HIF1A gene polymorphisms and human diseases: Graphical review of 97 association studies.

Hypoxia-inducible factors (HIFs) belong to a family of transcription factors (TF) responsive to a low O2 availability, which is often a characteristic feature of solid tumors. The alpha subunit of the HIF heterodimer is O2 -sensitive, and once stabilized in hypoxia, it functions as a master regulator of various genes involved in hypoxia pathway. Changes in the HIF1A (hypoxia inducible factor 1, alpha subunit) nucleotide sequence or expression has been shown to be associated with the development of several diseases. Because of increasing research interest in HIF1A gene a review of association studies was needed. We here reviewed published data on single nucleotide polymorphisms (SNPs) in HIF1A in various diseases; in total, 34 SNPs were tested for an association with 49 phenotypes, and the results were visualized using the Cytoscape software. Among all collected polymorphisms 16 SNPs showed significant associations with 40 different phenotypes, including six SNPs associated with 14 cancer types. Missense SNPs (rs11549465 and rs11549467) within the oxygen-dependent degradation domain were most frequently studied. The study provides a comprehensive tool for researchers working in this area and may contribute to more accurate disease diagnosis and identification of therapeutic targets.

PPAR𝛾 Gene and Atherosclerosis: Genetic Polymorphisms, Epigenetics and Therapeutic Implications.

Atherosclerosis is the leading cause of mortality and morbidity in the developed world. It is characterized by the formation of a plaque in the walls of middle and large arteries leading to macrovascular complications. Several risk factors are included, with diabetes being one of the most important for the onset and development of atherosclerosis. Due to an increase in the prevalence of diabetes in the world, the incidence of diabetic complications (microvascular and macrovascular) is increasing. Peroxisome proliferator-activated receptor γ (PPARγ) plays a important role in atherosclerotic processes. Peroxisome proliferator activated receptor γ belongs to the superfamily of nuclear receptors, has a great presence in fat tissue, macrophages, and regulates gene expression and most of the processes that lead to the onset and development of atherosclerosis. In this review, we discuss the basic patho-physiological mechanisms of atherosclerosis in type 2 diabetes mellitus (T2DM). Furthermore, we discuss the impact of PPARγ polymorphisms, and the epigenetic mechanisms affecting the onset of atherosclerosis, i.e, DNA methylation and demethylation, histone acetylation and deacetylation, and RNA-based mechanisms. Moreover, we add therapeutic possibilities for acting on epigenetic mechanisms in order to prevent the onset and progression of atherosclerosis.

FTO gene variants are associated with growth and carcass traits in cattle.

An important aim in animal breeding is the improvement of growth and meat quality traits. Previous studies have demonstrated that genetic variants in the fat mass and obesity associated (FTO) gene have a relatively large effect on human obesity as well as on body composition in rodents and, more recently, in livestock. Here, we examined the effects of the FTO gene variants on growth and carcass traits in the Slovenian population of Simmental (SS) and Brown (SB) cattle. To validate and identify new polymorphisms, we used sequencing, PCR-RFLP analysis and TaqMan assays in the SS breed and FTO gene variants data from the Illumina BovineSNP50 v1 array for the SB breed. Sequencing of the eight samples of progeny-tested SS sires detected 108 single nucleotide polymorphisms (SNPs) in the bovine FTO gene. Statistical analyses between growth and carcass traits and 34 FTO polymorphisms revealed significant association of FTO variants with lean meat percentage in both breeds. Additionally, FTO SNPs analyzed in SS cattle were associated with fat percentage, bone weight and live weight at slaughter. The FTO gene can thus be regarded as a candidate gene for the marker-assisted selection programs in our and possibly other populations of cattle. Future studies in cattle might reveal novel roles for the FTO gene in shaping carcass traits in livestock species as well as body composition control in other mammals.

Genome-wide in silico screening for microRNA genetic variability in livestock species.

MicroRNAs are a class of non-coding RNAs that post-transcriptionally regulate target gene expression. Previous studies have shown that microRNA gene variability can interfere with its function, resulting in phenotypic variation. Polymorphisms within microRNA genes present a source of novel biomarkers for phenotypic traits in animal breeding. However, little is known about microRNA genetic variability in livestock species, which is also due to incomplete data in genomic resource databases. Therefore, the aim of this study was to perform a genome-wide in silico screening of genomic sources and determine the genetic variability of microRNA genes in livestock species using mirna sniper 3.0 (http://www.integratomics-time.com/miRNA-SNiPer/), a new version of our previously developed tool. By examining Ensembl and miRBase genome builds, it was possible to design a tool-based generated search of 16 genomes including four livestock species: pig, horse, cattle and chicken. The analysis revealed 65 polymorphisms located within mature microRNA regions in these four species, including 28% within the seed region in cattle and chicken. Polymorphic microRNA genes in cattle and chicken were further examined for mapping to quantitative trait loci regions associated with production and health traits. The developed bioinformatics tool enables the analysis of polymorphic microRNA genes and prioritization of potential regulatory polymorphisms and therefore contributes to the development of microRNA-based biomarkers in livestock species. The assembled catalog and the developed tool can serve the animal science community to efficiently select microRNA SNPs for further quantitative and molecular genetic evaluations of their phenotypic effects and causal associations with livestock production traits.

