Genome-Wide Expression of Azoospermia Testes Demonstrates a Specific Profile and Implicates ART3 in Genetic Susceptibility

Infertility affects about one in six couples attempting pregnancy, with the man responsible in approximately half of the cases. Because the pathophysiology underlying azoospermia is not elucidated, most male infertility is diagnosed as idiopathic. Genome-wide gene expression analyses with microarray on testis specimens from 47 non-obstructive azoospermia (NOA) and 11 obstructive azoospermia (OA) patients were performed, and 2,611 transcripts that preferentially included genes relevant to gametogenesis and reproduction according to Gene Ontology classification were found to be differentially expressed. Using a set of 945 of the 2,611 transcripts without missing data, NOA was further categorized into three classes using the non-negative matrix factorization method. Two of the three subclasses were different from the OA group in Johnsen's score, FSH level, and/or LH level, while there were no significant differences between the other subclass and the OA group. In addition, the 52 genes showing high statistical difference between NOA subclasses (p < 0.01 with Tukey's post hoc test) were subjected to allelic association analyses to identify genetic susceptibilities. After two rounds of screening, SNPs of the ADP-ribosyltransferase 3 gene (ART3) were associated with NOA with highest significance with ART3-SNP25 (rs6836703; p = 0.0025) in 442 NOA patients and 475 fertile men. Haplotypes with five SNPs were constructed, and the most common haplotype was found to be under-represented in patients (NOA 26.6% versus control 35.3%, p = 0.000073). Individuals having the most common haplotype showed an elevated level of testosterone, suggesting a protective effect of the haplotype on spermatogenesis. Thus, genome-wide gene expression analyses were used to identify genes involved in the pathogenesis of NOA, and ART3 was subsequently identified as a susceptibility gene for NOA. These findings clarify the molecular pathophysiology of NOA and suggest a novel therapeutic target in the treatment of NOA

A conditionally immortalized cell line from murine proximal tubule

A conditionally immortalized cell line from murine proximal tubule. We have developed a conditionally immortalized murine cell line with proximal tubule characteristics (tsMPT) and a background suitable for genetic manipulations. tsMPT was derived from the F1 progeny of crosses between: [1] a transgenic mouse harboring a γ-interferon (IFN-γ)-inducible, temperature sensitive SV40 large T antigen gene (tsA58) and [2] mice of the 129/SvEv strain, the background from which most embryonic stem (ES) cells are derived. Under permissive conditions (33°C and in the presence of IFN-γ), tsMPT cells grow rapidly as monolayers with a doubling time of 23 hours; the large T antigen can be detected by immunocytochemistry and by Western blotting. When transferred to non-permissive conditions (39°C, without IFN-γ), the cells undergo differentiation coinciding with the disappearance of the large T antigen. By electron microscopy, tsMPT cells are polarized and show microvilli at their apical surface. tsMPT cells express brush border enzymes γ-glutamyl transpeptidase and carbonic anhydrase IV. They possess Na+-dependent transport systems for Pi, D-glucose and L-proline as well as an amiloride-insensitive Na+-H+ exchanger. Intracellular cAMP generation is stimulated by parathyroid hormone but not by arginine vasopressin. Angiotensinogen mRNA and protein are present in tsMPT with markedly higher levels at non-permissive conditions. tsMPT cells should be a useful model for investigation of the functional features of the proximal tubule epithelium in relation to cellular differentiation

Phase-defined complete sequencing of the HLA genes by next-generation sequencing

Background: The human leukocyte antigen (HLA) region, the 3.8-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, mostly autoimmune diseases. Due to the complex nature of HLA genes, there are difficulties in elucidating complete HLA gene sequences especially HLA gene haplotype structures by the conventional sequencing method. We propose a novel, accurate, and cost-effective method for generating phase-defined complete sequencing of HLA genes by using indexed multiplex next generation sequencing. Results: A total of 33 HLA homozygous samples, 11 HLA heterozygous samples, and 3 parents-child families were subjected to phase-defined HLA gene sequencing. We applied long-range PCR to amplify six HLA genes (HLA-A, -C, -B, DRB1, -DQB1, and –DPB1) followed by transposase-based library construction and multiplex sequencing with the MiSeq sequencer. Paired-end reads (2 × 250 bp) derived from the sequencer were aligned to the six HLA gene segments of UCSC hg19 allowing at most 80 bases mismatch. For HLA homozygous samples, the six amplicons of an individual were pooled and simultaneously sequenced and mapped as an individual-tagging method. The paired-end reads were aligned to corresponding genes of UCSC hg19 and unambiguous, continuous sequences were obtained. For HLA heterozygous samples, each amplicon was separately sequenced and mapped as a genetagging method. After alignments, we detected informative paired-end reads harboring SNVs on both forward and reverse reads that are used to separate two chromosomes and to generate two phase-defined sequences in an individual. Consequently, we were able to determine the phase-defined HLA gene sequences from promoter to 3′- UTR and assign up to 8-digit HLA allele numbers, regardless of whether the alleles are rare or novel. Parent–child trio-based sequencing validated our sequencing and phasing methods. Conclusions: Our protocol generated phased-defined sequences of the entire HLA genes, resulting in high resolution HLA typing and new allele detection

Gene expression in a canine basilar artery vasospasm model: a genome-wide network-based analysis

