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PubMed2006

Common variants in maturity-onset diabetes of the young genes contribute to risk of type 2 diabetes in Finns.

Prior reports have suggested that variants in the genes for maturity-onset diabetes of the young (MODY) may confer susceptibility to type 2 diabetes, but results have been conflicting and coverage of the MODY genes has been incomplete. To complement our previous studies of HNF4A, we examined the other five known MODY genes for association with type 2 diabetes in Finnish individuals. For each of the five genes, we selected 1) nonredundant single nucleotide polymorphisms (SNPs) (r(2)< 0.8 with other SNPs) from the HapMap database or another linkage disequilibrium map, 2) SNPs with previously reported type 2 diabetes association, and 3) nonsynonymous coding SNPs. We tested 128 SNPs for association with type 2 diabetes in 786 index cases from type 2 diabetic families and 619 normal glucose-tolerant control subjects. We followed up 35 of the most significant SNPs by genotyping them on another 384 case subjects and 366 control subjects from Finland. We also supplemented our previous HNF4A results by genotyping 12 SNPs on additional Finnish samples. After correcting for testing multiple correlated SNPs within a gene, we find evidence of type 2 diabetes association with SNPs in five of the six known MODY genes: GCK, HNF1A, HNF1B, NEUROD1, and HNF4A. Our data suggest that common variants in several MODY genes play a modest role in type 2 diabetes susceptibility.

Basic Helix-Loop-Helix Proteins↗
PubMed2006

Common variants in MODY genes increase the risk of gestational diabetes mellitus.

AIMS/HYPOTHESIS: Impaired beta cell function is the hallmark of gestational diabetes mellitus (GDM) and MODY. In addition, women with MODY gene mutations often present with GDM, but it is not known whether common variants in MODY genes contribute to GDM. SUBJECTS AND METHODS: We genotyped five common variants in the glucokinase (GCK, commonly known as MODY2), hepatocyte nuclear factor 1-alpha (HNF1A, commonly known as MODY3) and 4-alpha (HNF4A commonly known as MODY1) genes in 1,880 Scandinavian women (648 women with GDM and 1,232 pregnant non-diabetic control women). RESULTS: The A allele of the GCK -30G-->A polymorphism was more common in GDM women than in control subjects (odds ratio [OR] 1.28 [95% CI 1.06-1.53], p=0.008, corrected p value, p=0.035). Under a recessive model [AA vs GA+GG], the OR increased further to 2.12 (95% CI 1.21-3.72, p=0.009). The frequency of the L allele of the HNF1A I27L polymorphism was slightly higher in GDM than in controls (1.16 [95% CI 1.001-1.34], p=0.048, corrected p value, p=0.17). However, the OR increased under a dominant model (LL+IL vs II; 1.31 [95% CI 1.08-1.60], p=0.007). The rs2144908, rs2425637 and rs1885088 variants, which are located downstream of the primary beta cell promoter (P2) of HNF4A, were not associated with GDM. CONCLUSIONS/INTERPRETATION: The -30G-->A polymorphism of the beta-cell-specific promoter of GCK and the I27L polymorphism of HNF1A seem to increase the risk of GDM in Scandinavian women.

Adult↗
PubMed2006

Aetiological heterogeneity of asymptomatic hyperglycaemia in children and adolescents.

