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Nateglinide is a meglitinide used for the treatment of type 2 diabetes mellitus. Individual studies demonstrated the association of CYP2C9, SLCO1B1, and MTNR1B variants with the safety and efficacy of nateglinide. The current study aimed to develop a pharmacogenomic algorithm to optimize nateglinide therapy.Multiple linear regression (MLR) and classification and regression tree (CART) were used to develop a pharmacogenomic algorithm for nateglinide dosing based on the published nateglinide pharmacokinetic data on the area under the curve data (AUC) and CThe MLR models of AUC and CCYP2C9, SLCO1B1, and MTNR1B genotyping help in optimizing nateglinide therapy based on this algorithm and ensuring safety and efficacy.

Mucopolysaccharidoses (MPSs) is a major group of the Lysosomal storage disorders (LSDs) with defective degradation of glycosaminoglycans (GAGs) due to deficiency of certain lysosomal enzymes. Enzyme replacement therapy (ERT) or bone marrow transplantation are the key therapeutic options available for MPS disorders. Early diagnosis and appropriate intervention improve the therapeutic efficacy. To establish a genotype-phenotype correlation of MPS disorders, a combination of bioinformatic tools including FATHMM, I-Mutant, PolyPhen-2, PATHER, PHD-SNP, SNP&GO, SIFT, PROVEAN, CUPSAT, SNAP2 are utilized. These in silico tools and urinary GAG levels helped in monitoring the response to enzyme replacement therapy (ERT). Enzyme activity was inversely associated with SNAP2 (r= -0.36, p = 0.04), Polyphen-2 (r = − 0.44, p = 0.009) and Evolutionary preservation time (r= -0.396, p = 0.02). This suggests that subjects having mutations with higher SNAP2 and Polyphen-2 score tend to have lower enzyme activity. ERT lead to 7–31% decrease in urinary GAG levels in seven MPS I patients. The determined pathogenicity scores using the bioinformatic tools are serving as prognostic markers indicating a response to therapy. Urinary GAG excretion is the primary end point to monitor the therapeutic efficacy.

Glioblastoma multiforme (GBM) is the most dangerous cancers of the brain. Despite availability of various treatment modalities, GBM chemotherapy remains obscure. Cancer metabolism is considered as one of the important factors for the tumor aggressiveness. Glucose is an important energy source for the cellular metabolism and was found to affect the GBM cancer aggressiveness, and chemo-resistance. Studies have found that GBM cancer is driven by epigenetic proteins. HDACs are important epigenetic proteins that regulate the gene expression by chromatin epigenetics changes, and there by involved in gene transcription in cancer cells. In this study, we have evaluated the role of glucose on GBM cancer cells and identified the cell viability effects. Further, the cell-cycle studies have indicated the apoptotic effects of high dose of glucose. Further the histone deacetylase (HDAC) gene expression was examined during increased glucose availability. We have observed a drastic enhancement in HDAC gene expression. Further, the cancer cell metabolism was analysed by studying the gene expression pertaining to mammalian target of rapamycin (mTOR) pathway. Glucose has induced changes in gene expression of class I HDACs and mTOR pathway genes. Furthermore, the study has also identified the microRNA modulatory effect of glucose. The molecular modelling studies have indicated the interaction of glucose with mTOR, Rictor and caspase-3 proteins suggesting the functional regulatory role of glucose on the expression of genes. The caspase-3 (i. e. the effector caspase) studies confirmed the effect of glucose on caspase-3 activity and the effect was enhanced by the treatment with mTOR complex inhibitors. Proteomic study has identifed the involvement of MAPK, Rho kinase, S6 kinase pathways, Bromodomain, histone acetyl transferases during combined treatment of mTOR complex inhibitor and high glucose combination treatment. Thus, the present study has elucidated the role of glucose on GBM cancer proliferation, and molecular modulatory effect mediated by glucose by varying the chromatin epigenetics, and microRNA modulation.

Men with loss-of-function (LOF) variants of toll-like receptor 7 (TLR7) are more susceptible to critical COVID-19. We aimed to determine the pathogenicity and binding affinity changes of TLR7 variants towards SARS-CoV2 RNA, MyD88, imiquimod, and N-acetylcysteine (NAC). TLR7 deleterious mutations increase the risk of critical COVID-19 by 16-folds (95% CI: 2.40–106.73, p = 0.005). LOF-TLR7 variants had impaired SARS COV-2 viral RNA sensing (-292.09 ± 11.86 Kcal/mol) compared to hypofunctional (-304.65 +/- 8.84 Kcal/mol), and neutral (-310.01 ± 5.29 Kcal/mol) TLR7 variants (p

Mucopolysaccharidoses (MPSs) is a major group of the lysosomal storage disorders (LSDs) with defective degradation of glycosaminoglycans (GAGs). Enzyme replacement therapy or bone marrow transplantation are the key therapeutic options available. Early diagnosis and appropriate intervention improve the therapeutic efficacy. We have used FATHMM, I-Mutant, PolyPhen-2, PATHER, PHD-SNP, SNP&GO, SIFT, PROVEAN, CUPSAT, SNAP2 for in silico analysis. These in silico tools and urinary GAG levels helped in monitoring the response to enzyme replacement therapy (ERT). Enzyme activity was inversely associated with SNAP2 (r= -0.36, p=0.04), Polyphen-2 (r= - 0.44, p=0.009) and Evolutionary preservation time (r= -0.396, p=0.02). This suggests that subjects having mutations with higher SNAP2 and Polyphen-2 score tend to have lower enzyme activity. ERT lead to 7 – 31% decrease in urinary GAG levels in seven MPS I patients. The determined pathogenicity scores are serving as prognostic markers indicating a response to therapy. Urinary GAG excretion is the primary end point to monitor the therapeutic efficacy.

