PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells

Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.

AB0151 THE ROLE OF PLASMA MICROVESICLES IN LVVs: NOT ONLY BIOLOGICAL MARKERS

Background

Microvesicles (MVs) are membrane enclosed extracellular vesicles released upon cellular activation and stress, which maintains features and maintain features and constituents of their parental cells. Large vessel vasculitides (LVVs) are inflammatory conditions of the wall of large-sized arteries, mainly represented by giant cell arteritis (GCA) and Takayasu arteritis (TA). Arterial stenosis and dilatation directly affect prognosis and, according to latest EULAR guidelines can be investigated by positron emission tomography and magnetic resonance angiography. Endothelial cells are believed to play a role in the pathogenesis of LVVs and circulating microvesicles could be a biomarker of vessel wall injury.

Objectives

To verify whether arterial wall derived-MVs detectable in the blood of TA patients and expressing bioactive molecules potentially involved in arterial injury, inflammation and remodeling could correlate with clinical and radiological features of those patients.

Methods

Platelet was obtained from 112 LVV pts (73 TA, 39 GCA). Plasma flow cytometry was performed with anti-CD14, CD16, anti-CD144 (VE-cadherin, an endothelial marker), anti-CD140a/b (PDGF receptor A/B a vascular stromal marker), anti-HMGB1, anti-PTX3, Mitotracker green and MitoSox, which are expression of mitochondrial moieties and ROS. Vascular imaging was carried out by angio-RM and PET. Circulating microvesicles from LVVs patients were correlated with disease characteristics, namely CRP, NIH activity, PGA, ITAS2010, ITAS2011 activity, immunosuppressant intake (IS), intake of glucocorticoids (yes/no) and biologics, and daily dose of glucocorticoids as well as radiological parameters. Pearson’s and Spearman’s correlation tests were used for parametric and non-parametric analysis. The SPSS IBM Software was used for statistics.

Results

The number of total MVs negatively correlate to CRP levels positively correlate to IS (p 0.052 and 0.013). CD 14 and 16 + MVs do not correlate with disease activity, extent or vascular inflammation at either MR or PET. PTX3+ MVs positively correlate to disease activity (NIH criteria and VAS), steroid intake, and disease extent (number of vessels at imaging). CD144+ MVs negatively correlate to IS and positively to SUV max at FDG PET. CD140a+ MVs significantly correlate to disease activity (PGA, VAS, and ITAS2010). Mitotracker+ Mvs negatively correlate to SNR max and positively to FDG-PET positivity.

Conclusion

Monocyte-derived MVs, despite being increased in LVV, do not correlate with disease activity, extent and vascular inflammation. Despite this, endothelial and stromal-derived MVs reflect some disease-related domains including clinical activity and imaging activity at PET. Furthermore, bioactive signals on MVs such as the long pentraxin PTX3 and mitochondria are more promising biomarkers. Accordingly, other studies have shown that systemic pentraxin-3 levels reflect vascular enhancement and progression in Takayasu arteritis, being PCR and ESR more a mirror of the burden of systemic inflammation. However, further studies are required to verify the pathogenic role of MVs in LVVs and to assess the impact of potential confounders such as therapy.

References

[1]van Niel G et al, Nat Rev Mol Cell Biol. 2018

[2]Mason JC. Nat Rev Rheumatol. 2010

[3]Tombetti et al, Arthirtis Research therapy 2014

Disclosure of Interests

None declared

OP0056 PLASMA MICROVESICLES AS LIQUID BIOPSIES OF THE ARTERIAL WALL IN LARGE VESSEL VASCULITIS

Background:

Large-vessel vasculitides comprise Takayasu arteritis (TA)and giant cell arteritis (GCA). Arterial stenosis and dilatation directly affect prognosis but the mechanism(s) underlying remodeling of the vessel wall have not been identified. Microvesicles (MVs) are membrane-enclosed extracellular vesicles released upon cellular activation and stress and as a consequence of environmental inflammation. MVs maintain features and constituents of their parental cells. They have been proposed to serve as potential liquid biopsies in oncology.

Objectives:

To verify whether arterial wall derived-MVs are recognizable in the blood of TA patients and express bioactive molecules potentially involved in arterial injury, inflammation and remodeling.

