Genome Research Group

Kainan, Japan

Genome Research Group

Kainan, Japan
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Masson E.,French Institute of Health and Medical Research | Masson E.,University of Health Sciences | Masson E.,Institute Federatif Of Recherche Ifr 148 | Paliwal S.,Genome Research Group | And 18 more authors.
Pancreas | Year: 2010

Objectives: The aim of this study was to evaluate whether variations in the glycoprotein 2 gene (GP2) may potentially affect the risk of chronic pancreatitis. Methods: Six hundred sixty-one French white patients (idiopathic chronic pancreatitis, n = 590; familial chronic pancreatitis, n = 42; hereditary pancreatitis, n = 29), 445 Dravidian patients from India (tropical calcific pancreatitis, n = 306; idiopathic chronic pancreatitis, n = 139), and 962 unrelated healthy subjects (French white, n = 500; Dravidian, n = 462) participated in this case-control association study. The entire coding sequence of the GP2 gene was searched for conventional genetic variations by direct sequencing, whereas all 12 exons of the GP2 gene were screened for copy number variations by quantitative fluorescent multiplex-polymerase chain reaction. Results: Only 3 rare missense mutations (p.A137T, p.E250D, and p.V432M; only p.E250D was not detected in any control subjects) and 3 common synonymous polymorphisms (c.348C>T, c.714G>C, and c.1275A>G) were identified. The c.348C>T and c.1275A>G variations were found to be contradictorily associated with the disease (ranging from protective effects to disease-predisposing effects) in the French white and Indian populations. CONCLUSION: The paucity of patient-specific missense mutations and contradictory findings with respect to 2 common polymorphisms in the 2 contrasting populations suggest that the GP2 gene is unlikely to play a major role in the etiology of chronic pancreatitis. Copyright © 2010 by Lippincott Williams & Wilkins.


Boulling A.,French Institute of Health and Medical Research | Boulling A.,University of Western Brittany | Witt H.,TU Munich | Chandak G.R.,Genome Research Group | And 10 more authors.
European Journal of Human Genetics | Year: 2011

The SPINK1 gene, encoding the human pancreatic secretory trypsin inhibitor, is one of the major genes involved in predisposition to chronic pancreatitis (CP). In this study we have assessed the potential functional impact of 11 SPINK1 promoter variants by means of both luciferase reporter gene assay and electrophoretic mobility shift assay (EMSA), using human pancreatic COLO-357 cells as an expression system. The 11 promoter variants were found to be separable into three distinct categories on the basis of the reporter gene assay results viz loss-of-function, gain-of-function and functionally neutral. These findings, which were validated by EMSA, concurred with data from previous deletion studies and DNase I footprinting assays. Further, binding sites for two transcription factors, HNF1 and PTF1, were newly identified within the SPINK1 promoter by virtue of their being affected by specific variants. Combining the functional data with epidemiological data (derived by resequencing the SPINK1 promoter region in French, German and Indian CP patients and controls), then allowed us to make meaningful inferences as to each variant's likely contribution to CP. We conclude that only the three promoter variants associated with a loss-of-function (ie, 53CT, 142TC and 147AG) are likely to be disease-predisposing alterations. © 2011 Macmillan Publishers Limited All rights reserved.


Uno Y.,Genome Research Group | Fujino H.,Health Science University | Iwasaki K.,Genome Research Group | Utoh M.,Genome Research Group
Current Drug Metabolism | Year: 2010