INTRODUCTION: Randomly estimated fasting hyperglycaemia in an asymptomatic individual may represent the first sign of pancreatic beta-cell dysfunction. OBJECTIVE: We aimed at specifying the genetic aetiology of asymptomatic hyperglycaemia in a cohort of children and adolescents. SUBJECTS AND METHODS: We analysed the aetiological diagnosis in 82 non-obese paediatric subjects (38 males) aged 0.2-18.5 years (median: 13.1) who were referred for elucidation of a randomly found blood glucose level above 5.5 mmol/l. In addition to fasting glycaemia and circulating levels of insulin and C-peptide, the subjects were tested by an oral glucose tolerance test and an intravenous glucose tolerance test and screened for mutations in the genes encoding glucokinase (GCK), HNF-1alpha (TCF1), Kir6.2 (KCNJ11) (if aged <2 years) and HNF-4alpha (HNF4A) (those with a positive family history of diabetes). RESULTS AND DISCUSSION: We identified 35 carriers of GCK mutations causing MODY2, two carriers of TCF1 mutations causing MODY3, one carrier of a HNF4A mutation causing MODY1 and one carrier of a KCNJ11 mutation causing permanent neonatal diabetes mellitus. Of the remaining patients, 11 progressed to type 1 diabetes mellitus (T1DM) and 9 had impaired glucose tolerance or diabetes mellitus of unknown origin. In 23 subjects, an impairment of blood glucose levels was not confirmed. We conclude that 39 of 82 paediatric patients (48%) with randomly found fasting hyperglycaemia suffered from single gene defect conditions, MODY2 being the most prevalent. An additional 11 patients (13%) progressed to overt T1DM. The aetiological diagnosis in asymptomatic hyperglycaemic children and adolescents is a clue to introducing an early and effective therapy or, in MODY2, to preventing any future extensive re-investigations.

Adolescent↗
PubMed2026

Tissue-derived extracellular matrix hydrogels instruct epigenetic adaptation in metastatic colonization.

The extracellular matrix (ECM) plays a central role in regulating tumor progression and metastatic colonization by providing biochemical and mechanical signals that shape cancer cell fate. However, most organoid culture systems rely on basement membrane extracts that fail to reproduce the tissue-specific extracellular environments encountered during metastasis. Here, we develop tissue-derived decellularized matrix hydrogels to reconstruct organ-specific microenvironments and investigate epigenetic adaptation to ECM cues during metastatic colonization. Patient-derived colorectal cancer organoids cultured in colon-derived matrices exhibited enhanced maintenance of stem-like phenotypes and colon-specific chromatin accessibility landscapes compared with cultures grown in basement membrane extracts, demonstrating improved physiological relevance for primary tumor modeling. When exposed to matrices derived from secondary organs, the organoids showed distinct growth phenotypes accompanied by rapid, tissue-dependent chromatin accessibility remodeling, indicating that ECM composition alone can reshape regulatory programs governing metastatic adaptation. Notably, liver-derived matrices selectively activated hepatocyte nuclear factor 4 alpha (HNF4A)-associated transcriptional networks and created a context-specific dependence on c-MET signaling for survival. Functional perturbation of HNF4A or c-MET signaling confirmed that both are required for organoid formation specifically within the liver matrix environment. Together, these findings establish tissue-derived matrix hydrogels as instructive bioactive materials that actively regulate cancer cell epigenetic states and reveal microenvironment-specific therapeutic vulnerabilities during early metastatic colonization.

Journal Article↗
PubMed2004

Genetic variation near the hepatocyte nuclear factor-4 alpha gene predicts susceptibility to type 2 diabetes.

The Finland-United States Investigation Of NIDDM Genetics (FUSION) study aims to identify genetic variants that predispose to type 2 diabetes by studying affected sibling pair families from Finland. Chromosome 20 showed our strongest initial evidence for linkage. It currently has a maximum logarithm of odds (LOD) score of 2.48 at 70 cM in a set of 495 families. In this study, we searched for diabetes susceptibility variant(s) at 20q13 by genotyping single nucleotide polymorphism (SNP) markers in case and control DNA pools. Of 291 SNPs successfully typed in a 7.5-Mb interval, the strongest association confirmed by individual genotyping was with SNP rs2144908, located 1.3 kb downstream of the primary beta-cell promoter P2 of hepatocyte nuclear factor-4 alpha (HNF4A). This SNP showed association with diabetes disease status (odds ratio [OR] 1.33, 95% CI 1.06-1.65, P = 0.011) and with several diabetes-related traits. Most of the evidence for linkage at 20q13 could be attributed to the families carrying the risk allele. We subsequently found nine additional associated SNPs spanning a 64-kb region, including the P2 and P1 promoters and exons 1-3. Our results and the independent observation of association of SNPs near the P2 promoter with diabetes in a separate study population of Ashkenazi Jewish origin suggests that variant(s) located near or within HNF4A increases susceptibility to type 2 diabetes.