Comparative genomics approach to identify candidate genetic loci for male fertility.

The article presents multi-species, genome-wide, comparative approach to review male fertility-associated loci to contribute to the development of new genetic markers that could be of interest for functional studies and have the potential to be implemented in farm animal breeding programmes. We reviewed 835 male fertility-associated candidate loci from seven species and presented them as bovine orthologues where possible. The candidate loci were identified exploiting seven different research approaches: (i) data from animal models: mouse transgenics and knock-outs (569 genes) and random chemical mutagenesis of mouse genome (31); (ii) animal QTL (69); (iii) genes differentially expressed between fertile and subfertile phenotype in humans and mouse (95); (iv) DNA sequence variations that show specific allele-phenotype interactions (43 in human and 13 in farm animals); (v) germ line-specific small non-coding RNAs (47); (vi) testes expressed genes controlling complex differentiation process of mammalian spermatogenesis (6); and (vii) epigenetically regulated genes (4). According to the number of different research approaches reporting effects of individual genes, we selected 33 most promising candidate genes, which were further in silico analysed for expression levels in testes, genetic variability and top biological functions in functional networks. The aim of this study was to review systematically male fertility-associated candidate loci using integrated information from different study approaches and species, which will further facilitate development of novel genetic markers for selection towards improved fertility in domestic animals.

Database of cattle candidate genes and genetic markers for milk production and mastitis.

A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3'UTRs of candidate genes.

Polymorphisms in the kappa casein (CSN3) gene in horse and comparative analysis of its promoter and coding region.

The major parts of the coding region and promoter of the equine kappa casein (CSN3) gene were sequenced and compared among several species. Four SNPs were identified in the CSN3 gene: two in exon 1 and two in exon 4. The SNPs were genotyped in six Slovenian horse breeds using RFLP and two different PCR-based methods. The highest variation in genotype frequencies was found in the Slovenian cold-blood breed. The SNPs in exon 4 may cause a change in the amino acid sequence and may alter chemical/functional properties of the protein. Using horse-specific primers, we obtained 400 bp of exon 4 sequence from zebra and donkey. Two SNPs within the zebra exon 4 sequence were discovered; both presumably caused amino acid substitutions. Within the equine promoter sequence, 15 SNPs were found and 12 of them could be involved in the gain/loss of potential transcription factor (TF) binding sites. Using a comparative genomics approach, we obtained 1482 bp of the promoter sequence from zebra and donkey. Sequence alignment revealed highly conserved blocks of promoter sequence among nine species (sheep, goat, cow, zebra, donkey, horse, chimp, macaque and human) and clustered these species in three distinct groups. Consensus binding sites for TFs STAT5, C/EBP, NF1 and STAT6, previously demonstrated to be associated with expression, were located within conserved regions. Four promoter regions were tested for specific binding of TFs using electrophoretic mobility shift assays. Predicted binding sites for C/EBP and NF1 were confirmed and one conserved region was specifically detected by a yet-uncharacterized TF.

Molecular mechanisms of cryptorchidism development: update of the database, disease comorbidity, and initiative for standardization of reporting in scientific literature.

Cryptorchidism is a frequent urogenital abnormality that may be present at birth (congenital form) or develop later in life (acquired form). It represents 2-4% full-term male births. It has a potential effect on health; defects in testes descent usually cause impaired spermatogenesis resulting in reduced fertility and increased rates of testicular neoplasia, and testicular torsion. In our previous study, we developed a cryptorchidism gene database which consists of 217 genomic variations associated with development of cryptorchidism in seven mammalian species. The number of studies and study approaches in this field are increasing; therefore, update of the database was needed. The search of multi-omics data was performed and the updated database includes 280 genomic variations associated with cryptorchidism in seven species. The catalog has been complemented with additional data including: number of participants (patients/controls), race/ethnicity, clinical data (age period at diagnosis), congenital/acquired cryptorchidism, unilateral (left/right)/bilateral cryptorchidism, disease comorbidity, and disease ontology. Collected data revealed that cryptorchidism has been reported to be co-present with 150 comorbid conditions, including several syndromes, reproductive, cardiovascular, ophthalmologic, dermatologic, mental, and bone disorders, deafness, and cancer. However, updating the database is time-consuming because of the heterogeneity of results and methodology in scientific literature. The field lacks a standardized format for reporting associations between genotype and phenotype which would enable faster development of the database, data integration, sharing, and facilitate biomarker development. Therefore, in this study, we updated a database of cryptorchidism genes and suggested a first step toward standardization of the format for reporting results of original as well as review studies which we suggest implementing into the scientific literature that reports genotype-cryptorchidism associations.

