Recently it has become clear that only a small percentage (7%) of disease-associated single nucleotide polymorphisms (SNPs) are located in protein-coding regions, while the remaining 93% are located in gene regulatory regions or in intergenic regions. Thus, the understanding of how genetic variations control the expression of non-coding RNAs (in a tissue-dependent manner) has far-reaching implications. We tested the association of SNPs with expression levels (eQTLs) of large intergenic non-coding RNAs (lincRNAs), using genome-wide gene expression and genotype data from five different tissues. We identified 112 cis-regulated lincRNAs, of which 45% could be replicated in an independent dataset. We observed that 75% of the SNPs affecting lincRNA expression (lincRNA cis-eQTLs) were specific to lincRNA alone and did not affect the expression of neighboring protein-coding genes. We show that this specific genotype-lincRNA expression correlation is tissue-dependent and that many of these lincRNA cis-eQTL SNPs are also associated with complex traits and diseases.

IntroductionThe use of the 5-alpha reductase inhibitors (5-ARIs) finasteride and dutasteride for prostate cancer prevention is still under debate. The FDA recently concluded that the increased prevalence of high-grade tumors among 5-ARI-treated patients must not be neglected, and they decided to disallow the use of 5-ARIs for prostate cancer prevention. This study was conducted to verify the effects of finasteride on prostate cell migration and invasion and the related enzymes/proteins in normal human and tumoral prostatic cell lines.Materials and MethodsRWPE-1, LNCaP, PC3 and DU145 cells were cultivated to 60% confluence and exposed for different periods to either 10 µM or 50 µM finasteride that was diluted in culture medium. The conditioned media were collected and concentrated, and MMP2 and MMP9 activities and TIMP-1 and TIMP-2 protein expression were determined. Cell viability, migration and invasion were analyzed, and the remaining cell extracts were submitted to androgen receptor (AR) detection by western blotting techniques. Experiments were carried out in triplicate.ResultsCell viability was not significantly affected by finasteride exposure. Finasteride significantly downregulated MMP2 and MMP9 activities in RWPE-1 and PC3 cells and MMP2 in DU145 cells. TIMP-2 expression in RWPE-1 cells was upregulated after exposure. The cell invasion of all four tested cell lines was inhibited by exposure to 50 µM of finasteride, and migration inhibition only occurred for RWPE-1 and LNCaP cells. AR was expressed by LNCaP, RWPE-1 and PC3 cells.ConclusionsAlthough the debate on the higher incidence of high-grade prostate cancer among 5-ARI-treated patients remains, our findings indicate that finasteride may attenuate tumor aggressiveness and invasion, which could vary depending on the androgen responsiveness of a patient’s prostate cells.

Objective Multiple single‐nucleotide polymorphisms ( SNP s) conferring susceptibility to osteoarthritis ( OA ) mark imbalanced expression of positional genes in articular cartilage, reflected by unequally expressed alleles among heterozygotes (allelic imbalance [ AI ]). We undertook this study to explore the articular cartilage transcriptome from OA patients for AI events to identify putative disease‐driving genetic variation. Methods AI was assessed in 42 preserved and 5 lesioned OA cartilage samples (from the Research Arthritis and Articular Cartilage study) for which RNA sequencing data were available. The count fraction of the alternative alleles among the alternative and reference alleles together ( φ ) was determined for heterozygous individuals. A meta‐analysis was performed to generate a meta‐ φ and P value for each SNP with a false discovery rate ( FDR ) correction for multiple comparisons. To further validate AI events, we explored them as a function of multiple additional OA features. Results We observed a total of 2,070 SNP s that consistently marked AI of 1,031 unique genes in articular cartilage. Of these genes, 49 were found to be significantly differentially expressed (fold change <0.5 or >2, FDR <0.05) between preserved and paired lesioned cartilage, and 18 had previously been reported to confer susceptibility to OA and/or related phenotypes. Moreover, we identified notable highly significant AI SNP s in the CRLF 1 , WWP 2 , and RPS 3 genes that were related to multiple OA features. Conclusion We present a framework and resulting data set for researchers in the OA research field to probe for disease‐relevant genetic variation that affects gene expression in pivotal disease‐affected tissue. This likely includes putative novel compelling OA risk genes such as CRLF 1 , WWP 2 , and RPS 3 .

Taken together, the use of decellularized bioscaffold and subcutaneous MSCs seems to be a potential approach to obtain bioengineered blood vessels, in the presence of EIGF supplementation.