Basic Helix-Loop-Helix Leucine Zipper Transcriptio↗
PubMed2026

Comprehensive bioinformatics analysis identifies candidate ciliogenesis-related genes preferentially associated with N0-stage lung squamous cell carcinoma.

PURPOSE: There is few research on which genes play an important role in tumors without lymph metastasis. This study aimed to identify candidate molecular alterations preferentially associated with N0-stage LUSC. METHODS: we conducted a comprehensive bioinformatics analysis using publicly available The Cancer Genome Atlas (TCGA) data. Differentially expressed genes (DEGs) were identified separately by comparing N0 tumors and N+ tumors with normal lung tissues. Genes dysregulated in both N0 and N+ tumors were excluded to identify candidate N0-associated genes PPI networks were constructed using STRING and Cytoscape, with module analysis performed via MCODE. Hub genes were identified using multiple Cytohubba algorithms. Functional enrichment analyses were conducted using GO, and KEGG pathways using DAVID. Gene interaction networks were further explored using GeneMANIA. Immune cell infiltration was evaluated with TIMER. Associations with pathological stage and patient survival were assessed using GEPIA and other relevant tools. RESULTS: A total of 1103 candidate N0-associated DEGs were identified, including 748 upregulated and 355 downregulated genes. The PPI network contained five major MCODE clusters. One cluster (MCODE 4) included TTC30A, TTC30B, BBS7, and KIF3B genes implicated in ciliogenesis. TTC30B showed significant differential expression across pathological stages in the overall LUSC cohort. Seven consensus hub genes (ERBB2, CHUK, CASP8, NOTCH1, HNF4A, CREBBP, and IRS1) were identified based on their consistent ranking across multiple CytoHubba algorithms. Upregulated candidate N0-associated genes were primarily enriched in immune-related processes, including B-cell-mediated immunity and humoral responses, whereas downregulated genes were enriched in lysosomal and trans-Golgi network-related pathways. Exploratory immune infiltration analyses identified associations between the four ciliogenesis-related genes and several immune cell populations. CONCLUSIONS: This study identified candidate molecular signatures preferentially associated with N0-stage LUSC, including ciliogenesis-related genes and consensus hub genes. These findings provide hypotheses regarding molecular features of N0-stage LUSC and warrant further validation in independent cohorts and experimental studies.

Humans↗
PubMedDate not supplied

The role of transcription factors in maturity-onset diabetes of the young.

The study of maturity-onset diabetes of the young (MODY), an autosomal dominant form of early-onset diabetes mellitus characterised by defective insulin secretion has been extremely successful in two ways. Firstly it has enabled definitive diagnosis for patients. This allows more accurate prediction of disease and treatment requirements. Secondly it has facilitated an increased understanding of the genes and pathways that are crucial for normal beta-cell function. Five of the six MODY genes, TCF1 (encoding HNF-1alpha), TCF2 (encoding HNF-1beta) HNF4A, insulin promoter factor (IPF)1, and NEUROD1, are transcription factors that operate in a complex network of gene regulation. Several genes have been shown to be regulated by the MODY transcription factors in a beta-cell specific manner. This includes the co-regulation of HNF-1alpha and HNF-4alpha by each other. The exact mechanism of how mutations in these transcription factors result in diabetes in humans remains unknown. However, current opinion favours pleiotropic adverse effects on many genes; extensive in vitro and in vivo studies of these genes has highlighted their importance in both glucose sensing-insulin secretion coupling and maintaining the fully differentiated beta-cell phenotype.

Alleles↗
PubMed2003

The orphan nuclear receptor HNF4alpha determines PXR- and CAR-mediated xenobiotic induction of CYP3A4.

