Estrogen receptor α (ERα) and estrogen receptor β (ERβ) regulate different sets of gene expression, and have different ligand responses, which make the estrogen tissue-specific. Thus, the estrogen receptor (ER) subtype-selective ligands can improve the target-site selectivity and decrease the off-target effect. In order to discover the selective ER subtype ligands with novel scaffolds, in this work three-dimensional (3D) pharmacophore models of the ERα ligands (Hypo 1) and the ERβ ligands (Hypo 2) were established (correlation coefficients were 0.959 and 0.966) and validated (R=0.936 and 0.879; enrichment factors (EFs) at 2% were 16.2 and 8.4; areas under the concentration–time curve (AUC) of the receiver operating curve (ROC) were 0.88 and 0.91) using the Discovery Studio 4.0 software package. Hypo 1 and Hypo 2 were then employed for virtual screening and ten hits were found as potential candidate leads. Based on their ERα/ERβ binding affinity results by fluorescence polarization technology, two of these leads, AH-262/34334025 (AH) and AG-670/08803023 (AG) with novel scaffolds were identified as selective ERα ligands. A molecular docking study was also performed, which provided the explanation for the ER subtype preferences for AH and AG.
Emerging evidence demonstrates that microRNAs, as important endogenous posttranscriptional regulators, are essential for bone remodeling and regeneration. Undoubtedly, microRNA-based gene therapies show great potential to become novel approaches against bone-related diseases, including osteoporosis and associated fractures. The major obstacles for continued advancement of microRNA-based therapies in clinical application include their poor in vivo stability, nonspecific biodistribution, and unwanted side effects. Appropriate chemical modifications and delivery vectors, which improve the biological performance and potency of microRNA-based drugs, hold the key to translating miRNA technologies into clinical practice. Thus, this review summarizes the current attempts and existing deficiencies of chemical modifications and delivery systems applied in microRNA-based therapies for osteoporosis and osteoporotic fractures to inform further explorations.
High throughput analyses were performed to detect epistatic QTL in 17 body dimension and organ weight traits from a large F2 pig population derived from a White Duroc and Erhualian intercross. The analyses used a nested test framework to handle multiple tests and a combined search algorithm to map epistatic QTL with empirical genome-wide thresholds derived via prior permutation. Alternative statistical models (e.g. including vs. excluding carcass weight as a covariate) were tested to develop an in-depth understanding of the role of epistasis in these kinds of traits. Epistasis signals were detected in only two or three traits under each statistical model studied. The interaction component of each pair of epistatic QTL explained a small proportion (0.7 to 2.1%) of the phenotypic variance in general. About half of the detected epistatic QTL pairs involved one of the two major QTL on porcine chromosomes 7 and 4. In those traits, the Erhualian allele consistently increased the phenotypes for the chromosome 7 QTL but decreased them for the chromosome 4 QTL. Models including carcass weight as covariate detected epistasis in body dimension traits whereas those excluding carcass weight found epistasis in organ weight traits. In addition, the epistasis results suggested that a QTL on chromosome 14 could be important for a number of organ weight traits. Using the high-throughput analysis tool to examine different statistical models was essential for the generation of a complete picture of epistasis in a whole category of traits.
Abstract Background We applied a range of genome-wide association (GWA) methods to map quantitative trait loci (QTL) in the simulated dataset provided by the 12 th QTLMAS workshop in order to derive an effective strategy. Results A variance component linkage analysis revealed QTLs but with low resolution. Three single-marker based GWA methods were then applied: Transmission Disequilibrium Test and single marker regression, fitting an additive model or a genotype model, on phenotypes pre-corrected for pedigree and fixed effects. These methods detected QTL positions with high concordance to each other and with greater refinement of the linkage signals. Further multiple-marker and haplotype analyses confirmed the results with higher significance. Two-locus interaction analysis detected two epistatic pairs of markers that were not significant by marginal effects. Overall, using stringent Bonferroni thresholds we identified 9 additive QTL and 2 epistatic interactions, which together explained about 12.3% of the corrected phenotypic variance. Conclusion The combination of methods that are robust against population stratification, like QTDT, with flexible linear models that take account of the family structure provided consistent results. Extensive simulations are still required to determine appropriate thresholds for more advanced model including epistasis.