Cynomolgus monkey is used in the study of drug metabolism and toxicity due to its evolutionary closeness to human as compared with other non-human primate species. However, it has become certain that drug metabolism in monkeys is different than in humans. Such species differences have not been fully investigated at a molecular level largely due to the scarcity of information on drug-metabolizing enzyme genes. In cynomolgus monkey, we have identified cDNAs for 21 kinds of cytochromes P450 (CYPs), among which CYP2C76 does not correspond to any human CYP isozymes and is partly responsible for the difference in pitavastatin metabolism between cynomolgus monkey and human. In cynomolgus monkey CYP2C76, we identified numerous genetic variants including a null genotype. Heterozygotes for this null genotype are expected to be poor metabolizers in CYP2C76-mediated drug metabolism. To provide new clues to CYP2C76 function, here, we have taken advantage of sequence information that has been recently deposited to public databases to assess the presence of CYP2C76 orthologs in primate species. In this assessment, we found the CYP2C76 cDNA sequence in rhesus monkey, and a gene sequence highly homologous to cynomolgus monkey CYP2C76 in the marmoset and orangutan genomes, raising the possibility that CYP2C76 could also play a role in these primate species. This review paper gives an overview of CYP2C76 from isolation to molecular characterization, and its implication in drug metabolism. © 2010 Bentham Science Publishers Ltd.


Godbole K.,Kem Hospital | Hemavathi J.,Genome Research Group | Vaid N.,Kem Hospital | Pandit A.N.,Kem Hospital | And 2 more authors.
Indian Journal of Otolaryngology and Head and Neck Surgery | Year: 2010

Objectives: To identify the prevalence of GJB2 (Cx 26)and GJB6 (Cx 30) mutations in hearing impaired individuals from Western and South India. Study design: Cross-sectional study. Methods: Families with hearing impaired individuals (prelingual, non-syndromic, sensori-neural hearing loss) were enrolled and genomic DNA was extracted. Primers were designed for amplifying the coding and non-coding exons including flanking splice sites of the Cx 26 gene. Probands heterozygous or negative for Cx 26 mutations were further analyzed for the 342Kb deletion encompassing D13S1830 microsatellite marker on Cx 30. Results: Two hundred and eighty-eight patients were enrolled in the study and 116 (40. 3%) were diagnosed to have mutations in the coding exon 2 of Cx 26 gene. Fifty-four (18.8%) probands were found to have mutations in both the alleles while the remaining 62 (21.5%) were heterozygous for Cx 26 mutations. W24X, and W77X were the common mutations identified. The prevalence of familial deafness was similar in both consanguineous and non-consanguineous families (33% and 34. 9% respectively). Mutations in the non-coding exon 1 and intron 1 as well as the 342 kb deletion involving D13S1830 marker on Cx 30 were ruled out in two hundred and thirty-four deaf individuals carrying none or only one mutation in the exon 2 of Cx 26 gene. Conclusion: Cx30 mutations do not contribute to the autosomal recessive non-syndromic hearing loss (NSHL) in the Indian population. Homozygous Cx26 mutations account only for about 1/5th (18.8%) of autosomal recessive non-syndromic hearing implying the need to explore other contributory loci. © 2010 Association of Otolaryngologists of India.


Uno Y.,Pharmacokinetics and Bioanalysis Center | Uno Y.,Genome Research Group | Uehara S.,Pharmacokinetics and Bioanalysis Center | Uehara S.,Showa Pharmaceutical University | And 2 more authors.
Drug Metabolism and Disposition | Year: 2014

Carboxylesterase (CES) is important for detoxification of a wide range of drugs and xenobiotics and catalyzes cholesterol and fatty acid metabolism. Cynomolgus macaques are widely used in drug metabolism studies; however, cynomolgus CES has not been fully investigated at molecular levels, partly due to the lack of gene information. In this study, we isolated and characterized cDNAs for CES homologous to human CES1, CES2, and CES5A in cynomolgus macaques. By genome analysis, in the cynomolgus macaque genome, three gene sequences were found for CES1(v1 - 3) and CES2(v1 - 3) , whereas one gene sequence was found for CES5A. Cynomolgus CES1 , CES2 , and CES5A genes were located in the genomic regions corresponding to the human genes. We successfully identified CES1v1, CES1v2, CES2v1, CES2v3, and CES5A cDNAs from cynomolgus liver. Sequence analysis showed that amino acid sequences of each CES were highly homologous to that of the human homolog. All five CESs had sequences characteristic for CES enzymes, including the catalytic triad and oxyanion hole loop. By quantitative polymerase chain reaction, the most abundant expression of CES mRNAs among the 10 tissue types analyzed was observed in liver (CES1v1 and CES2v3 mRNAs), jejunum (CES2v1 mRNAs), and kidney (CES1v2 and CES5A mRNA), the organs important for drug metabolism and excretion. The results indicated that cynomolgus macaques express at least five CES genes, which potentially encode intact CES proteins. © 2014 by The American Society for Pharmacology and Experimental Therapeutics.