Diagnostic test for Y chromosome microdeletion screening in male infertility.

Despite the current lack of understanding the mechanism of deleterious effects of Y chromosome microdeletions and their prognostic influence on male subfertility, the Y chromosome microdeletion test is widely used in the diagnostic evaluation of male subfertility. However, currently used diagnostic schemes have not been sufficiently evaluated for their diagnostic performance. The purpose of this study was to analyze a large database of published Y chromosome microdeletions to develop the optimal screening strategy for male subfertility. Therefore, we created a database from genetic and clinical data published in 52 peer-reviewed studies reporting on 512 cases with Y chromosome microdeletions. We developed a computerized procedure with the goal of minimizing the number of genetic markers included in the diagnostic set while maximizing the detection rate in patients with microdeletions. We estimate that 85.6% of all published Y chromosome microdeletions can be covered by a set of six genetic markers (sY84, sY127, sY152, RBMY1, sY147, sY254-DAZ). Inclusion of additional markers brings relatively little to the sensitivity of the test and is potentially related to the population origin.

A Gly482Ser polymorphism of the peroxisome proliferator-activated receptor-gamma coactivator-1 (PGC-1) gene is associated with type 2 diabetes in Caucasians.

The PGC-1 gene has been implicated in the regulation of several genes controlling energy metabolism. The prevalent Gly482Ser polymorphism of the PGC-1 gene has been shown to be associated with type 2 diabetes in some but not all studies. The aim of this study was to analyse whether the Gly482Ser variant is a risk factor for development of type 2 diabetes in Slovene population (Caucasians). Genotyping of the Gly482Ser polymorphism was performed for 545 subjects: 305 patients with type 2 diabetes and 240 non-diabetic controls. The Gly482Ser genotype distribution in patients with type 2 diabetes (AA = 11.5%, AG = 42.3%, GG = 46.2%) differed from genotype distribution in non-diabetic controls (AA = 6.3%, AG = 46.3%, GG = 47.5%), and the AA genotype was associated with 1.9-times increased risk of type 2 diabetes (95% confidence interval 1.0-3.6; P = 0.036). In conclusion, we suggest that the AA genotype of the Gly482Ser polymorphism of the PGC-1 gene should be considered as a risk factor for the development of type 2 diabetes in Caucasians.

A data mining approach to the development of a diagnostic test for male infertility.

The paper presents a database of published Y chromosome deletions and the results of analyzing the database with data mining and other heuristic techniques with the goal of developing a diagnostic test for male infertility. The database describes 382 patients for which 177 markers were tested. Two data mining techniques, clustering and decision tree induction were used, as well as a heuristic set cover algorithm. Clustering was used to group markers according to their appearance across patients, while a heuristic set covering algorithm was used to select as small a set of markers that cover as many patients with deletions as possible. This algorithm created a diagnostic set of 13 markers that cover more than 90% of the patients with deletions. Finally, decision tree induction was used to relate deletion patterns to the severity of the clinical phenotype. A decision tree induced from the data uses 5 markers, all of which are also in the diagnostic set of 13 markers, to show relations between the severity of the clinical phenotype and deletion patterns which have not been known previously.

HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts.

Recent data have linked hypoxia, a classic feature of the tumor microenvironment, to the function of specific microRNAs (miRNAs); however, whether hypoxia affects other types of noncoding transcripts is currently unknown. Starting from a genome-wide expression profiling, we demonstrate for the first time a functional link between oxygen deprivation and the modulation of long noncoding transcripts from ultraconserved regions, termed transcribed-ultraconserved regions (T-UCRs). Interestingly, several hypoxia-upregulated T-UCRs, henceforth named 'hypoxia-induced noncoding ultraconserved transcripts' (HINCUTs), are also overexpressed in clinical samples from colon cancer patients. We show that these T-UCRs are predominantly nuclear and that the hypoxia-inducible factor (HIF) is at least partly responsible for the induction of several members of this group. One specific HINCUT, uc.475 (or HINCUT-1) is part of a retained intron of the host protein-coding gene, O-linked N-acetylglucosamine transferase, which is overexpressed in epithelial cancer types. Consistent with the hypothesis that T-UCRs have important function in tumor formation, HINCUT-1 supports cell proliferation specifically under hypoxic conditions and may be critical for optimal O-GlcNAcylation of proteins when oxygen tension is limiting. Our data gives a first glimpse of a novel functional hypoxic network comprising protein-coding transcripts and noncoding RNAs (ncRNAs) from the T-UCRs category.