Abstract Gout is a chronic disease of monosodium urate crystal deposition in the setting of hyperuricemia that typically presents with recurrent flares of acute inflammatory arthritis that occur due to innate immune response to deposited crystals. The molecular mechanism of the progression from hyperuricemia to clinical gout is poorly understood. Here we provide insights into this progression from a genetic study of 2.6 million people, including 120,282 people with gout. We detected 376 loci and 410 genetically independent signals (148 new loci in urate and gout). We identified 1,768 candidate genes with subsequent pathway analysis revealing urate metabolism, type 2 diabetes, and chromatin modification and structure as top pathways in gout. Genes located within or statistically linked to significant GWAS loci were prioitized for their potential to control the progression from hyperuricemia to gout. This identified strong candidate immune genes involved in epigenetic remodelling, cell osmolarity, and regulation of NLRP3-inflammasome activity. The genetic association signal at XDH , encoding the urate-producing enzyme xanthine oxidoreductase (XOR), co-localizes with genetic control of XDH expression, but only in the prostate. We demonstrate XOR activity and urate production in the mouse prostate, and use single-cell RNA sequence data to propose a model of urate reuptake, synthesis, and secretion by the prostate. The gout-associated loci were over-represented for genes implicated in clonal hematopoeiesis of indeterminate potential (CHIP) and Mendelian randomization analysis provided evidence for a causal role of CHIP in gout. In concert with implication of epigenomic regulators, this provides support for epigenomic remodelling as causal in gout. We provide new insights into the molecular pathogenesis of gout and identify an array of candidate genes for a role in the inflammatory process of gout.
Loss-of-function mutations in the X-linked gene FLNA can lead to abnormal neuronal migration, vascular and cardiac defects, and congenital intestinal pseudo-obstruction (CIPO), the latter characterized by anomalous intestinal smooth muscle layering. Survival in male hemizygotes for such mutations is dependent on retention of residual FLNA function but it is unclear why a subgroup of males with mutations in the 5′ end of the gene can present with CIPO alone. Here, we demonstrate evidence for the presence of two FLNA isoforms differing by 28 residues at the N-terminus initiated at ATG+1 and ATG+82. A male with CIPO (c.18_19del) exclusively expressed FLNA ATG+82, implicating the longer protein isoform (ATG+1) in smooth muscle development. In contrast, mutations leading to reduction of both isoforms are associated with compound phenotypes affecting the brain, heart, and intestine. RNA-seq data revealed three distinct transcription start sites, two of which produce a protein isoform utilizing ATG+1 while the third utilizes ATG+82. Transcripts sponsoring translational initiation at ATG+1 predominate in intestinal smooth muscle, and are more abundant compared with the level measured in fibroblasts. Together these observations describe a new mechanism of tissue-specific regulation of FLNA that could reflect the differing mechanical requirements of these cell types during development.
Sero-negative rheumatoid arthritis (RA) is a highly heterogeneous disorder with only a few additive loci identified to date. We report a genotypic variability-based genome-wide association study (vGWAS) of six cohorts of sero-negative RA recruited in Europe and the US that were genotyped with the Immunochip. A two-stage approach was used: (1) a mixed model to partition dichotomous phenotypes into an additive component and non-additive residuals on the liability scale and (2) the Levene's test to assess equality of the residual variances across genotype groups. The vGWAS identified rs2852853 (P = 1.3e-08, DHCR7) and rs62389423 (P = 1.8e-05, near IRF4) in addition to two previously identified loci (HLA-DQB1 and ANKRD55), which were all statistically validated using cross validation. DHCR7 encodes an enzyme important in cutaneous synthesis of vitamin D and DHCR7 mutations are believed to be important for early humans to adapt to Northern Europe where residents have reduced ultraviolet-B exposure and tend to have light skin color. IRF4 is a key locus responsible for skin color, with a vitamin D receptor-binding interval. These vGWAS results together suggest that vitamin D deficiency is potentially causal of sero-negative RA and provide new insights into the pathogenesis of the disorder.
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