Uno Y.,Genome Research Group | Uehara S.,Genome Research Group | Uehara S.,Showa Pharmaceutical University | Kohara S.,Genome Research Group | And 2 more authors.
Drug Metabolism and Disposition | Year: 2014

Cynomolgus macaques and rhesus macaques are nonhuman primate species widely used in drug metabolism studies. Cynomolgus CYP2D17, highly homologous to human CYP2D6, metabolizes human CYP2D6 substrates such as bufuralol and dextromethorphan, and the gene is expressed predominantly in liver. Although human CYP2D6 variants account for the variability of the enzyme properties among individuals and populations, genetic variants have not been investigated in CYP2D17. In the present study, CYP2D17 from 87 cynomolgus and 40 rhesus macaques was resequenced. The analysis found a total of 36 nonsynonymous variants, among which 5 were located in substrate recognition sites, the region important for protein function. Twenty-two variants were unique to cynomolgus macaques, of which 11 and 9 were found only in Indochinese and Indonesian cynomolgus macaques, respectively. Eight variants were unique to rhesus macaques. The functional characterization showed that two variant proteins (S188Y and V227I) heterologously expressed in Escherichia coli did not show substantial differences in the rate of bufuralol 1′-hydroxylation as compared with wild-type. However, measuring catalytic activities of the genotyped liver microsomes revealed that I297M and N337D were together significantly associated with higher rates, approximately 2.3- and 11.5-fold, of bufuralol 1′-hydroxylation and dextromethorphan O-demethylation, respectively, in the homozygotes than wild-type animals. The present study provided the first evidence that variability of a CYP2D-dependent metabolism in macaque liver is partly accounted for by CYP2D genotypes. Copyright © 2014 by The American Society for Pharmacology and Experimental Therapeutics.


Ganesan M.,Genome Research Group | Ganesan M.,Osmania University | Bhaskar S.,Genome Research Group | Bhaskar S.,Osmania University | And 11 more authors.
Journal of Diabetes and its Complications | Year: 2011

Introduction: Hypertension and dyslipidemia have been associated with cardiovascular disease (CVD). We investigated the association of candidate gene polymorphisms in angiotensin-converting enzyme (ACE) and cholesterol ester transfer protein (CETP) genes in a cohort of Asian Indian patients with and those without type 2 diabetes. Methods: PCR-based genotyping of insertion/deletion (I/D) polymorphism of ACE (rs4646994) and -629C>A of CETP (rs1800775) was carried out in 520 individuals, of whom 160 had CVD+type 2 diabetes mellitus (T2DM), 90 were CVD patients without T2DM, 150 had T2DM with no cardiovascular complications, and 120 were age- and sex-matched healthy controls. Results: With respect to the ACE gene I/D polymorphism, there was a higher percentage of D/D genotype in CVD+T2DM patients, but it was not statistically significant, while the CETP -629A allele was significantly associated with CVD+T2DM patients (P=.000007; odds ratio=0.46; 95% confidence interval=0.32-0.65) as compared with the normal controls and not with CVD alone. Additive interactions between the AA+I/I genotypes, AC+I/D genotypes, and AC+D/D were identified between the patients and the controls with P values of.0052,.0009, and.0078, respectively. Conclusions: Our study suggests that candidate gene polymorphism -629C>A of CETP may serve as a susceptibility biomarker for CVD in T2DM patients. Analyzing the combined effect of both ACE and CETP genotypes would enhance the sensitivity and specificity of CVD risk estimation in the T2DM patients in our population. © 2011 Elsevier Inc.


