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PubMed1986

[hGH and molecular biology].

This review summarizes the progress recently made through the approaches provided by DNA recombinant technology in the knowledge of the human growth hormone (hGH) gene and of the molecular basis of hGH deficiencies. The growth hormone gene is part of a family of five structural genes located on the long arm of human chromosome 17, over a distance of 55 kilobases (kb), and oriented in the same transcriptional 5' to 3' direction in the order 5' hGH-N, hCS-L, hCS-A, hGH-V, and hCS-B 3'. The five genes contain five exons interrupted by four introns, and they display a high sequence homology. GH and CS genes show class differences on their 3' side, approximately 100 base pairs beyond the polyadenylation sites. Analysis of homology regions has permitted to define duplication units useful to trace the evolution process of the cluster. The hGH-N gene codes for the normal, pituitary, 22K human growth hormone. The hGH-V genes codes for a variant peptide that can be expressed in vitro in transgenomic systems, but that is not known to be expressed in vivo. The hCS-A and -B genes each code for human chorionic somatomammotropin. They specify the same mature hormone and are expressed at different levels in term placenta. The hCS-L gene appears to be an unexpressed pseudogene and has a single base substitution, located in a splicing site, that would preclude normal mRNA maturation.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed2002

Mutation screening and association of human retinoid X receptor gamma variation with lipid levels in familial type 2 diabetes.

Both type 2 diabetes (T2DM) and familial combined hyperlipidemia have been mapped to human chromosome 1q21-q24. This region includes the retinoid X receptor gamma (RXRgamma), which is a strong candidate for both glucose and lipid metabolism. Retinoid X receptors form heterodimers with a variety of nuclear receptors, including peroxisome-proliferator-activated receptors alpha and gamma (PPARalpha and PPARgamma), and are synergistic targets for drugs that alter glucose and lipid metabolism. We hypothesized that RXRgamma variation could explain the linkage of diabetes and lipid disorders to this region. We screened each of the 10 exons, the flanking intronic sequences, the 3' untranslated region, and the 5' flanking region. We identified 14 variants, none of which altered the coding sequence. Of the 10 variants examined in a diabetes case-control study, three showed nominal (p < 0.05) associations with T2DM. We subsequently typed four variants in all members of the 63 multiplex families used in our previous linkage analysis. No individual variant showed excess transmission to offspring with T2DM using a transmission disequilibrium test and only a single rare haplotype showed evidence of an association with T2DM. Likewise, neither individual variants nor haplotypes were associated with either fasting or post-challenge glucose in non-diabetic subjects. In contrast, three of the four variants were associated with fasting free fatty acid (FFA) levels (p = 0.024-0.00044) and two variants were associated with triglyceride levels (p < 0.05). These findings were supported by the association of several haplotypes with FFA and triglyceride levels. RXRgamma haplotypes were also associated with several measures of pancreatic beta-cell function, consistent with the proposed role of lipid metabolism in insulin secretion. These data suggest that RXRgamma may contribute to disordered lipid metabolism in members of familial T2DM kindreds, but this gene is unlikely to explain the linkage of T2DM with this region.

Blood Glucose↗
PubMed2001

Empirical comparison of DRG variants using cardiovascular surgery data: initial results of a project at 18 German hospitals.

In 2000, the responsibility for selecting a DRG variant for use in Germany was assigned to a body comprising representatives of hospitals and insurers called the Self-Administration Board (or Board in this paper). To help the Board, we applied cardiac surgery data from 18 German hospitals to eight different DRG variants. The error caused by bad coding quality could be minimized this way, since all diagnoses and procedures in cardiac surgery must be recorded for quality assurance purposes. To match the German code to the appropriate code required by the DRG variant, we created mapping tables whenever needed. As far as cardiac surgery is concerned, the Australian AR-DRG and the French GHM variants provided the best medical relevance, while the AR-DRG variant considered the level of severity better. Other variants would have to be updated to better reflect the level of medical complexity. Three main causes for wrong grouping could be identified for all systems: incomplete mapping, not enough reference to multidisciplinary treatments, and system construction problems.

Cardiovascular Diseases↗
PubMed1982

An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.

Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

Animals↗
PubMed2026

Neurodegeneration risk variants promote lysosomal TMEM106B fibril accumulation.

Variants in TMEM106B and GRN, which encode lysosomal proteins, interact through unknown mechanisms to increase the risk of age-related cognitive decline and neurodegeneration. Here, we show that these variants converge on a single molecular intermediate: the cleaved intra-lysosomal fibril core of TMEM106B, a precursor to amyloid fibrils that accumulate in the aging brain. A protein-coding TMEM106B risk variant (p.T185) drives fibril core accumulation by impairing its degradation and GRN risk variants amplify this effect. Mice over-expressing the fibril core develop hallmarks of neurodegeneration, and cryo-electron tomography reveals intra-lysosomal fibrils in cultured neurons, mice, and diseased human brain. In GRN-mutation carriers, in whom fibril burden is greatest, fibrils extrude through ruptured lysosomal membranes. These findings identify intra-lysosomal TMEM106B fibrillization as a convergent neurodegeneration mechanism and potential therapeutic target.

