases until December 2013. Genotype distribution data were collected to calculate the pooled odds ratios (ORs) and 95% confidence intervals (95%CIs) to examine the strength of the association. A total of 8,590 cancer cases and 9,601 controls were included from twenty nine eligible case control studies. Overall pooled analysis suggested significantly reduced risk associated with heterozygous genotype (CT vs CC: OR=0.758, 95%CI=0.637 to 0.902, p=0.002) and dominant model (TT+CT vs CC: OR=0.816, 95%CI=0.678 to 0.982, p=0.032) genetic models. However, allelic (T vs C: OR=0.882, 95%CI=0.738 to 1.055, p=0.169), homozygous (TT vs CC: OR=1.185, 95%CI=0.825 to 1.700, p=0.358) and recessive (TT vs CC+CT: OR=1.268, 95%CI=0.897 to 1.793, p=0.179) models did not show any risk. No evidence of publication bias was detected during the analysis. The results of present meta-analysis suggest that the MMP2 -1306 C>T polymorphism is significantly associated with reduced risk of cancer. However, further studies with consideration of different populations will be required to evaluate this relationship in more detail.

Genetic variants of chemokine CCL2 and chemokine receptor CCR2 genes and risk of prostate cancer

Chemokines and their receptors acts as mediators of migration of immune cells to the site of inflammation and deregulated inflammatory response is associated with increased risk of cancer. We performed a case-control study to analyze the frequencies of CCL2 (I/D, rs3917887), -2518 (A > G, rs1024611), and CCR2 (G > A, rs1799864) polymorphisms for prostate cancer (PCa) risk. In this hospital-based case-control study, histologically confirmed 195 PCa patients and 250 unrelated healthy controls of similar ethnicity were genotyped by PCR-RFLP. The result showed that heterozygous ID (odds ratio (OR) = 1.71; p = 0.010) carrier genotype of CCL2 gene were at increased risk for developing PCa. Variant allele D carriers (ID + DD) demonstrated a 1.67-fold increased risk (OR = 1.67; p = 0.010), suggesting a dominant effect model involved in PCa risk. Similarly, variant allele D of CCL2 gene also had a higher risk (OR = 1.53; p = 0.040) for developing PCa. High risk to PCa was also observed with respect to diplotypes, I-G (OR = 1.83; Bonferroni corrected p value (P c) = 0.004) and D-A (OR = 2.11; P c = 0.004) of CCL2 I/D and -2518 (A > G). In association of genotypes with clinic-pathological grade of tumor, homozygous DD (OR = 7.40; P c = 0.042) and variant allele carrier ID + DD (OR = 2.42; P c = 0.036) genotypes of CCL2 gene conferred risk in high Gleason grade tumor of PCa. We observed a significantly enhanced risk for PCa due to interaction between CCL2 I/D, -2518 (A > G), and CCR2 (G > A) genotypes. However, -2518 (A > G) and CCR2 V64I (G > A) gene polymorphisms were not significantly associated with PCa risk. Our results supported that CCL2 I/D gene variant contribute to the susceptibility and clinic-pathological characteristic of PCa and could be considered as an important risk factor for this malignancy in North Indian men.

Evaluating the Association between TaqI Variant of Vitamin D Receptor Gene and Susceptibility to Tuberculosis: A Meta-analysis

OBJECTIVES

Vitamin D has been shown to hamper the growth of Mycobacterium tuberculosis in macrophages. The actions of vitamin D are exerted through a vitamin D receptor (VDR). The genetic variant TaqI of VDR has been implicated in tuberculosis (TB) risk in several case-control studies. However, these studies have shown inconsistent results. Hence, a meta-analysis was conducted to investigate the potential relationship between VDR TaqI polymorphism and risk of developing TB.

MATERIALS AND METHODS

We performed a quantitative synthesis for published studies based upon the relationship between TaqI polymorphism and TB risk from PubMed (Medline) and Embase databases. The meta-analysis was performed and pooled odds ratios (ORs) and 95% confidence intervals (CIs) were estimated for all genetic models.