Background: Methotrexate (MTX) is an antirheumatic drug, transported by reduced folate carrier-1 (RFC1). The most common RFC1 gene variant, c.80 A>G (rs1051266) is ambiguously linked to adverse effects of MTX therapy in some rheumatoid arthritis (RA) patients. Objective: The purpose of meta-analysis was to summarize all major published studies on c.80 A>G SNP to clarify this ambiguity in MTX therapy. Methods: A total of 18 studies representing 3592 RA patients comprising 699 men and 2893 women were included. Both fixed and random effect models were applied to study the data. Results: The RFC1 80A-allele showed null association with MTX-mediated toxicity in both fixed (odds ratio [OR] = 0.91; 95% CI = 0.80-1.03) and random effects (OR = 0.89; 95% CI: 0.71-1.11) models. Because heterogeneity was observed in this association ( P = 0.0006), data were segregated based on use of folate therapy. In 7 studies (n = 1191) where folate was used along with MTX, RFC1 AA patients showed reduced risk for MTX-mediated toxicity (OR = 0.67; 95% CI: 0.50-0.89; P = 0.0006). The RFC1 80A-allele was found to increase the efficacy of MTX therapy by 1.53-fold (95% CI: 1.24-1.88), whereas the 80AA-genotype increased the efficacy by 1.85-fold (95% CI: 1.41-2.42). No publication bias was observed in these associations. Conclusion and Relevance: RFC1 c.80 A>G is an important pharmacogenetic determinant of MTX therapy in RA. The RFC1 80A-allele robustly increased therapeutic efficacy and safety when folate was used along with MTX. Findings are relevant to decision-making in the clinical use of MTX as a treatment for RA patients harboring the RFC1 gene variant.

High prevalence of congenital hypothyroidism (CH) among Indian newborns prompted us to establish population-specific reference ranges of TSH and to explore the contribution of the common genetic variants in TSHR, TPO, TG and DUOX2 genes towards CH. A total of 1144 newborns (593 males and 551 females) were screened for CH. SNV profiling (n = 22) spanning three candidate genes, i.e. TSHR, TPO and TG was carried out in confirmed CH cases (n = 45). In screen negative cases (n = 700), ten TSHR variants were explored to establish association with CH. No mutation found in DUOX2. The 2.5th to 97.5th percentiles of TSH in these newborns were 0.5 to 12.2 mU/L. In newborns with optimal birth weight, the cut-off was 10 mU/L. Lower or higher birth weight resulted in slightly higher TSH. Two TSHR variants, i.e. rs7144481 and rs17630128 were associated with agenesis, hypoplasia and goiter. The rs2268477 was associated with agenesis and hypoplasia. The rs1991517, rs2075176 and rs2241119 were associated with agenesis only. The rs7144481, rs17630128, rs1991517 and rs2268477 were associated with 2.17, 4.62, 2.91 and 2.29-fold increased risk for CH, respectively. Among the TPO variants, rs867983 and rs2175977 were associated with agenesis and goiter, respectively. Among the TG variants, rs2076740 showed association with agenesis and goiter. Two rare variants i.e. TPO g.IVS14-19 G>C and TG c.1262 C>T were observed in CH cases. No genetic variant identified in the two exons of DUOX2. To conclude, the current study established Indian population-specific normative values for TSH and demonstrates specific genotype–phenotype correlations among three candidate genes.

Several genetic variants of thiopurine metabolic pathway are associated with 6-thiopurine-mediated leucopenia. A population-based evaluation of these variants lays the foundation for Pharmacogenetic-guided thiopurine therapy. A total of 2000 subjects were screened for the pharmacogenetic determinants using the infinium global screening array (GSA). The functional relevance of these variants was deduced using SNAP2, SIFT, Provean, Mutalyzer, Mutation Taster, Phyre2, SwissDock, AGGRESCAN, and CUPSAT. The minor allele frequencies of NUDT15*3, NUDT15*5, TPMT*3C, TPMT*3B variant alleles were 6.78%, 0.11%, 1.98% and 0.69%, respectively. TPMT*3A genotype was observed in 0.35% subjects. No gender-based differences were observed in the incidence of these variants. Data from studies of the Indian population showed that 92.86% subjects heterozygous for NUDT15*3 and 60% subjects heterozygous for TPMT*3C exhibit thiopurine-mediated hematological toxicity. NUDT15 variants have no impact on the binding of ‘dGTP’ to the NUDT protein. NUDT15*3 variant increases aggregation ‘hot spot’ region and induces unfavourable torsion in the protein. NUDT15*5 destabilizes the protein and impairs Mg/Mn binding. TPMT*3A, TPMT*3B and TPMT*3C variants lower binding affinity to 6-mercaptopurine compared to the wild protein. TPMT*3C variant destabilizes the TPMT protein in the thermal experiment. Compared to the data of European and African/African American populations, NUDT15*3 frequency is higher and TPMT*3C frequency is lower in our population. TPMT variants were less frequent in Indian population, while NUDT15*3 is more frequent compared to European and African/African American populations. NUDT15*3 increases aggregation ‘hot spot’ and induces unfavourable torsion in the protein. NUDT15*5 and TPMT*3C destabilize the respective proteins. TPMT*3A, TPMT*3B and TPMT*3C are associated with a lower binding affinity towards 6-mercaptopurine.