Journal Article↗
PubMed2026

Germline noncoding risk variants influence clonal hematopoiesis through altered hematopoietic enhancer activity.

Clonal hematopoiesis of indeterminate potential (CHIP) is a precursor condition characterized by the expansion of mutant hematopoietic stem and progenitor cell (HSPC) clones that increases the risk of hematologic malignancies. Although genome-wide association studies have identified multiple non-coding loci associated with CHIP susceptibility, their mechanisms remain unclear. We hypothesized that CHIP risk variants alter enhancer activity in HSPCs. To test this, we screened 1,374 non-coding variants from 51 CHIP-associated loci using a Massively Parallel Reporter Assay (MPRA) in the CD34+ fraction of MUTZ-3 cells. We identified 87 regulatory variants across 32 loci. Targeted genome editing in hematopoietic cells and complementary reporter assays in primary human HSPCs validated enhancer activity for variants regulating NKD2, FLT3, and MSI2. Functional studies demonstrated that increased MSI2 expression, modeling the effect of the CHIP risk allele, promotes clonal expansion of TET2-deficient HSPCs, providing a mechanistic link between inherited non-coding variation and CHIP clonal expansion.

Journal Article↗
PubMed2001

The hormone sensitive lipase gene in familial combined hyperlipidemia and insulin resistance.

BACKGROUND: Insulin resistance in the most common familial dyslipidemia, familial combined hyperlipidemia (FCHL), could be due to variations in the hormone sensitive lipase (HSL) gene. MATERIALS AND METHODS: The coding region of the HSL gene was screened with the single strand conformation polymorphism analysis in probands of 27 FCHL families with 228 members. In addition, the C-60G promoter substitution of the HSL gene was determined by the restriction fragment length polymorphism analysis in these subjects. RESULTS: No variants in the coding region of the HSL gene were found and the allele frequencies of the C-60G promoter substitution and the silent variant (G3138A) in the 3' untranslated region did not differ between 110 control subjects and 27 probands with FCHL. However, in control women the C-60G substitution was associated with high body mass index [30.6 +/- 0.9 kg m(-2) (mean +/- SD) in subjects with the C/G genotype and 24.8 +/- 4.6 in subjects with the C/C genotype, P = 0.012], and in control men with high rates of insulin-stimulated whole body glucose uptake (70.1 +/- 14.7 vs. 56.7 +/- 14.2 micromol kg(-1) min(-1), P = 0.014). In 228 FCHL family members this substitution was associated with high low-density lipoprotein cholesterol levels in men (4.51 +/- 1.12 vs. 5.17 +/- 1.28 mmol L(-1), P = 0.049), but not in women. CONCLUSIONS: The HSL gene is not a major gene for FCHL. However, the - 60G allele of this gene may affect body weight, insulin sensitivity and serum cholesterol levels.

Adult↗
PubMed1997

Cloning and characterization of human cDNAs encoding a protein with high homology to rat intestinal development protein OCI-5.

We constructed a lambda complementary DNA expression library from the mitoxantrone-resistant human gastric carcinoma cell line EPG85-257RNOV. The library was screened by differential hybridization (resistant cell line against non-resistant cell variant). By this procedure we found five independent cDNA clones representing one single gene that has much higher expression in the mitoxantrone-resistant cell line EPG85-257RNOV than in the non-resistant variant EPG85-257P. One of the cDNA clones (MXR7) contains a complete open reading frame (ORF) encoding a 580-amino acid polypeptide. Amino acid and nucleotide sequence analysis revealed that this gene codes the human variant of a rat intestinal development protein OCI-5.

Amino Acid Sequence↗
PubMed1999

Mutational analysis of the proopiomelanocortin gene in Caucasians with early onset obesity.

