Rheumatoid arthritis specific anti-Sa antibodies target citrullinated vimentin

Antibodies directed to the Sa antigen are highly specific for rheumatoid arthritis (RA) and can be detected in approximately 40% of RA sera. The antigen, a doublet of protein bands of about 50 kDa, is present in placenta and in RA synovial tissue. Although it has been stated that the Sa antigen is citrullinated vimentin, experimental proof for this claim has never been published. In this study, we investigated the precise nature of the antigen. Peptide sequences that were obtained from highly purified Sa antigen were unique to vimentin. Recombinant vimentin, however, was not recognized by anti-Sa reference sera. In vivo, vimentin is subjected to various post-translational modifications, including citrullination. Since antibodies to citrullinated proteins are known to be highly specific for RA, we investigated whether Sa is citrullinated and found that Sa indeed is citrullinated vimentin. Anti-Sa antibodies thus belong to the family of anticitrullinated protein/peptide antibodies. The presence of the Sa antigen in RA synovial tissue, and the recent observation that vimentin is citrullinated in dying human macrophages, make citrullinated vimentin an interesting candidate autoantigen in RA and may provide new insights into the potential role of citrullinated synovial antigens and the antibodies directed to them in the pathophysiology of RA

Redirecting splicing with bifunctional oligonucleotides

Abstract: Ectopic modulators of alternative splicing are important tools to study the function of splice variants and for correcting mis-splicing events that cause human diseases. Such modulators can be bifunctional oligonucleotides made of an antisense portion that determines target specificity, and a nonhybridizing tail that recruits proteins or RNA/protein complexes that affect splice site selection (TOSS and TOES, respectively, for targeted oligonucleotide silencer of splicing and targeted oligonucleotide enhancer of splicing). The use of TOSS and TOES has been restricted to a handful of targets. To generalize the applicability and demonstrate the robustness of TOSS, we have tested this approach on more than 50 alternative splicing events. Moreover, we have developed an algorithm that can design active TOSS with a success rate of 80%. To produce bifunctional oligonucleotides capable of stimulating splicing, we built on the observation that binding sites for TDP-43 can stimulate splicing and improve U1 snRNP binding when inserted downstream from 50 splice sites. A TOES designed to recruit TDP-43 improved exon 7 inclusion in SMN2. Overall, our study shows that bifunctional oligonucleotides can redirect splicing on a variety of genes, justifying their inclusion in the molecular arsenal that aims to alter the production of splice variants

Conditioned spin and charge dynamics of a single electron quantum dot

In this article we describe the incoherent and coherent spin and charge dynamics of a single electron quantum dot. We use a stochastic master equation to model the state of the system, as inferred by an observer with access to only the measurement signal. Measurements obtained during an interval of time contribute, by a past quantum state analysis, to our knowledge about the system at any time $t$ within that interval. Such analysis permits precise estimation of physical parameters, and we propose and test a modification of the classical Baum-Welch parameter re-estimation method to systems driven by both coherent and incoherent processes.Comment: 9 pages, 9 figure

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma

Protein families encoded by transcripts that are differentially spliced in various types of HCC. Table S2. Bioinformatical prediction of functional changes caused by some of ASEs identified. Table S3. List of tumor suppressors for which AS is dysregulated in various types of HCC. Table S4. List of oncogenes for which AS is dysregulated in various types of HCC. Table S5. List of kinases for which AS is dysregulated in various types of HCC. Table S6. List of transcription factors for which AS is dysregulated in various types of HCC. Table S7. List of genes for which AS is dysregulated in all types of HCC. Table S8. List of genes uniquely dysregulated in HBV-associated HCC. Table S9. List of genes uniquely dysregulated in HCV-associated HCC. Table S10. List of genes uniquely dysregulated in HBV&HCV-associated HCC. Table S11. List of genes uniquely dysregulated in virus-free HCC. Figure S1. Characterization of splicing mysregulation in HCC. Figure S2. Characterization of ASEs that are modified in HBV- and HCV-associated HCC. Figure S3. AS modifications in transcripts encoded by kinases and transcriptions factores in HBV- and HCV-associated HCC. Figure S4. Global profiling of ASE modifications in both HBV&HCV-associated HCC and virus-free-associated HCC. Figure S5. RNA splicing factors in HCC. Figure S6. Modifications to AS of 96 transcripts in response to knockdown of splicing factors with specific siRNAs (PDF 6675 kb

Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells

© 2018 The Author(s). Background: Mounting evidence suggests that one of the ways that cells adapt to hypoxia is through alternative splicing. The aim of this study was firstly to examine the effect of hypoxia on the alternative splicing of cancer associated genes using the prostate cancer cell line PC3 as a model. Secondly, the effect of hypoxia on the expression of several regulators of splicing was examined. Methods: PC3 cells were grown in 1% oxygen in a hypoxic chamber for 48 h, RNA extracted and sent for high throughput PCR analysis at the RNomics platform at the University of Sherbrooke, Canada. Genes whose exon inclusion rate PSI (ψ) changed significantly were identified, and their altered exon inclusion rates verified by RT-PCR in three cell lines. The expression of splice factors and splice factor kinases in response to hypoxia was examined by qPCR and western blotting. The splice factor kinase CLK1 was inhibited with the benzothiazole TG003. Results: In PC3 cells the exon inclusion rate PSI (ψ) was seen to change by >25% in 12 cancer-associated genes; MBP, APAF1, PUF60, SYNE2, CDC42BPA, FGFR10P, BTN2A2, UTRN, RAP1GDS1, PTPN13, TTC23 and CASP9 (caspase 9). The expression of the splice factors SRSF1, SRSF2, SRSF3, SAM68, HuR, hnRNPA1, and of the splice factor kinases SRPK1 and CLK1 increased significantly in hypoxia. We also observed that the splice factor kinase CLK3, but not CLK2 and CLK4, was also induced in hypoxic DU145 prostate, HT29 colon and MCF7 breast cancer cell lines. Lastly, we show that the inhibition of CLK1 in PC3 cells with the benzothiazole TG003 increased expression of the anti-apoptotic isoform caspase 9b. Conclusions: Significant changes in alternative splicing of cancer associated genes occur in prostate cancer cells in hypoxic conditions. The expression of several splice factors and splice factor kinases increases during hypoxia, in particular the Cdc-like splice factor kinases CLK1 and CLK3. We suggest that in hypoxia the elevated expression of these regulators of splicing helps cells adapt through alternative splicing of key cancer-associated genes. We suggest that the CLK splice factor kinases could be targeted in cancers in which hypoxia contributes to resistance to therapy

Caractérisation du système autoantigène/autoanticorps Sa dans la polyarthrite rhumatoïde

La polyarthrite rhumatoïde (PR) est une maladie inflammatoire des articulations caractérisée par la présence de plusieurs autoanticorps dans le sérum des patients atteints. Un de ces autoanticorps, associés spécifiquement aux patients souffrant de PR, se lie à un autoantigène d'environ 50 kD, l'autoantigène Sa. La nature de cet autoantigène est restée jusqu'à présent nébuleuse, étant donné les difficultés de caractérisation. La connaissance des antigènes ciblés par les autoanticorps peut donner des indices importants sur l'étiologie d'une maladie. C'est donc afin de purifier et caractériser cet antigène que les manipulations ont été effectuées. Trois protéines différentes ont pu être identifiées: la vimentine, la calréticuline et la protéine disulfure isomérase. Par étude d'absorption et de réactivité croisée, aucune de ces protéines n'a pu être associée hors de tout doute au Sa. Lors de ce travail des modifications post-traductionnelles ont été suggérées pour expliquer l'apparition d'épitoges auto-antigéniques. En particulier, il a été suggéré que des antigènes citrullinés seraient reconnus spécifiquement par les sérums de patients souffrant de PR. La protéine Sa semble donc être un antigène citrulliné. Des protéines tel l'histone et la MBP, possédant un plus grand pourcentage de résidus arginine sont plus réactives que la BSA qui a un faible pourcentage de résidus arginine. En conclusion, la réactivité de l'antigène Sa semble provenir d'une modification post-traductionnelle, la citrullination des protéines."--Résumé par UMI

Caractérisation du système autoantigène/autoanticorps Sa dans la polyarthrite rhumatoïde

La polyarthrite rhumatoïde (PR) est une maladie inflammatoire des articulations caractérisée par la présence de plusieurs autoanticorps dans le sérum des patients atteints. Un de ces autoanticorps, associés spécifiquement aux patients souffrant de PR, se lie à un autoantigène d'environ 50 kD, l'autoantigène Sa. La nature de cet autoantigène est restée jusqu'à présent nébuleuse, étant donné les difficultés de caractérisation. La connaissance des antigènes ciblés par les autoanticorps peut donner des indices importants sur l'étiologie d'une maladie. C'est donc afin de purifier et caractériser cet antigène que les manipulations ont été effectuées. Trois protéines différentes ont pu être identifiées: la vimentine, la calréticuline et la protéine disulfure isomérase. Par étude d'absorption et de réactivité croisée, aucune de ces protéines n'a pu être associée hors de tout doute au Sa. Lors de ce travail des modifications post-traductionnelles ont été suggérées pour expliquer l'apparition d'épitoges auto-antigéniques. En particulier, il a été suggéré que des antigènes citrullinés seraient reconnus spécifiquement par les sérums de patients souffrant de PR. La protéine Sa semble donc être un antigène citrulliné. Des protéines tel l'histone et la MBP, possédant un plus grand pourcentage de résidus arginine sont plus réactives que la BSA qui a un faible pourcentage de résidus arginine. En conclusion, la réactivité de l'antigène Sa semble provenir d'une modification post-traductionnelle, la citrullination des protéines."--Résumé par UMI