Association between the apolipoprotein B signal peptide gene insertion/deletion polymorphism and male infertility.

In male mice heterozygous for a null apolipoprotein B (apoB), allele infertility was noticed. These data led us to investigate a possible role of APOB gene polymorphism and male infertility in humans. In this case-control study, we searched for an association between the insertion/deletion (I/D) polymorphism of the APOB gene and male infertility in 560 Slovene Caucasian men. The study group consisted of 310 infertile patients: 115 with azoospermia and 195 with oligoasthenoteratozoospermia (OAT) and a control group of 250 fertile men. We found a statistically significant difference in the genotype distribution between the two groups (chi2 = 6.315, P = 0.043). A separate analysis of azoospermic and OAT patients demonstrated that significant differences in genotype distribution were limited to the OAT group (chi2 = 7.011, P = 0.030). The presence of the D allele (DD or ID genotypes) conferred a 1.6 risk [chi2 = 6.089, P = 0.014, 95% confidence interval (95% CI) = 1.102-2.347] for male infertility in the OAT group of patients. We did not find a correlation between the I/D polymorphism genotypes and the clinical characteristics of infertile men: sperm concentration (P = 0.102), rapid progressive motility (P = 0.449), normal morphology (P = 0.085) and Johnsen score (P = 0.531). These data suggest that genetic variation in the signal peptide of the APOB gene (I/D polymorphism) might be a risk factor for the development of male infertility.

Frequency distribution of a Cys430Ser polymorphism in peroxisome proliferator-activated receptor-gamma coactivator-1 (PPARGC1) gene sequence in Chinese and Western pig breeds.

Identification of major genes, that genetically impact fat tissue formation is important for successful selection of lean animals with good meat quality. Because of its central role in fat cell differentiation and muscle fibre type determination, PPARGC1 is a potential candidate gene affecting fattening traits and pig meat quality. In this study, a T/A substitution at position 1378 (GenBank accession no. AY346131) in the porcine PPARGC1 gene causing a Cys430Ser amino acid substitution at position 430 was genotyped on a total of 239 animals, including 101 from seven Chinese and 138 from six Western pig breeds. Bayesian analysis revealed that the mean frequency of allele T (Cys) was 92.64 +/- 4.82% in Chinese pigs, and 45.99 +/- 4.13% in Western pigs. The 95% interval of the posterior mean frequency of allele T was 0.82-1.00 in Chinese pigs and 0.38-0.54 in Western pigs, indicating these two groups of pigs diverged at this locus during genetic evolution of the breed. Because marked differences in fat and lean tissue deposition exist between Western and Chinese pig breeds, this Cys430Ser exchange in the PPARGC1 gene deserves further evaluation to determine its phenotypic effect on fattening and carcass traits in commercial pig populations.

Screening for Y chromosome microdeletions in 226 Slovenian subfertile men.

BACKGROUND: The objective of this study was to estimate the frequency of Y chromosome microdeletions in the Slovenian population of infertile men and to analyse the consequences of mutation in respect to clinical severity and prognosis. METHODS: In a controlled clinical study at the university-based medical genetics service and infertility clinic, 226 infertile men undergoing ICSI were tested. The main outcome measures included polymerase chain reaction amplification of 16 genes and gene families and 42 sequence-tagged sites in the non-recombining region of the Y chromosome, semen, testicular volume and testicular histological analysis, serum FSH concentrations, fertilization and respective pregnancy rates. RESULTS: The incidence of deletions was 4.4%: 8.6% in men with azoospermia and 1.5% in men with oligoasthenoteratozoospermia. Isolated gene deletions were not identified. No statistically significant differences in clinical outcome measures were found in patients with mutations versus patients without mutations. High fertilization (49%) and pregnancy (43%) rates with sperm of patients with Y chromosome deletions were obtained. CONCLUSIONS: Testing for gene-specific microdeletions does not contribute significantly to the sensitivity of microdeletion test. Fertilization and pregnancy rates obtained using sperm of patients with Y chromosome deletions were comparable with those achieved in conventional IVF.