OBJECTIVE: Mutations in the human gene encoding the polyhormone peptide proopiomelanocortin (POMC) are associated with obesity in rare cases and the gene co-localizes with a reported quantitative trait loci (QTL) for variations in circulating leptin levels and fat mass on human chromosome 2p21. In this study we have used polymerase chain reaction (PCR) and single strand conformation polymorphism (SSCP) analysis, to test whether variations in the human POMC gene are associated with human obesity. DESIGN AND SUBJECTS: Primary mutational analysis was performed on the coding region of the POMC gene and 500 bp of the putative promoter region, by single strand conformational analysis and sequencing, in 56 subjects with juvenile onset obesity (body mass index (BMI) > or = 31 kg/m2 at the draft board examination). The prevalence of two polymorphisms were further studied in 156 obese and 205 control subjects, and in a population based cohort of 380 extensively characterized young healthy subjects. RESULTS: We have identified a total of six gene variants, five were silent nucleotide substitutions (No51(promoter) g-->c, No670(5'UTR)g-->a, No4512(codon6)c-->t Cys/Cys, No7726(codon116)c-->t Leu/Leu) of which one was prevalent (No8246(3'UTR)c-->t) and one variant changed an amino acid (No8086(codon236)g-->c Arg/Gln). The amino acid substitution was only seen in one subject. Comparing the prevalence of the frequent No8246 silent polymorphism, in an association study comprising 156 subjects with juvenile onset obesity and 205 randomly sampled control subjects (mean BMI 23.5+/-4.7 kg/m2), did not show any relationship to obesity. Also, comparing the prevalence of a known 9bp insertion/deletion variant in the coding region of the gene between obese and lean, showed no association to obesity. Furthermore, analyzing a population based cohort of 380 young healthy Caucasians for the prevalent 3'UTR polymorphism as well as the 9 bp insertion/deletion variant did not show any association to deviations in body fat contents or fasting serum leptin concentrations. CONCLUSION: In conclusion, it is unlikely that variations in the coding region and the putative promoter of the POMC gene are a major cause of juvenile onset human obesity.

3' Untranslated Regions↗
PubMed1998

Structural and functional analysis of the porcine secretory carrier membrane protein 1 gene (SCAMP1).

The secretory carrier membrane proteins (SCAMPs) are highly conserved integral vesicle membrane components of the post-Golgi secretory and endocytic pathways. We have isolated and characterized the porcine SCAMP1 cDNA and gene coding for a variant of the SCAMP family. The SCAMP1 cDNA has a length of 3827 bp including a 133-bp 5' and 2701-bp 3' untranslated region. The mRNA has an open reading frame of 1014 nt coding for a protein of 338 amino acids with a calculated molecular mass of 37.9 kDa and a pI of 7.9. The porcine SCAMP1 is 97.04% identical with the human and rat paralogs, respectively. The SCAMP1 gene consists of nine exons with sizes ranging from 78 to 2842 bp and spans at least 70 kb of genomic DNA on porcine Chromosome (Chr) 2q21-q22. The promoter of the SCAMP1 gene is TATA-box-less, and transcription starts at a G-nucleotide 133 nt upstream the start codon.

Amino Acid Sequence↗
PubMed1999

Genetics of HIV-1 infection: chemokine receptor CCR5 polymorphism and its consequences.

The chemokine receptor gene, CCR5, has become a central theme in studies of host genetic effects on HIV-1 pathogenesis ever since the discovery that the CCR5 molecule serves as a major cell surface co-receptor for the virus. A growing number of genetic variants within the coding and 5' regulatory region of CCR5 have been identified, several of which have functional consequences for HIV-1 pathogenesis. Here we review the CCR5 literature describing CCR5 polymorphism and the functional ramifications that several of these variants have on HIV-1 infection and progression to AIDS. The multiplicity of CCR5 genetic effects on HIV-1 disease underscores the critical importance of this gene in controlling AIDS pathogenesis and provides the logic for develop-ment of therapeutic strategies that target the interaction of HIV-1 envelope and CCR5 in HIV-1 associated disease.

Genetic Variation↗
PubMed1999

A new amyloidogenic transthyretin variant, [D38A], detected by electrospray ionization/mass spectrometry.

A new variant of transthyretin (TTR) was detected by mass spectrometry (MS) in a 63-year-old Japanese female patient suffering from amyloidosis. TTR was analyzed by 2-dimensional liquid chromatography coupled with electrospray ionization MS. Variant TTR showed extra peaks in addition to normal TTR peaks. The extra peaks were about 44 Da smaller than normal TTR peaks, and the abundance of variant peaks showed about 80% of the corresponding normal free and adduct peaks. Direct genomic DNA sequencing of TTR exon 2 showed both adenine and cytosine in the position corresponding to the second base of codon 38. This codes for a variant alanine (GCT) as well as the normal aspartic acid (GAT), indicating that the case is heterozygous for the substitution, [D38A].

Amyloid↗
PubMed1998

Expression of estrogen receptor beta messenger RNA variant in breast cancer.