Depletion of S-adenosyl methionine and 5-methyltetrahydrofolate; and elevation of total plasma homocysteine were documented in CAD patients, which might modulate the gene-specific methylation status and alter their expression. In this study, we have aimed to delineate CAD-specific epigenetic signatures by investigating the methylation and expression of 11 candidate genes i.e. ABCG1, LIPC, PLTP, IL-6, TNF-α, CDKN2A, CDKN2B, F2RL3, FGF2, P66 and TGFBR3. The methylation-specific PCR and qRT-PCR were used to assess the methylation status and the expression of candidate genes, respectively. CAD patients showed the upregulation of IL-6, TNF-α, CDKN2A, CDKN2B, F2RL3, FGF2, P66, and TGFBR3. Hypomethylation of CDKN2A loci was shown to increase risk for CAD by 1.79-folds (95% CI 1.22–2.63). Classification and regression tree (CART) model of gene expression showed increased risk for CAD with F2RL3 > 3.4-fold, while demonstrating risk reduction with F2RL3

Background Heart failure is a complex cardiovascular disease with a variety of etiologies and heterogeneity. The N-terminal pro-B-type natriuretic peptide (NT-proBNP) value has limited usefulness in diagnosing heart failure with preserved ejection fraction (HFpEF). Aim The aim of the present study is to evaluate serum Galectin-3 as a diagnostic biomarker in patients with HFpEF and to compare Galectin-3 with NT-proBNP levels. Materials and Methods A cross-sectional case–control study including 63 cases of heart failure with ejection fraction ≥50% confirmed by echocardiography. NT-proBNP levels in serum were measured by electrochemiluminescence immunoassay and Galectin-3 levels in serum were measured by using an enzyme-linked-immunosorbent serologic assay kit. Results The median levels of serum Galectin-3 and NT-proBNP in patients were significantly higher than those of controls (26.59 vs. 5.27 and 927 vs. 49.3, p < 0.0001). A positive correlation was observed between serum levels of Galection-3 and NT-ProBNP (r: 0.21, p = 0.048). At cut-off values of 10.1 ng/mL and 160 pg/mL, serum Galectin-3 has 77.78% sensitivity, 95% specificity with an area under the curve (AUC) of 0.93, and serum NT-proBNP has 71.43% sensitivity, 100% specificity with an AUC of 0.87, respectively, for diagnosing HFpEF. The comparison of receiver operating characteristics curves showed that Galectin-3 has better AUC compared with NT-proBNP in diagnosing HFpEF. Serum Galectin-3 showed a positive correlation with NT-proBNP and lipid parameters. Conclusion Galectin-3 with higher sensitivity and AUC can be used as a valuable biomarker for the diagnosis of HFpEF. Simultaneous testing of both Galectin-3 and NT-proBNP can further improve the detection of patients with HFpEF.

Introduction: Diabetes Mellitus (DM) is a metabolic condition linked by the inability to produce enough insulin and/or to respond to insulin. This can lead to a number of acute and chronic health problems. In erythrocytes, transferrin is the main source of iron. Alterations in transferrin glycation affect transferrin saturation because the affinity of transferrin for Fe3+ is extremely high but it decreases progressively with increasing glycation. Aim: To investigate the influence of uncontrolled diabetes on transferrin glycation and iron metabolism. Materials and Methods: A total of 136 samples from 3 groups of HbA1c levels (8.0%-uncontrolled DM) were studied for the correlation pattern of iron with other variables. Chi square test and student’s t-test were performed to reveal the association between serum free iron levels and other variables with DM. Results: Serum iron has shown to be depleted significantly (p=0.02) along with percentage saturation (p=0.0006) with increase in diabetic severity. No significant differences were observed in serum ferritin in controlled DM and uncontrolled samples. Total Iron Binding Capacity (TIBC) was found to be significantly increased in uncontrolled DM samples (p=0.01). Abnormal transferrin was observed uncontrolled diabetes with subsequent depletion in transferrin, which in turn results in low serum iron, lower percentage saturation and high TIBC. Conclusion: Uncontrolled diabetes affects the glycation of transferrin also thus perturbating iron metabolism. The present study emphasises the need to monitor transferrin glycation status and iron deficiency anaemia in subjects with uncontrolled diabetes.

Background Joubert syndrome and related disorders are a group of ciliopathies characterized by mid-hindbrain malformation, developmental delay, hypotonia, oculomotor apraxia, and breathing abnormalities. Molar tooth sign in brain imaging is the hallmark for diagnosis. Joubert syndrome is a clinically and genetically heterogeneous disorder involving mutations in 35 ciliopathy-related genes. We present a large cohort of 59 patients with Joubert syndrome from 55 families. Molecular analysis was performed in 35 families (trio). Methods Clinical exome analysis was performed to identify causal mutations, and genotype-phenotype correlations were evaluated. Results All of the cases were stratified into pure Joubert syndrome (62.7%), Joubert syndrome with retinal disease (22.0%), polydactyly (8.5%), and liver (1.7%) and kidney (1.7%) involvement. Joubert syndrome-related disorders include Meckel-Gruber syndrome in 5.1% cases and Leber congenital amaurosis (1.7%). Of the 35 Joubert syndrome-related genes, 11 were identified in these patients, i.e., CEP290, C5ORF, TCTN1, CC2D2A, RPGRP1L, TCTN3, AHI1, INPP5E, TCTN2, NPHP1, and TMEM237. For the first time, we identified a ciliopathy gene, CCDC28B, as a causal gene in Joubert syndrome in one family. CEP290 accounted for 37.8% cases of pure Joubert syndrome, Joubert syndrome with retinal and renal disease, and Meckel-Gruber syndrome. The p.G1890∗ allele in CEP290 is highly recurrent. Of the six families with Joubert syndrome who had a prenatal diagnosis, one fetus was normal, two were carriers, and three were affected. Conclusions This is the largest study of Joubert syndrome from India. Although a high degree of locus and allelic heterogeneity was observed, CEP290 variants were the most common among these patients.