The drug metabolizing enzyme cytochrome P450 3A4 (CYP3A4) is thought to be involved in the metabolism of nearly 50% of all the drugs currently prescribed. Alteration in the activity or expression of this enzyme seems to be a key predictor of drug responsiveness and toxicity. Currently available studies indicate that the ligand-activated nuclear receptors pregnane X receptor (PXR; NR1I2) and constitutive androstane receptor (CAR; NR1I3) regulate CYP3A4 expression. However, in cell-based reporter assays, CYP3A4 promoter activity was most pronounced in liver-derived cells and minimal or modest in non-hepatic cells, indicating that a liver-specific factor is required for physiological transcriptional response. Here we show that the orphan nuclear receptor hepatocyte nuclear factor-4alpha (HNF4alpha; HNF4A) is critically involved in the PXR- and CAR-mediated transcriptional activation of CYP3A4. We identified a specific cis-acting element in the CYP3A4 gene enhancer that confers HNF4alpha binding and thereby permits PXR- and CAR-mediated gene activation. Fetal mice with conditional deletion of Hnf4alpha had reduced or absent expression of CYP3A. Furthermore, adult mice with conditional hepatic deletion of Hnf4alpha had reduced basal and inducible expression of CYP3A. These data identify HNF4alpha as an important regulator of coordinate nuclear-receptor-mediated response to xenobiotics.

Animals↗
PubMed2024

Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes.

Type 2 diabetes (T2D) genome-wide association studies (GWASs) often overlook rare variants as a result of previous imputation panels' limitations and scarce whole-genome sequencing (WGS) data. We used TOPMed imputation and WGS to conduct the largest T2D GWAS meta-analysis involving 51,256 cases of T2D and 370,487 controls, targeting variants with a minor allele frequency as low as 5&#x2009;&#xd7;&#x2009;10-5. We identified 12 new variants, including a rare African/African American-enriched enhancer variant near the LEP gene (rs147287548), associated with fourfold increased T2D risk. We also identified a rare missense variant in HNF4A (p.Arg114Trp), associated with eightfold increased T2D risk, previously reported in maturity-onset diabetes of the young with reduced penetrance, but observed here in a T2D GWAS. We further leveraged these data to analyze 1,634 ClinVar variants in 22 genes related to monogenic diabetes, identifying two additional rare variants in HNF1A and GCK associated with fivefold and eightfold increased T2D risk, respectively, the effects of which were modified by the individual's polygenic risk score. For 21% of the variants with conflicting interpretations or uncertain significance in ClinVar, we provided support of being benign based on their lack of association with T2D. Our work provides a framework for using rare variant GWASs to identify large-effect variants and assess variant pathogenicity in monogenic diabetes genes.

Diabetes Mellitus, Type 2↗
PubMed2006

Hepatocyte nuclear factor 4alpha is essential for embryonic development of the mouse colon.

BACKGROUND & AIMS: Hepatocyte nuclear factor 4 alpha (HNF4alpha) is a transcription factor that has been shown to be required for hepatocyte differentiation and development of the liver. It has also been implicated in regulating expression of genes that act in the epithelium of the lower gastrointestinal tract. This implied that HNF4alpha might be required for development of the gut. METHODS: Mouse embryos were generated in which Hnf4a was ablated in the epithelial cells of the fetal colon by using Cre-loxP technology. Embryos were examined by using a combination of histology, immunohistochemistry, DNA microarray, reverse-transcription polymerase chain reaction, electrophoretic mobility shift assays, and chromatin immunoprecipitation analyses to define the consequences of loss of HNF4alpha on colon development. RESULTS: Embryos were recovered at E18.5 that lacked HNF4alpha in their colons. Although early stages of colonic development occurred, HNF4alpha-null colons failed to form normal crypts. In addition, goblet-cell maturation was perturbed and expression of an array of genes that encode proteins with diverse roles in colon function was disrupted. Several genes whose expression in the colon was dependent on HNF4alpha contained HNF4alpha-binding sites within putative transcriptional regulatory regions and a subset of these sites were occupied by HNF4alpha in vivo. CONCLUSIONS: HNF4alpha is a transcription factor that is essential for development of the mammalian colon, regulates goblet-cell maturation, and is required for expression of genes that control normal colon function and epithelial cell differentiation.

Animals↗
PubMed2006

Expression of endoderm stem cell markers: evidence for the presence of adult stem cells in human thyroid glands.