To investigate the changes of gene expression on the cerebral vasospasm after subarachnoid hemorrhage, we used genome-wide microarray for a canine double-hemorrhage model and analyzed the data by using a network-based analysis. Six dogs were assigned to two groups of three animals: control and hemorrhage. The effects were assessed by the changes in gene expressions in the artery 7 days after the first blood injection. Among 23,914 genes, 447 and 66 genes were up-regulated more than two- and fivefold, respectively, and 332 and 25 genes were down-regulated more than two- and fivefold, respectively. According to gene ontology, genes related to cell communication (P = 5.28E-10), host–pathogen interaction (7.65E-8), and defense–immunity protein activity (0.000183) were significantly overrepresented. The top high-level function for the merged network derived from the network-based analysis was cell signaling, revealing that the subgroup that regulates the quantity of Ca2+ to have the strongest association significance (P = 4.75E-16). Canine microarray analysis followed by gene ontology profiling and connectivity analysis identified several functional groups and individual genes responding to cerebral vasospasm. Ca2+ regulation may play a key role in these gene expression changes and may be involved in the pathogenesis of cerebral vasospasm

Replication study and meta-analysis of human nonobstructive azoospermia in Japanese populations

Recently, a Chinese genomewide association study (GWAS) identified four autosomal single-nucleotide polymorphism (SNP) loci as being significantly associated with risk factors for nonobstructive azoospermia (NOA; P , 5 3 108 ). In the present study, we performed a replication study on two Japanese cohorts from different institutions in order to evaluate whether SNP loci are associated with NOA. The four SNPs (rs12097821, rs2477686, rs10842262, and rs6080550) reported in the Chinese GWAS were genotyped in 490 NOA patients and 1167 controls. To assess the significance of the associations between each of the four SNPs and NOA in the Japanese population, the association results for the two cohorts were combined by meta-analysis. In the meta-analysis, the combined per-allele odds ratios (ORs) for the four SNPs and their respective 95% confidence intervals (CIs) were as follows: rs12097821, OR ¼ 1.10 (CI ¼ 0.89–1.37); rs2477686, OR ¼ 1.11 (CI ¼ 0.87–1.43); rs10842262, OR ¼ 1.11 (CI ¼ 0.94–1.32); and rs6080550, OR ¼ 0.96 (CI ¼ 0.76–1.21). None of the SNPs was significantly associated with NOA (P . 0.05). However, three of four SNPs (rs12097821, rs2477686, and rs10842262) showed associations in the same direction in Japanese men as those reported in the Chinese GWAS. To determine whether the four SNPs are genetic risk factors for NOA, the effect sizes of NOA risk factors require further investigation using larger indepen dent sets of case-control samples of populations, including Japanese and Chinese populations

A Systems Genetics Approach Provides a Bridge from Discovered Genetic Variants to Biological Pathways in Rheumatoid Arthritis

Genome-wide association studies (GWAS) have yielded novel genetic loci underlying common diseases. We propose a systems genetics approach to utilize these discoveries for better understanding of the genetic architecture of rheumatoid arthritis (RA). Current evidence of genetic associations with RA was sought through PubMed and the NHGRI GWAS catalog. The associations of 15 single nucleotide polymorphisms and HLA-DRB1 alleles were confirmed in 1,287 cases and 1,500 controls of Japanese subjects. Among these, HLA-DRB1 alleles and eight SNPs showed significant associations and all but one of the variants had the same direction of effect as identified in the previous studies, indicating that the genetic risk factors underlying RA are shared across populations. By receiver operating characteristic curve analysis, the area under the curve (AUC) for the genetic risk score based on the selected variants was 68.4%. For seropositive RA patients only, the AUC improved to 70.9%, indicating good but suboptimal predictive ability. A simulation study shows that more than 200 additional loci with similar effect size as recent GWAS findings or 20 rare variants with intermediate effects are needed to achieve AUC = 80.0%. We performed the random walk with restart (RWR) algorithm to prioritize genes for future mapping studies. The performance of the algorithm was confirmed by leave-one-out cross-validation. The RWR algorithm pointed to ZAP70 in the first rank, in which mutation causes RA-like autoimmune arthritis in mice. By applying the hierarchical clustering method to a subnetwork comprising RA-associated genes and top-ranked genes by the RWR, we found three functional modules relevant to RA etiology: “leukocyte activation and differentiation”, “pattern-recognition receptor signaling pathway”, and “chemokines and their receptors”

HLA-DPB1*04:01 allele is associated with non-obstructive azoospermia in Japanese patients

Azoospermia is defined by absence of sperm in the semen and can either be caused by obstruction of the seminal tract (obstructive azoospermia) or by defects in spermatogenesis (non-obstructive azoospermia, NOA). Previous studies reported that specific alleles and single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA) region were associated with NOA in East Asians. We attempt to expand upon previous findings by genotyping more HLA genes and to replicate SNP associations by focusing on Japanese NOA patients. HLA typing of six genes (HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1) was done on 355 NOA patients using SSO-Luminex assay while genotyping of two previously reported SNPs (rs498422 and rs3129878) was done on 443 patients and 544 fertile males using TaqMan assay. Association was assessed with Chi squared and logistic regression tests. We found that HLA-DPB1*04:01 [corrected p value, Pc 7.13 9 10-6 ; odds ratio (OR) 2.52], DRB1*13:02 (Pc 4.93 9 10-4 , OR 1.97), DQB1*06:04 (Pc 8.94 9 10-4 , OR 1.91) and rs3129878 (p value 3.98 9 10-4 ; OR 1.32) showed significant association with NOA, however, these loci are in linkage disequilibrium with each other. The conditional logistic regression tests showed that DPB1*04:01 is independently associated with NOA, confirming the involvement of the HLA region in the etiology of NOA in Japanese patients