In the current study, we report three cases of Asparagine Synthetase (ASNS) Deficiency from two consanguineous families. Family 1 had two early neonatal deaths due to a novel mutation in the ASNS gene c.788C > T (p.S263F) and both the children presented with microcephaly and one of them had severe intracranial haemorrhage. The proband from the second family was homozygous for c.146G > A (p.R49Q) and manifested myoclonic seizures, developmental delay, coarse hair and diffuse cortical atrophy. Molecular docking studies of both the mutations revealed alteration in the ligand binding site. Till date, 26 mutations were reported in ASNS gene in 29 affected children indicating high degree of genetic heterogeneity and high mortality. Although asparagine depletion is not of diagnostic utility, multiple linear regression model suggested that asparagine levels vary to the extent of 20.6% based on glutamine and aspartate levels and ASNS deficiency results in depletion of asparagine synthesis. ASNS deficiency should be suspected in any neonate with microcephaly and epileptic encephalopathy.

Background: In majority of the studies inverse association between vitamin D and parathyroid hormone levels is documented. Objective: The rationale of the current study was to investigate whether this inverse association is agedependent and whether it has any role in modulating renal function and insulin resistance. Methods: To test this hypothesis, we have carried out a hospital based study enrolling 848 subjects (558 men and 290 women) with the mean age of 50.9 ± 15.9 y. Chemiluminometric competitive immune assays were performed using commercial kits to determine 25-OH vitamin D and Parathyroid Hormone (PTH) levels. Fasting glucose levels and serum creatinine were used to evaluate diabetes and renal function. Results: Vitamin D deficiency was predominant irrespective of age group (p = 0.21) and gender (p = 0.12). An inverse association between vitamin D and PTH was observed (r = -0.24) in middle age subjects (p = 0.02). The data segregation based on plasma vitamin D levels which were 30 ng/ml confirmed the inverse association between vitamin D and PTH levels (ptrend: 0.007). Subjects with low plasma vitamin D and increased PTH exhibited elevated blood urea, serum creatinine and blood glucose. Subjects with 25-OHD deficiency showed a 3.03-folds (95% CI: 2.26- 4.07) and 2.09-fold (1.41-3.10) increased risk for diabetes and renal disease, respectively. Conclusion: Based on the results of the present study, it is suggested that those with vitamin D deficiency need to be evaluated for possible presence of renal dysfunction, diabetes/insulin resistance in addition to assessing their PTH status.

The rationale of the current study was to develop 6-mercaptopurine (6-MP)-mediated hematological toxicity prediction model for acute lymphoblastic leukemia (ALL) therapeutic management. A total of 96 children with ALL undergoing therapy with MCP-841 protocol were screened for all the ten exons of TPMT, exon 2, exon 3 and intron 2 of ITPA using bidirectional sequencing. This dataset was used to construct prediction models of leucopenia grade by constructing classification and regression trees (CART) followed by smart pruning. The developed CART model indicated TPMT*12 and TPMT*3C as the key determinants of toxicity. TPMT int3, int4 and int7 polymorphisms exert toxicity when co-segregated with one mutated allele of TPMT*12 or TPMT*3C or ITPA exon 3. The developed CART model exhibited 93.6% accuracy in predicting the toxicity. The area under the receiver operating characteristic curve was 0.9649. TPMT *3C and TPMT*12 are the key determinants of 6-MP-mediated hematological toxicity while other variants of TPMT (int3, int4 and int7) and ITPA ex2 interact synergistically with TPMT*3C or TPMT*12 variant alleles to enhance the toxicity. TPMT and ITPA variants cumulatively are excellent predictors of 6-MP-mediated toxicity.

Several studies optimized the warfarin dose based on CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A, CYP4F2 V433M. But, the information on the rare variants is lacking. In this study, we have explored the prevalence of common and rare pharmacogenetic determinants of warfarin and determined their damaging nature. We have analyzed 2000 healthy adults using the Infinium global screening array (GSA) for 15 pharmacogenetic determinants of warfarin. In addition, we have elucidated the impact of these variants on protein function, stability, dynamics, evolutionary preservation, and ligand binding propensity. The GSA Analysis has revealed that CYP4F2 V433M (MAF: 39.425%), VKORC1 -1639 G > A (MAF: 20.5%), CYP2C9*3 (MAF:9.925%), and CYP2C9*2 (MAF:4.575%) are common, while CYP2C9*14 (MAF: 1.475%), CYP2C9*4 (0.175%), CYP2C9*5 (0.125%), and CYP2C9*11 (0.125%) are rare. Position-specific evolutionary preservation (PSEP) analysis has revealed that CYP2C9*4 is possibly damaging, while CYP2C9*5, CYP2C9*11, and CYP2C9*14 are probably damaging. CYP2C9*4 has high thermolability (−10.14 kcal/mol). Among the rare CYP2C9 variants, CYP2C9*4 and CYP2C9*11 exert destabilizing effects and may have increased molecular flexibility, while CYP2C9*5 and CYP2C9*14 exert stabilizing effects and may have decreased molecular flexibility. DNase I footprint analysis has revealed the loss of the E-box consensus sequence due to VKORC1 -1639 G > A polymorphism. CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A and CYP4F2 V433M are common; CYP2C9*4, CYP2C9*5, CYP2C9*11, and CYP2C9*14 variants are rare in Indian subjects. All the CYP2C9 variants are found to be damaging. DNase I footprint analysis provided the mechanistic rationale for the association of VKORC1 -1639 G > A with warfarin sensitivity.