OBJECTIVE: Adult stem cells have been detected in several human tissues. The object of this study was to investigate whether they also occur in the human thyroid gland. DESIGN: The expression of the stem cell marker Oct- 4 and the early endodermal markers GATA-4 and HNF4alpha was analyzed in histologic slides and cultured cells derived from goiters, in the FRTL5 cell line, and the HTh74, HTC, C643, and XTC133 thyroid carcinoma cell lines. MAIN OUTCOME: Stem cell markers were detectable in all primary cultures whereas in the differentiated FRTL5 cell line no expression was observed. Expression of stem cell marker mRNA was not affected by thyrotropin (TSH) stimulation and did not decrease when cells underwent several passages. Immunostaining of cultured cells and of histologic slides of goitrous tissues showed only single cells that were immunoreactive for Oct-4, GATA-4, and HNF4a. Expression of Oct-4 but not of endodermal marker GATA-4 was also detectable in some thyroid carcinoma cell lines. Fluorescence-activated cell sorter (FACS) analysis demonstrated cell populations that were positive for either Oct-4, GATA-4, or HNF4alpha but negative for thyroglobulin. When these putative, FACS-sorted stem cell populations were further analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR), expression of all stem cell markers and of Pax8 but not of thyroglobulin mRNA was detectable. CONCLUSIONS: These data provide evidence for the presence of adult stem and precursor cells of endodermal origin in the human thyroid gland.

Animals↗
PubMed2005

Temporal gene expression profiling of liver from periparturient dairy cows reveals complex adaptive mechanisms in hepatic function.

Long-term molecular adaptations in liver from high-producing dairy cows are virtually unknown. Liver from five Holstein cows was biopsied at -65, -30, -14, +1, +14, +28, and +49 days relative to parturition for transcript profiling using a microarray consisting of 7,872 annotated cattle cDNA inserts. More than 5,000 cDNA elements represented on the microarray were expressed in liver. From this set we identified 62 differentially expressed genes related to physiological state, with a false discovery rate threshold of P = 0.20. The dominant expression pattern consisted of upregulation from day -30 through day +1, followed by downregulation through day +28. There was a threefold decrease from day -65 through day +14 in expression of IGFBP3, GSTM5, and PDPK1. These genes mediate IGF-I transport, oxidative stress, and glucose homeostasis, respectively. IGFBP3, EIF4B, and GSTM5 mRNA levels were positively correlated with blood serum total protein. Correlation analysis showed positive associations between serum nonesterified fatty acids and mRNA expression for SAA1, CPT1A, ACADVL, and TFAP2A. Transcript levels of ACSL1, PPARA, and TFAP2A were positively correlated with serum beta-hydroxybutyrate. Expression patterns for certain genes (e.g., IGFBP3, HNF4A, GPAM) revealed adaptations commencing well ahead of parturition, suggesting they are regulated by factors other than periparturient hormonal environment. Results provide evidence that hepatic inflammatory responses occurring near parturition initiate or augment adipose catabolism. In this context, cytokines, acute-phase proteins, and serum nonesterified fatty acids are key players in periparturient cow metabolism. We propose a model for integrating gene expression, metabolite, and liver composition data to explain physiological events in placenta, adipose, and liver during the periparturient period.

Adaptation, Physiological↗
PubMed2003

Candidate gene association study in type 2 diabetes indicates a role for genes involved in beta-cell function as well as insulin action.