-The objective of this study was to describe daily body weight (BW) changes in the first 100 days of lactation in confined dairy cows and to associate BW loss with productive and reproductive performance. Data included 26,344 daily BW measurements of 372 Holsteins calving between June 2011 and June 2012 in a commercial herd in the South of Brazil. Cows were automatically weighed and were assigned according to parity. Individual measurements were smoothed using cubic splines, generating nadir BW, days to nadir BW and the BW loss (absolute and relative values). This approach used days in milk (DIM) as a single smoothing variable. Body weight at calving differed across parities: 570.5, 653.5, and 699.9 kg, for the 1st, 2nd and 3rd and subsequent parities, respectively. Body weight at nadir also differed across parities: 521.5, 608.8, and 647.3 kg, respectively. Mean days from calving BW to nadir BW and mean loss of BW (kg) from calving to nadir BW did not differ across parities, but relative BW change (kg/100 kg) was larger in animals in first parity (-8.4 kg/100 kg) than second parity (-6.6 kg/100 kg). However, cows in first parity had more chances for good reproduction than cows in third and subsequent parities (44.0% vs. 30.7%, respectively). There was no difference in the probability of adequate reproduction (pregnant until 180 DIM) among cows with low, medium, or high milk yield. Furthermore, cows with low and medium BW loss (below 60 kg of BW change) showed more likelihood to adequate reproduction than cows with high BW loss (above 60 kg of BW): 45.5 and 45.8% vs. 24.4%, respectively. Improvements in fertility of dairy cows should be achieved by minimizing body weight loss in early lactation.

Despite fast advances in genomics and proteomics, monoclonal antibodies (mAbs) are still a valuable tool for areas such as the evolution of basic research in stem cells and cancer, for immunophenotyping cell populations, diagnosing and prognosis of diseases, and for immunotherapy. To summarize different subtractive immunization approaches successfully used for the production of highly specific antibodies, we identified scientific articles in NCBI PubMed using the following search terms: subtractive immunization, monoclonal antibody, tolerization, neonatal, high-zone tolerance, masking immunization. Patent records were also consulted. From the list of results, we included all available reports, from 1985 to present, that used any enhanced immunization technique to produce either polyclonal or monoclonal antibodies. Our examination yielded direct evidence that these enhanced immunization techniques are efficient in obtaining specific antibodies to rare epitopes, with different applications, such as to identify food contaminants or tumor cells.

What is already known about this topic?  The multifactorial autoimmune blistering skin disease pemphigus foliaceus presents a genetic susceptibility component that is not fully understood.  Although pemphigus foliaceus is rare worldwide, it reaches the prevalence of 1.5% to 3% in some regions of Brazil, the highest ever reported for an autoimmune disease.  LncRNA polymorphisms have been associated with some complex diseases but were not yet studied in any form of pemphigus. What does this study add?  Genetic variation of lncRNA may influence susceptibility to pemphigus foliaceus via its effect on lncRNA structure, on transcription of nearby genes, and on microRNA-lncRNA interactions.

Objective: The aim of this study was to identify key determinants of the interactive osteoarthritis (OA) pathophysiological processes of subchondral bone and cartilage. Methods:We performed RNA sequencing on macroscopically preserved and lesioned OA subchondral bone of patients that underwent joint replacement surgery due to OA (N=24 pairs; 6 hips, 18 knees, RAAK-study). Unsupervised hierarchical clustering and differential expression analyses were performed. Results were combined with previously identified, differentially expressed genes in cartilage (partly overlapping samples) as well as with recently identified OA risk genes . Results:We identified 1569 genes significantly differentially expressed between lesioned and preserved subchondral bone, including CNTNAP2 (FC=2.4, FDR=3.36x10 -5 ) and STMN2 (FC=9.6, FDR=3.36x10 -3 ). Among the identified genes, 305 were also differentially expressed and with same direction of effects in cartilage, including IL11 and CHADL, recently acknowledged OA susceptibility genes. Upon differential expression analysis stratifying for joint site, we identified 509 genes exclusively differentially expressed in subchondral bone of the knee, such as KLF11 and WNT4. These exclusive knee genes were enriched for involvement in epigenetic processes, characterized by for instance HIST1H3J and HIST1H3H. Conclusion:To our knowledge, we are the first to report on differential gene expression patterns of paired OA subchondral bone tissue using RNA sequencing. Among the most consistently differentially expressed genes with OA pathophysiology in both bone and cartilage were IL11 and CHADL. As these genes were recently also identified as robust OA risk genes they classify as attractive druggable targets acting on two OA disease relevant tissues.