Chemoresistance is considered as one of the major obstacles in the postgenomic era of cancer treatment. Recent studies envisaged the crucial regulatory role of long noncoding RNA (lncRNA)/microRNA (miRNA) and their interaction in cancer chemotherapy and personalized medicine. Glioblastoma (GBM) is one of the devastating brain cancers and is highly malignant and resistant to therapy. LncRNAs are long noncoding RNAs with nucleotide length of more than 200 bp, lack protein-coding potential, and were found to regulate cellular processes such as chromatin epigenetics, posttranscriptional mRNA processing, gene regulation, glioma cancer stem cell (GCSC) self-renewal, drug metabolism, and chemoresistance. In GBM, the survival period of most of the patients is less than 15 months. The most common drug utilized for treating GBM is temozolomide as a part of first-line therapy. Resistance to temozolomide results in tumor recurrence, epithelial to mesenchymal transition (EMT), and therapy failure. This chapter describes how various lncRNAs contribute to drug resistance to temozolomide in GBM patients and interaction of lncRNA with miRNAs, modulation of chromatin epigenetics by lncRNA, the role of RNA modifications such as m6A and m5C in mRNA in GBM cancer progression and TMZ-drug resistance.

Purpose CYP2C19 metabolizes the antiplatelet and antiepileptic drugs. Any alteration in CYP2C19 activity might influence the therapeutic efficacy. The objective of this study was to identify CYP2C19 variants prevalent in Indians and perform their in silico characterization. Methods Infinium global screening array (GSA) was used for CYP2C19 genotyping in 2000 healthy Indians. In addition, we performed in silico characterization of the identified variants. Results Out of the 11 variants covered (*2, *3, *4,*5,*6, *7,*8, *9,*10,*11, and *17), five were identified in Indians (*2, *3, *6,*8 and *17). The *2 and *17 were the most prevalent alleles (minor allele frequencies, MAF: 32.0% and 13.95%). The *3, *6 and *8 were rare (MAFs: 0.425%, 0.025% and 0.05%). The *2 variant is shown to affect the splicing at the fifth exon–intron boundary. The *3 variant is a non-sense variant that is predicted to be deleterious. On the otherhand, the *17 variant showed more binding affinity for GATA binding protein 1 (GATA1), myocyte enhancer factor 2 (MEF2) and ectotropic viral integration site 1 (EVI1). The *6 and *8 variants predicted to be deleterious. The *2, *3 and *7 variants showed lesser probability of exon skipping, while *17 showed more probability. The genotype distribution of Indian subjects is comparable with that of South Asians (SAS) (1000 genome project, phase 3). Conclusion The *2, *3 and *17 variants are the key pharmacogenetic determinants in Indians. The *2 and *3 are loss-of-function variants. The *17 is a gain-of-function variant with increased binding of transcriptional factors.

Background The present study aimed to delineate the pharmacologically relevant dihydropyrimidine dehydrogenase (DPYD) variants in the Indian population. Methods We screened 2000 Indian subjects for DPYD variants using the Infinium Global Screening Array (GSA) (Illumina Inc., San Diego, CA, USA). Results The GSA analysis identified seven coding, two intronic and three synonymous DPYD variants. Level 1A alleles (rs75017182, rs3918290, P633Qfs*5 and D949V) were found to be rare (minor allele frequency: 1.889%), whereas Level 3 alleles were observed to be predominant (C29R: 24.91%, I543V: 9.047%, M166V: 8.993% and V732I: 8.44%). In silico predictions revealed that all Level 1A alleles were deleterious, whereas three (M166V, S534N and V732I) of seven Level 3 alleles were damaging. CUPSAT analysis revealed that two Level 1A (P633Qfs*, D949V) and three Level 3 (I543V, V732I and S534N) variants were thermolabile. The pooled Indian data showed that V732I, S534N and rs3918290 variants were associated with 5-FU/capecitabine toxicity, whereas C29R, I543V and M166V variants exhibited the null association. A comparison of our data with other population data from the 'Allele Frequency Aggregator' (https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/) database showed similarities with the South Asian data. Conclusions We have identified four Level 1A (non-functional/dysfunctional) and seven Level 3 variants in the DPYD gene. The pooled Indian data revealed the association of V732I, S534N and rs3918290 variants with 5-FU/capecitabine toxicity. Clustering analysis revealed the similarities in the DPYD profiles of the Indian and South Asian populations.