RESULTS

A total of 21 studies including 2,960 TB cases and 3,894 controls were included in this study. The pooled analysis demonstrated no evidence of association between VDR TaqI genotypes and risk of TB in any of the genetic models; variant (t vs T: P = 0.618; OR = 1.051, 95% CI = 0.864-1.278), homozygous (tt vs TT: P = 0.120; OR = 1.336, 95% CI = 0.927-1.924), heterozygous (Tt vs TT: P = 0.925; OR = 0.988, 95% CI = 0.774-1.262), dominant model (tt + Tt vs TT: P = 0.805; OR = 1.032, 95% CI = 0.805-1.322), and recessive model (tt vs TT + Tt: P = 0.180; OR = 1.229, 95% CI = 0.909-1.660). No publication bias was detected during the analysis.

CONCLUSIONS

Overall findings of this meta-analysis suggest that genetic polymorphism TaqI of VDR gene may not contribute to the risk of TB. However, future larger studies with group of populations are warranted to analyze this relationship.

High serum level of matrix metalloproteinase 9 and promoter polymorphism - 1562 C:T as a new risk factor for metabolic syndrome

The altered matrix metalloproteinases (MMPs) have been suggested in the pathophysiology of metabolic syndrome (MetS). Genetic variants in the promoter region of MMP1 and MMP9 genes may modulate an individual's susceptibility to MetS. The aim of this study was to determine the frequency of MMP1 -519 A:G and MMP9 -1562 C:T polymorphisms and the correlation with serum levels of MMP1 and MMP9 in MetS susceptibility. On the basis of anthropometric profile and laboratory investigations, 180 confirmed MetS patients and 190 unrelated healthy controls of similar ethnicity were genotyped for MMP1 -519 A:G and MMP9-1562 C:T polymorphisms by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods. In addition, serum levels of MMP1 and MMP9 were quantified by ELISA. We found that the serum level of MMP9 was significantly higher in MetS patients. Variant genotype TT of MMP9 -1562 demonstrated increased risk (odds ratio [OR]=3.70, p=0.015) of MetS. Similarly, variant allele T (OR=1.77, p=0.002) and combined genotype CT+TT (OR=1.81, p=0.057) also showed a significantly higher risk. The CT and TT genotypes of MMP9 -1562 polymorphism contributed to high serum levels of MMP9 in MetS patients. However, no such association was observed with the MMP1 serum level and -519 A:G polymorphism. Our results suggest that a higher serum level of MMP9 in the presence of MMP9 polymorphism -1562 C:T might be a risk factor for the development of MetS. The MMP9 enzyme activity might be a significant indicator in the screening of MetS patients.

No correlation between TIMP2 -418 G>C polymorphism and increased risk of cancer: evidence from a meta-analysis

Aim

Tissue inhibitor of metalloproteinase (TIMP2) is involved in the regulation of matrix metalloproteinase 2 (MMP2) and shown to implicate in cancer development and progression. The results from the published studies based on the association between TIMP2 -418 G>C polymorphism and cancer risk are inconsistent. In this meta-analysis, we aimed to evaluate the potential association between TIMP2 -418 G>C polymorphism and cancer risk.

Methodology

We searched PubMed (Medline) and EMBASE web databases to cover all studies based on relationship of TIMP2 -418 G>C polymorphism and risk of cancer until October 2013. The meta-analysis was performed for selected case-control studies and pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for all genetic models.

Results

A total of 2225 cancer cases and 2532 controls were included from ten eligible case-control studies. Results from overall pooled analysis suggested no evidence of significant risk between TIMP2 -418 G>C polymorphism and cancer risk in any of the genetic models, such as, allele (C vs. G: OR = 1.293, 95% CI = 0.882 to 1.894, p = 0.188), homozygous (CC vs. GG: OR = 0.940, 95% CI = 0.434 to 2.039, p = 0.876), heterozygous (GC vs. GG: OR = 1.397, 95% CI = 0.888 to 2.198, p = 0.148), dominant (CC+GC vs. GG: OR = 1.387, 95% CI = 0.880 to 2.187, p = 0.159) and recessive (CC vs. GG+GC: OR = 0.901, 95% CI = 0.442 to 1.838, p = 0.774) models. No evidence of publication bias was detected during the analysis.