Ramakrishnan L.,All India Institute of Medical Sciences | Sachdev H.S.,Sitaram Bhartia Institute of Science and Research | Sharma M.,Indian Council of Medical Research | Abraham R.,All India Institute of Medical Sciences | And 8 more authors.
Lipids in Health and Disease | Year: 2011

Background: Triglycerides is an independent risk factor for coronary artery disease (CAD) and is especially important in Indians because of high prevalence of hypertriglyceridemia in this population. Both genetic and environmental factors determine triglyceride levels. In a birth cohort from India, hypertriglyceridemia was found in 41% of men and 11% of women. Subjects who had high triglycerides had more rapid body mass index (BMI) or weight gain than rest of the cohort throughout infancy, childhood and adolescence. We analysed polymorphisms in APOA5, hepatic lipase and PPARγ genes and investigated their association with birth weight and serial changes in BMI. Results: Polymorphisms in APOA5 (-1131T > C, S19W), PPARγ (Pro12Ala) and hepatic lipase (-514C > T) were studied by polymerase chain reaction (PCR) followed by restriction digestion in 1492 subjects from the New Delhi Birth Cohort (NDBC). We assessed whether these polymorphisms influence lipid and other variables and serial changes in BMI, both individually and together. The risk allele of APOA5 (-1131C) resulted in 23.6 mg/dl higher triglycerides as compared to normal allele (P < 0.001). Risk allele of HL (-514T) was associated with significantly higher HDL2 levels (P = 0.002). Except for the marginal association of PPARγ Pro12Ala variation with a lower conditional weight at 6 months, (P = 0.020) and APOA5 S19W with a higher conditional BMI at 11 yrs of age (P = 0.030), none of the other associations between the gene polymorphisms and serial changes in body mass index from birth to young adulthood were significant. Conclusion: The promoter polymorphism in APOA5 was associated with raised serum triglycerides and that of HL with raised HDL2 levels. None of the polymorphisms had any significant relationship with birth weight or serial changes in anthropometry from birth to adulthood in this cohort. © 2011 Ramakrishnan et al; licensee BioMed Central Ltd.


PubMed | Genome Research Group
Type: Journal Article | Journal: Genetic testing and molecular biomarkers | Year: 2011

Type 2 diabetes mellitus (T2DM) is a major cause of coronary artery disease (CAD) and is responsible for a great deal of morbidity and mortality in Asian Indians. Several gene polymorphisms have been associated with CAD and T2DM in different ethnic groups. This study will give an insight about the association of two selected candidate gene polymorphisms; paraoxonase1 (PON1) Q192R and apolipoprotein A5 (APOA5) -1131T>C were assessed in a cohort of South Indian patients having CAD with and without T2DM. Polymerase chain reaction-based genotyping of PON1 Q192R (rs662) and APOA5-1131T>C (rs662799) polymorphism was carried out in 520 individuals, including 250 CAD patients (160 with T2DM and 90 without T2DM), 150 T2DM patients with no identified CAD, and 120 normal healthy sex- and age-matched individuals as controls. The PON1 192RR genotype and R allele frequency were elevated in both CAD and T2DM patients when compared with controls; however, only CAD patients with T2DM showed a statistical significance (p=0.023; OR=1.49; 95% CI: 1.04-2.12) when compared with controls. The APOA5-1131CC genotype and C allele also showed a significant association between the CAD+T2DM patients when compared with CAD without T2DM and healthy controls (p=0.012; OR=1.71; 95% CI: 1.0-2.67). An additive interaction between the PON1 RR and APOA5 TC genotypes was identified between the T2DM and CAD patients (p=0.028 and 0.0382, respectively). PON1 and APOA5 polymorphisms may serve as biomarkers in the South Indian population to identify T2DM patients who are at risk of developing CAD.

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