Glutaric acidemia type 1 (GA-1, OMIM 231670) is an autosomal recessive inborn error of metabolism caused by the deficiency of glutaryl-coenzyme A (CoA) dehydrogenase with most children presenting in infancy with encephalopathy, dystonia, and macrocephaly. In this article, we presented the clinical characteristics, molecular profile, and outcomes in 29 unrelated families with affected children (30 cases total). The mean age at onset of illness was 10 months (±14.58), whereas the mean age at referral for molecular diagnosis was 29.44 months (±28.11). Patients were residents of nine different states of India. Clinical presentation varied from acute encephalitis followed by neuroregression and chronic/insidious developmental delay. Neurological sequelae varied from asymptomatic (no sequelae, 2 patients) to moderate (5 patients) and severe (23 patients) sequelae. All patients underwent blood tandem mass spectrometry (TMS on dried blood spots) and/or urine gas chromatography mass spectrometry (GCMS). Neuroimaging demonstrated batwing appearance in 95% cases. Sanger's sequencing of GCDH, covering all exons and exon–intron boundaries, was performed for all patients. Variants identified include 15 novel coding variants: p.Met100Thr, p.Gly107Ser, p.Leu179Val, p.Pro217Ser, p. Phe236Leufs*107, p.Ser255Pro, p.Met266Leufs*2, p.Gln330Ter, p.Thr344Ile, p.Leu345Pro, p.Lys377Arg, p.Leu424Pro, p.Asn373Lys, p.Lys377Arg, p.Asn392Metfs*9, and nine known genetic variants such as p.Arg128Gln, p.Leu179Arg, p.Trp225Ter, p.Met339Val, p.Gly354Ser, p.Arg402Gln, p.Arg402Trp, p.His403Tyr, and p.Ala433Val (Ensembl transcript ID: ENST00000222214). Using in silico analysis, genetic variants were shown to be affecting the residues responsible for homotetramer formation of the glutaryl-CoA dehydrogenase protein. Treatment included oral carnitine, riboflavin, protein-restricted diet, lysine-deficient special formulae, and management of acute crises with intravenous glucose and hydration. However, the mortality (9/30, 27.58%) and morbidity was high in our cohort with only two patients affording the diet. Our study is the largest multicentric, genetic variant–proven series of glutaric aciduria type 1 from India till date.

The objective of the current study is to explore the association of thyroid-stimulating hormone receptor (TSHR) rs1991517 polymorphism (c.2337 C > G, p.D727E) with congenital hypothyroidism (CH) through a case–control study followed by a meta-analysis. The case–control study was based on 45 CH subjects and 700 healthy controls. Meta-analysis comprised of seven published studies and our current findings (1044 CH cases and 1649 healthy controls). The allele contrast model showed that the presence of G- allele increased CH risk by 45% (OR: 1.45, 95% CI 1.20–1.76) and 41% (OR: 1.41, 95% CI 1.03–1.93) in fixed effect and random effect models, respectively. The GG- genotype is associated with 2.3-fold (95% CI 1.32–3.99) increased risk for CH in the fixed-effect model. I(2) (0.58) and Cochran’s Q test (Q: 16.72, p = 0.02) revealed evidence of heterogeneity in the association. No publication bias was observed by Egger’s test (p = 0.70). Sensitivity analysis revealed that even after excluding any study this polymorphism is associated with risk for CH. The rs1991517 mutation alters the binding affinity to cAMP (ΔG of 727D vs.727E: − 7.27 vs. − 7.34 kcal/mol). In conclusion, rs1991517 is a genetic risk factor for CH and exerts its impact by altering cAMP-mediated signal transduction.

In view of high mortality associated with coronary artery disease (CAD), development of an early predicting tool will be beneficial in reducing the burden of the disease. The database comprising demographic, conventional, folate/xenobiotic genetic risk factors of 648 subjects (364 cases of CAD and 284 healthy controls) was used as the basis to develop CAD risk and percentage stenosis prediction models using ensemble machine learning algorithms (EMLA), multifactor dimensionality reduction (MDR) and recursive partitioning (RP). The EMLA model showed better performance than other models in disease (89.3%) and stenosis prediction (82.5%). This model depicted hypertension and alcohol intake as the key predictors of CAD risk followed by cSHMT C1420T, GCPII C1561T, diabetes, GSTT1, CYP1A1 m2, TYMs 5′-UTR 28 bp tandem repeat and MTRR A66G. MDR and RP models are in agreement in projecting increasing age, hypertension and cSHMTC1420T as the key determinants interacting in modulating CAD risk. Receiver operating characteristic curves exhibited clinical utility of the developed models in the following order: EMLA (C = 0.96) > RP (C = 0.83) > MDR (C = 0.80). The stenosis prediction model showed that xenobiotic pathway genetic variants i.e. CYP1A1 m2 and GSTT1 are the key determinants of percentage of stenosis. Diabetes, diet, alcohol intake, hypertension and MTRR A66G are the other determinants of stenosis. These eleven variables contribute towards 82.5% stenosis. To conclude, the EMLA model exhibited higher predictability both in terms of disease prediction and stenosis prediction. This can be attributed to higher number of iterations in EMLA model that can increase the prediction accuracy.

In view of well-documented association of hyperhomocysteinaemia with a wide spectrum of diseases and higher incidence of vitamin deficiencies in Indians, we proposed a mathematical model to forecast the role of demographic and genetic variables in influencing homocysteinemetabolism and investigated the influence of life style modulations in controlling homocysteine levels. Total plasma homocysteine levels were measured in fasting samples using reverse phase HPLC. Multiple linear regression (MLR) and neuro-fuzzy models were developed. The MLR model explained 64% variability in homocysteine, while the neurofuzzy model showed higher accuracy in predicting homocysteine with a mean absolute error of 0.00002 μmol/L. Methylene tetrahydrofolate reductase (MTHFR) C677T, 5-methyltetrahydrofolate homocysteine methyltransferase (MTR) A2756G and 5- methyltetrahydrofolate homocysteine methyltransferase reductase (MTRR) A66G were shown to be positively associatiated with homocysteine, while nonvegetarian diet, serine hydroxymethyltransferase 1 (SHMT1) C1420T and TYMS 5'-UTR 28 bp tandem repeat exhibited negative association with homocysteine. The protective role of SHMT1 C1420T was attributed to more H-bonding interactions in the mutant modelled compared to the wild type, as shown through in silico analysis. To conclude, polymorphisms in genes regulating remethylation of homocysteine strongly influence homocysteine levels. The restoration of one-carbon homeostasis by SHMT1 C1420T or increased flux of folate towards remethylation due to TYMS 5'-UTR 28 bp tandem repeat or nonvegetarian diet can lower homocysteine levels.