Estrogen receptor (ER) beta is expressed in a number of tissues, including the breast. We have recently shown that ER-beta mRNA is regulated by estradiol (E2) and that antiestrogens antagonize E2 induction of ER-beta mRNA. Here, we identify by reverse transcription-PCR and by the RNase protection assay a mRNA coding for a variant of ER-beta that is coexpressed with wild-type ER-beta in the ER-alpha-negative, estrogen-independent breast cancer cell line MDA-MB-231 and in malignant breast tumor specimens. In contrast, this variant was not seen in the tested normal breast tissue. Sequence analysis of the ER-beta variant PCR product revealed the absence of 139 bp within the hormone-binding domain. This ER-beta deletion corresponds precisely to the entire exon 5 of ER-alpha. The ER-beta variant protein is predicted to lack part of the hormone-binding domain and may bind E2 with lower affinity than the wild-type ER-beta protein.

Base Sequence↗
PubMed1993

Variants of the MMPI 2-7-8 code type: schizotypal correlates of high point 2, 7, or 8.

Our study sought to evaluate whether examination of the high-point scale among subjects with a 2-7-8 parent configuration on the MMPI could assist in the identification of individuals with schizotypal features. Additionally, this study compared male 2-7-8 subjects to female 2-7-8 subjects to determine whether gender mediates endorsement of items associated with these features. Subjects (N = 106) who produced a 2-7-8 parent profile were subdivided according to high point (2, 7, or 8), and the three subgroups were subsequently compared on other self-report measures associated with schizotypal attributes. Subgroup comparisons revealed that the High 8 and High 2 groups produced a pattern of responding consistent with schizotypal characteristics. In contrast, the at-risk status of the High 7 group appears doubtful. Comparisons based on gender generally revealed no differences among female and male 2-7-8 subjects.

Adolescent↗
PubMed2002

Analysis of the relationship between mannose-binding lectin (MBL) genotype, MBL levels and function in an Australian blood donor population.

The mannose-binding lectin (MBL) pathway of complement activation is an important component of innate host defence. Numerous studies have described associations between the MBL genotype, MBL levels and disease susceptibility. However, genotyping and quantitative assays used in these studies have frequently been limited, and comprehensive data examining the interaction between structural and coding MBL genetic variants, MBL antigenic levels and MBL functional activity are lacking. Such data may be important for accurate planning and interpretation of studies of MBL and disease. This study has examined MBL in a cohort of 236 Australian blood donors. Five MBL promoter and coding single nucleotide polymorphisms were genotyped using polymerase chain reaction-sequence-specific priming (PCR-SSP). Plasma levels of MBL antigen were quantified using a double-antibody enzyme-linked immunosorbent assay (ELISA), and functional MBL levels were quantified using a mannan-binding assay. Activation of the complement pathway by MBL was measured in a C4-deposition assay. Significant associations were found between both coding and promoter polymorphisms and MBL antigenic and functional levels. There was significant correlation between the results of MBL double-antibody, mannan-binding and C4-deposition assays. Comprehensive MBL genotyping and functional MBL quantitation using mannan-binding and C4-deposition assays have the potential to be highly informative in MBL disease association studies.

Australia↗
PubMed2002

Lack of SCN1A mutations in familial febrile seizures.

PURPOSE: Mutations in the voltage-gated sodium channel subunit gene SCN1A have been associated with febrile seizures (FSs) in autosomal dominant generalized epilepsy with febrile seizures plus (GEFS+) families and severe myoclonic epilepsy of infancy. The present study assessed the role of SCN1A in familial typical FSs. METHODS: FS families were selected throughout a collaborative study of the Italian League Against Epilepsy. For each index case, the entire coding region of SCN1A was screened by denaturant high-performance liquid chromatography. DNA fragments showing variant chromatograms were subsequently sequenced. RESULTS: Thirty-two FS families accounting for 91 affected individuals were ascertained. Mutational analysis detected a single coding variant (A3169G) on exon 16. The extended analysis of all family members and 78 normal controls demonstrated that A3169G did not contribute to the FS phenotype. CONCLUSIONS: Our study demonstrated that SCN1A is not frequently involved in common FSs and suggested the involvement of specific FS genes.

Adolescent↗
PubMed1994

Expression of two variants of the human mu opioid receptor mRNA in SK-N-SH cells and human brain.

A partial mu opioid receptor gene was isolated from a human genomic library using a mouse delta opioid receptor cDNA as a probe. Using information from this genomic clone and the published human mu receptor, MOR1, a cDNA was isolated from SK-N-SH mRNA that codes for a variant of the MOR1 mRNA, MOR1A. The presence of MOR1A is also shown in human brain using RT-PCR. MOR1A differs from MOR1 in that the 3' terminal intron has not been removed. An in-frame termination codon is found four amino acids after the 5' consensus splice site, making MOR1A eight amino acids shorter than MOR1. Both receptors show similar ligand binding and coupling to cAMP in CHO-K1 cells. The C-terminal differences between MOR1 and MOR1A could have effects on receptor coupling or receptor transport and localization.

Alternative Splicing↗