Type 2 diabetes is an increasingly common, serious metabolic disorder with a substantial inherited component. It is characterised by defects in both insulin secretion and action. Progress in identification of specific genetic variants predisposing to the disease has been limited. To complement ongoing positional cloning efforts, we have undertaken a large-scale candidate gene association study. We examined 152 SNPs in 71 candidate genes for association with diabetes status and related phenotypes in 2,134 Caucasians in a case-control study and an independent quantitative trait (QT) cohort in the United Kingdom. Polymorphisms in five of 15 genes (33%) encoding molecules known to primarily influence pancreatic beta-cell function-ABCC8 (sulphonylurea receptor), KCNJ11 (KIR6.2), SLC2A2 (GLUT2), HNF4A (HNF4alpha), and INS (insulin)-significantly altered disease risk, and in three genes, the risk allele, haplotype, or both had a biologically consistent effect on a relevant physiological trait in the QT study. We examined 35 genes predicted to have their major influence on insulin action, and three (9%)-INSR, PIK3R1, and SOS1-showed significant associations with diabetes. These results confirm the genetic complexity of Type 2 diabetes and provide evidence that common variants in genes influencing pancreatic beta-cell function may make a significant contribution to the inherited component of this disease. This study additionally demonstrates that the systematic examination of panels of biological candidate genes in large, well-characterised populations can be an effective complement to positional cloning approaches. The absence of large single-gene effects and the detection of multiple small effects accentuate the need for the study of larger populations in order to reliably identify the size of effect we now expect for complex diseases.

ATP-Binding Cassette Transporters↗
PubMed2006

Association studies of variants in the genes involved in pancreatic beta-cell function in type 2 diabetes in Japanese subjects.

Because impaired insulin secretion is characteristic of type 2 diabetes in Asians, including Japanese, the genes involved in pancreatic beta-cell function are candidate susceptibility genes for type 2 diabetes. We examined the association of variants in genes encoding several transcription factors (TCF1, TCF2, HNF4A, ISL1, IPF1, NEUROG3, PAX6, NKX2-2, NKX6-1, and NEUROD1) and genes encoding the ATP-sensitive K(+) channel subunits Kir6.2 (KCNJ11) and SUR1 (ABCC8) with type 2 diabetes in a Japanese cohort of 2,834 subjects. The exon 16 -3c/t variant rs1799854 in ABCC8 showed a significant association (P = 0.0073), and variants in several genes showed nominally significant associations (P < 0.05) with type 2 diabetes. Although the E23K variant rs5219 in KCNJ11 showed no association with diabetes in Japanese (for the K allele, odds ratio [OR] 1.08 [95% CI 0.97-1.21], P = 0.15), 95% CI around the OR overlaps in meta-analysis of European populations, suggesting that our results are not inconsistent with the previous studies. This is the largest association study so far conducted on these genes in Japanese and provides valuable information for comparison with other ethnic groups.

ATP-Binding Cassette Transporters↗
PubMed2002

Searching for type 2 diabetes genes on chromosome 20.

Genome scans in families with type 2 diabetes identified a putative locus on chromosome 20q. For this study, linkage disequilibrium mapping was used in an effort to narrow a 7.3-Mb region in an Ashkenazi type 2 diabetic population. The region encompassed a 1-logarithm of odds (LOD) interval around the microsatellite marker D20S107, which gave a LOD score of >3 in linkage analysis of a combined Caucasian population. This 7.3-Mb region contained 25 known and 99 predicted genes. Predicted single nucleotide polymorphisms (SNPs) were chosen from public databases and validated. Two SNPs were unique to the Ashkenazi. Here, 91 SNPs with a minor allele frequency of >or=10% were genotyped in pooled DNA from 150 case subjects and 150 control subjects of Ashkenazi Jewish descent. The SNP association study showed that SNP rs2664537 in the TIX1 gene had a significant P value of 0.035, but the finding did not replicate in an additional case pool. In addition, HNF4a and Mybl2 were screened for mutations and new polymorphisms. No mutations were identified, and a new nonsynonymous SNP (R687C in exon 14 of Mybl2) was found. The limits to this type of association study are discussed.

Aged↗
PubMed2003

Genetic variation in the small heterodimer partner gene and young-onset type 2 diabetes, obesity, and birth weight in U.K. subjects.