Scriptaid (SCR), a well-known histone deacetylase inhibitor, cause various cellular effects such as cell growth inhibition and apoptosis. In this study, we have evaluated the anti-cancer effects of Scriptaid in HeLa cells, IMR-32 and HepG2 cells. Scriptaid inhibited the growth of HeLa cells with IC50 of 2μM at 48h in a dose-dependent manner. Flow-cytometric analysis indicated that SCR induced apoptosis. Scriptaid was found to inhibit HDAC-8 effectively than other HDAC inhibitor such as TSA as observed by HDAC-8 assay, Western blotting and modelling study. This observation was further strengthened by an artificial neuronal network (ANN) model.

The rationale of the current study was to elucidate the contributing factors for the gender-based differences in total plasma homocysteine levels. A total of 413 subjects comprising of 293 men and 120 women were enrolled for the study. Chemiluminescence technology for vitamin B12, folate and total plasma homocysteine; ELISA for estradiol and 8-oxo-2-deoxyguanosine; Ellman's method for total glutathione; and PCR-RFLP analysis for the detection of methylene tetrahydrofolate reductase (MTHFR) C677T polymorphism were employed. No statistically significant differences were observed between the men and women in the distribution of age (p = 0.82), vitamin B12 (p = 0.23), folate (p = 0.36) and MTHFR C677T polymorphism (p = 0.35). However, the total plasma homocysteine levels were higher in men compared to women (28.4 ± 17.9 vs. 20.6 ± 13.6 μmol/L, p

Background: The deficiency of vitamin D receptor (VDR) or its ligand, vitamin D3, is linked to the development of renal diseases. The TaqI (rs731236) and ApaI (rs7975232) polymorphisms of VDR gene are widely studied for their association with renal disease risk. However, studies have largely been ambiguous. Objectives: Here, a meta-analysis comprising 2669 renal disease cases and 3342 controls was carried out to clarify the association of TaqI and ApaI polymorphisms with nephrolithiasis (NL), diabetic nephropathy (DN) and end stage renal disease (ESRD). Methods and Results: The VDR TaqI C-allele under allele contrast and fixed effect models was significantly associated with NL and ESRD, and Apal T-allele with ESRD only under fixed effect model. Cochrane Q-test showed no evidence of heterogeneity for TaqI polymorphism and a significant heterogeneity for Apa I polymorphism. No publication bias was observed for both the polymorphisms. Interestingly, increased disease penetrance with an increase in latitude from south to north across the globe was found only in the case of Taql polymorphism but not with Apal. Conclusions and Implications: The present meta-analysis identifies TaqI and ApaI polymorphisms of VDR gene as significant risk factors for renal diseases. Besides, increased disease penetrance with Taql polymorphism from south to north may corroborate with combined effect of defective VDR expression and decreased vitamin D synthesis due shorter durations of sun exposure with increasing latitude. On the other hand, possibility of Apal polymorphism in linkage disequilibrium with an adjacent functional polymorphism and lack of their co-segregation may have resulted in reduced disease penetrance. Present findings may have implications in understanding the role of gene-environmental interaction in renal disease risk.

Background The deficiency of vitamin D receptor (VDR) or its ligand, vitamin D3, is linked to the development of renal diseases. The TaqI (rs731236) and ApaI (rs7975232) polymorphisms of VDR gene are widely studied for their association with renal disease risk. However, studies have largely been ambiguous. Methods Meta-analysis was carried out to clarify the association of TaqI (2777 cases and 3522 controls) and ApaI (2440 cases and 3279 controls) polymorphisms with nephrolithiasis (NL), diabetic nephropathy (DN) and end stage renal disease (ESRD). Results The VDR TaqI C-allele under allele contrast was significantly associated with ESRD in both fixed effect and random effect models, and ApaI C-allele with ESRD only under fixed effect model. Cochrane Q-test showed no evidence of heterogeneity for TaqI polymorphism and a significant heterogeneity for Apa I polymorphism. No publication bias was observed for both the polymorphisms. Conclusions The present meta-analysis identifies TaqI and ApaI polymorphisms of VDR gene as risk factors for renal diseases.

Introduction: Association of serum folate, Vitamin B6 and B12 deficiencies with hyperhomocysteinemia are well-documented. Several studies on Indian population, address the association of hyperhomocysteinemia with numerous diseases, but populationspecific baseline levels of homocysteine in healthy population have not been elucidated till date. Aim: To establish Indian-population specific reference ranges for total plasma homocysteine in healthy adults in accordance to variation in dietary factors, serum B12 and folate status. The study also aimed to assess the contribution of cofactors in modulating homocysteine levels, and to evaluate the impact of higher homocysteine levels on the oxidative DNA damage. Materials and Methods: In this retrospective study, 151 apparently healthy non-diabetic, non-hypertensive individuals with normal thyroid, renal and cardiac function were recruited. Vitamin B12, Folate, and Homocysteine assays were performed on ADVIA Centaur® XP Immunoassay system. Plasma 8-oxo2deoxyguanosine levels were estimated by using commercially available ELISA kit. Student’s t-test, ANOVA, Spearman rank correlation was used to establish the associations between variables. The p45 yr, n=93) and gender. In both the age groups, homocysteine and 8-oxo-2deoxyguanosine levels were found to be elevated in men (p=0.003) while no gender-specific differences were observed in the levels of folate and B12. Post-menopausal women had higher oxidative DNA damage as compared to the pre-menopausal women. Positive correlation was observed between total plasma homocysteine and plasma 8-oxo-2deoxyguanosine (r=0.35, p=0.03). An inverse correlation was observed between plasma B12 levels and total plasma homocysteine in men (r=-0.24, p=0.02) while no such correlation was observed in women (r=0.22, p=0.10). No significant correlation was observed between plasma folate levels and total plasma homocysteine in both genders (male: r=-0.10, p=0.33; female: r=-0.23, p=0.09). Non-vegetarians had higher plasma B12 levels (p