Conclusions

The present meta-analysis suggests that the TIMP2 -418 G>C polymorphism may not be involved in predisposing risk factor for cancer in overall population. However, future larger studies with group of populations are needed to analyze the possible correlation.

Genetic variation of TBX21 gene increases risk of asthma and its severity in Indian children

T-box transcription factor protein (TBX21) is encoded by the TBX21 gene in human. It is crucial for naive T lymphocyte development, interferon-γ production, airway hyperresponsiveness and regulation of corticosteroid response in asthmatics. Polymorphisms rs4794067 and rs16947078 of TBX21 were found to be associated with acetylsalicylic acid-induced and allergic asthma, respectively. We examined whether sequence variants of TBX21 gene are associated with asthma and its severity in Indian population. In a hospital-based case-control study, 240 asthmatic children and 240 healthy controls were investigated for the association of TBX21 rs4794067 (C>T) and rs16947078 (G>A) polymorphisms with asthma and its severity using PCR-restriction fragment length polymorphism method. Heterozygous (CT) (odds ratio (OR)=2.33; P=0.001) and variant (TT) (OR=6.25; P=0.001) genotypes of rs4794067 were demonstrated significant risk of asthma. However, in asthma severity variant (TT) genotype revealed significant increase risk (intermittent: OR=5.9, P=0.001; mild: OR=8.0, P=0.001; moderate: OR=3.2, P=0.041; and severe: OR=43.6, P=0.001) in all subgroups. Furthermore, haplotypes TG (OR=2.83; P=0.001) and TA (OR=2.54; P=0.001) of TBX21 were associated with an increased risk of asthma. Conversely, rs16947078 G>A polymorphism was not associated with any asthma/asthma severity risk. These data suggest that TBX21 gene variation may modify individual's susceptibility to asthma and its severity in Indian population. However, further validation in large population-based studies is needed to confirm the finding.

Evaluating the association between p53 codon 72 Arg>pro polymorphism and risk of ovary cancer: a meta-analysis

Aim

Allelic polymorphism in codon 72 of the p53 tumor suppressor gene causes imbalance of p53 protein expression. Earlier studies have shown association between allelic polymorphism in codon 72 of the p53 gene with risk of ovary cancer (OC); however the results are inconclusive and conflicting. Therefore, we performed this meta-analysis to investigate the relation between p53 codon 72 Arg>Pro polymorphism and overall OC susceptibility.

Methods

We searched all eligible published studies based on the association between codon 72 of the p53 Arg>Pro polymorphism and risk of OC. Data were pooled together from individual studies and meta-analysis was performed. Pooled odds ratios (ORs) and 95% CI were calculated for allele contrast, homozygous, heterozygous, dominant and recessive genetic models.

Results

A total of twelve studies comprising of 993 OC cases and 1264 healthy controls were included in this meta-analysis. Overall, no significant association was detected for Pro allele carrier (Pro vs. Arg: p = 0.916; OR = 0.980, 95% CI = 0.677 to 1.419), homozygous (Pro/Pro vs. Arg/Arg: p = 0.419; OR = 0.731, 95% CI = 0.341 to 1.564), heterozygous (Arg/Pro vs. Arg/Arg: p = 0.248; OR = 1.237, 95% CI = 0.862 to 1.773), dominant (Pro/Pro+Arg/Pro vsArg/Arg: p = 0.699; OR = 1.089, 95% CI = 0.706 to 1.681), and recessive (Pro/Pro vs Arg/Arg+Arg/Pro: p = 0.329; OR = 0.754, 95% CI = 0.428 to 1.329) genetic models, respectively. Also, in the stratified analysis by ethnicity, no significant association of this polymorphism with risk of OC was found in the Caucasian population.

Conclusions

This meta-analysis suggested that codon 72 of the p53 Arg>Pro polymorphism may not significantly contribute in ovary cancer susceptibility. However, future large studies with gene-gene and gene-environment interactions are needed to validate these findings.