The orphan receptor small heterodimer partner (SHP, NR0B2) modulates the transcription activity of the MODY1 gene HNF4a. Mutations in SHP were found in 7% of Japanese obese young-onset type 2 diabetic patients and were associated with moderate obesity and increased birth weight. We investigated SHP in 1927 U.K. subjects, examining relationships with type 2 diabetes, obesity, and birth weight. Sequencing of the coding region of SHP in 122 obese, young-onset type 2 diabetic patients detected the polymorphism G171A. The polymorphism was not associated with diabetes in case control or familial association studies. The A allele (frequency 0.07) was not associated with obesity in type 2 diabetic subjects (n = 348), their parents (n = 272), or young nondiabetic adults (n = 925). However, the rare (<1%) AA homozygotes had a raised BMI in each cohort; this was significant when all cohorts were combined (Z score = 0.67 AA vs. -0.05 G/x, P = 0.02). There was no association with corrected birth weight in 382 normal babies, but the only AA baby was 4,069 g. Our study suggests that genetic variation in SHP is unlikely to be common in the predisposition to diabetes, obesity, or increased birth weight in U.K. Caucasians.

Adolescent↗
PubMed2005

Polymorphisms in the SLC2A2 (GLUT2) gene are associated with the conversion from impaired glucose tolerance to type 2 diabetes: the Finnish Diabetes Prevention Study.

Impaired insulin secretion is a fundamental defect in type 2 diabetes. The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) in the genes regulating insulin secretion (SLC2A2 [encoding GLUT2], GCK, TCF1 [encoding HNF-1alpha], HNF4A, GIP, and GLP1R) are associated with the conversion from impaired glucose tolerance (IGT) to type 2 diabetes in participants of the Finnish Diabetes Prevention Study. With the exception of SLC2A2, other genes were not associated with the risk of type 2 diabetes. All four SNPs of SLC2A2 predicted the conversion to diabetes, and rs5393 (AA genotype) increased the risk of type 2 diabetes in the entire study population by threefold (odds ratio 3.04, 95% CI 1.34-6.88, P = 0.008). The risk for type 2 diabetes in the AA genotype carriers was increased in the control group (5.56 [1.78-17.39], P = 0.003) but not in the intervention group. We conclude that the SNPs of SLC2A2 predict the conversion to diabetes in obese subjects with IGT.

Analysis of Variance↗
PubMed2005

Comparative genomics on Wnt3-Wnt9b gene cluster.

WNT signals, transduced through Frizzled (FZD) receptors with extracellular WNT-binding domain and cytoplasmic Dishevelled-binding domain, are implicated in carcinogenesis and embryogenesis. WNT3-WNT9B (WNT14B) locus (17q21.31) and WNT3A-WNT9A (WNT14) locus (1q42.13) are paralogous regions within the human genome. Here, the rat Wnt3 and Wnt9b genes were identified and characterized by using bioinformatics. Wnt3 and Wnt9b genes at rat chromosome 10q32.1 were clustered in head-to-head manner with an interval of about 24 kb within AC105632.3 genome sequence. The rat Wnt3 gene, consisting of five exons, encoded a 355-aa protein with N-terminal signal peptide, 24 conserved Cys residues and two Asn-linked glycosylation sites. The rat Wnt9b gene, consisting of four exons, encoded a 359-aa protein with N-terminal signal peptide, 24 conserved Cys residues and one Asn-linked glycosylation site. The rat Wnt3 core promoter showed 80.5% nucleotide identity with human WNT3 core promoter, while rat Wnt9b core promoter showed 45.6% nucleotide identity with human WNT9B core promoter. MYB (c-Myb), ELK1, POU2F1 (OCT1), HNF4A (HNF-4), COMP1, NFYA (NF-Y) and NKX2-5 binding sites were conserved between rat Wnt3 and human WNT3 core promoters. The Wnt3-Wnt9b intergenic conserved region (IGCR), corresponding to nucleotide position 124747-125252 of AC105632.3 genome sequence, showed 85.6% nucleotide identity with human WNT3-WNT9B IGCR. GC content of rat Wnt3-Wnt9b IGCR was 59.5%. Wnt3-Wnt9b IGCR was predicted as regulatory element rather than gene because cDNA or EST derived from Wnt3-Wnt9b IGCR was not identified. This is the first report on the rat Wnt3 and Wnt9b genes as well as on comparative genomics on the Wnt3-Wnt9b gene cluster.

Amino Acid Sequence↗