This study was aimed to construct classification and regression tree (CART) model of glycosaminoglycans (GAGs) for the differential diagnosis of Mucopolysaccharidoses (MPS). Two-dimensional electrophoresis and liquid chromatography–tandem mass spectrometry (LC–MS/MS) were used for the qualitative and quantitative analysis of GAGs. Specific enzyme assays and targeted gene sequencing were performed to confirm the diagnosis. Machine learning tools were used to develop CART model based on GAG profile. Qualitative and quantitative CART models showed 96.3% and 98.3% accuracy, respectively, in the differential diagnosis of MPS. The thresholds of different GAGs diagnostic of specific MPS types were established. In 60 MPS positive cases, 46 different mutations were identified in six specific genes. Among 31 different mutations identified in IDUA, nine were nonsense mutations and two were gross deletions while the remaining were missense mutations. In IDS gene, four missense, two frameshift, and one deletion were identified. In NAGLU gene, c.1693C > T and c.1914_1914insT were the most common mutations. Two ARSB, one case each of SGSH and GALNS mutations were observed. LC–MS/MS-based GAG pattern showed higher accuracy in the differential diagnosis of MPS. The mutation spectrum of MPS, specifically in IDUA and IDS genes, is highly heterogeneous among the cases studied.

Cardiovascular disease (CVD) is one of the most common causes of deaths globally. Oxidative stress is documented to be one of the potential risk factors for CVD. This review focuses on genetic and epigenetic factors contributing toward CVD risk. Certain genetic variants in oxidants, i.e., NADPH oxidase p22Phox rs4673, eNOS (-786 T>C, 894 G>T, and 27bp VNTR), MPO (-463 and -129 GA-genotypes), XO 69901 A>C, COX2 (rs5277 and rs20417), and ALOX15 (rs2619112 and rs7217186), were reported to increase CVD risk. Similarly, genetic variants in antioxidants, i.e., SOD1 (rs9974610, rs10432782, rs1041740), SOD2 (V16A, C24T), GPX1 Pro198Leu, NQO1 C609T, PON1 Q192R, and TXNIP (rs7212 and rs7211), were also shown to exhibit positive association with CVD risk. Apart from oxidants and antioxidants, folate and xenobiotic metabolic pathways were also investigated due to their direct influence on synthesis, methylation, and repair of DNA. Among the functional variants of folate pathway, GCPII H475Y, MTHFR C677T, and MTRR A66G were reported to increase CVD risk, thus influencing S-adenosylmethionine/S-adenosyl homocysteine ratio. Two genetic variants, i.e., cSHMT C1420T and TYMS 5’-UTR 28bp tandem repeat, were shown to confer protection by inducing the futile folate cycle and by increasing the flux of folate toward remethylation of homocysteine, respectively. Among the xenobiotic variants, CYP1A1 CAC and TAC haplotypes and GSTT1 and GSTM1 null variants contribute toward CVD risk by inducing quinone and semiquinone synthesis and by preventing conjugation of glutathione, respectively. These two process trigger mutagenicity. CYP1A1 TAC haplotype and CYP4F2 rs2108622 confer protection against CVD. Hypermethylation of ER-alpha, ER-beta, p15(INK4b), FOXP3, and DDAH2 was associated with CVD risk, which is attributed to altered ER-signaling, increased oxidative stress, and impaired synthesis of Treg cells. Factor VII hypermethylation confers protection against CVD. In a nut shell, interplay of genetic and epigenetic factors in oxidant–antioxidant system modulates susceptibility to CVD.

Incense smoke is reported to increase cardiovascular disease (CVD) risk in exposed individuals. However, the mechanism underlying the toxic effect of incense smoke on cardiovascular system is unclear. To test this, we chronically exposed male albino rats to two different types of Arabian incense smoke and studied their effects on oxidative stress, inflammation, and endothelial function. Rats exposed to either of incense smoke showed a significant increase in malondialdehyde (MDA) and a significant decline in superoxide dismutase (SOD) and reduced glutathione (GSH). Endothelial functional marker, nitric oxide (NO) was significantly decreased while endothelin-1 was significantly increased in rats exposed to both the incense types. Incense smoke exposure also led to a significant increase in chemokines and inflammatory mediators including monocyte chemoattractant protein-1 (MCP-1), granulocyte-macrophage-colony stimulating factor (GM-CSF), regulated on activation normal T cell expressed and secreted (RANTES), interleukin-4 (IL-4), C-reactive protein (CRP), and tumor necrosis factor-alpha (TNF-α). Besides, incense smoke-exposed rats demonstrated a significant increase in the expression of intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecules-1 (VCAM-1), and E-selectin. Importantly, cessation of incense smoke exposure for 30 days led to a significant reversal in the levels of all the studied markers. Collectively, this study describes oxidative stress, endothelial dysfunction, and inflammation as possible underlying mechanisms in the toxic effects of incense smoke on increased CVD risk in exposed individuals. Findings also underscore that avoiding incense smoke exposure may have beneficial health effects.