Methods:

Platelet was obtained from 112 LVV pts (73 TA, 39 GCA), 42 age and age- and sex-matched healthy controls (HC) and 30 pts with severe carotid atherosclerosis requiring vascular surgery. Plasma flow cytometry was performed with anti-CD14, CD16, anti-CD144 (VE-cadherin, an endothelial marker), anti-CD140a/b (PDGF receptor A/B a vascular stromal marker), anti-HMGB1, anti-PTX3, mitotracker green (that identifies mithochondrial moieties) and mitosox (that revels mitochondrial reactive oxygen species). MVs were identified by physical parameters using Gigamix beads. Medium- to large-sized MVs were defined as MVs with >240nm-eq diameter.

Results:

Preliminary results are available for 49 LVV (42 TA, 7 GCA), 8 severe carotidatherosclerosis and 14 age- and sex-matched HC. As compared to HC or CA, LVV plasma contains a higher number of MVs and in particular of medium- to large- sized MVs (p<0.001 for all comparisons) (Figure, panels A-B). Next, we evaluated the MVs surface expression of markers of leukocytic, endothelial and stromal/vascular stromal lineages. Total counts of CD14+, CD16+, CD66b+, CD140a+, CD140b+, CD144+ MVs were increased in LVV plasma with very high level of significance (Figure, panels C-G) while higher percentage of CD16+ and CD140a+ medium-to large-sized MVs was found in atherosclerosis. Expression of molecules involved in inflammation or repair, PTX3 or HMGB1 mitochondrial antigens and mitochondrial ROS all were consistently higher in LVV (Figure, panels H-M).

Conclusion:

MVs, including those expressing arterial stromal biomarkers, are increased in LVV plasma, suggesting a communication between the vessel wall and peripheral blood. MV express signals that may in turn contribute to persisting vascular inflammation in large vessel vascultis Further analysis is required to dissect their potential use as disease biomarkers

References:

[1]van Niel G et al, Nat Rev Mol Cell Biol. 2018

[2]Mason JC. Nat Rev Rheumatol. 2010

Disclosure of Interests:

None declared

Promoter-like epigenetic signatures in exons displaying cell type-specific splicing

BACKGROUND

Pre-mRNA splicing occurs mainly co-transcriptionally, and both nucleosome density and histone modifications have been proposed to play a role in splice site recognition and regulation. However, the extent and mechanisms behind this interplay remain poorly understood.

RESULTS

We use transcriptomic and epigenomic data generated by the ENCODE project to investigate the association between chromatin structure and alternative splicing. We find a strong and significant positive association between H3K9ac, H3K27ac, H3K4me3, epigenetic marks characteristic of active promoters, and exon inclusion in a small but well-defined class of exons, representing approximately 4 % of all regulated exons. These exons are systematically maintained at comparatively low levels of inclusion across cell types, but their inclusion is significantly enhanced in particular cell types when in physical proximity to active promoters.

CONCLUSION

Histone modifications and other chromatin features that activate transcription can be co-opted to participate in the regulation of the splicing of exons that are in physical proximity to promoter regions.

Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing

The OLR1 gene encodes the oxidized low-density lipoprotein receptor (LOX-1), which is responsible for the cellular uptake of oxidized LDL (Ox-LDL), foam cell formation in atheroma plaques and atherosclerotic plaque rupture. Alternative splicing (AS) of OLR1 exon 5 generates two protein isoforms with antagonistic functions in Ox-LDL uptake. Previous work identified six single nucleotide polymorphisms (SNPs) in linkage disequilibrium that influence the inclusion levels of OLR1 exon 5 and correlate with the risk of cardiovascular disease. Here we use minigenes to recapitulate the effects of two allelic series (Low- and High-Risk) on OLR1 AS and identify one SNP in intron 4 (rs3736234) as the main contributor to the differences in exon 5 inclusion, while the other SNPs in the allelic series attenuate the drastic effects of this key SNP. Bioinformatic, proteomic, mutational and functional high-throughput analyses allowed us to define regulatory sequence motifs and identify SR protein family members (SRSF1, SRSF2) and HMGA1 as factors involved in the regulation of OLR1 AS. Our results suggest that antagonism between SRSF1 and SRSF2/HMGA1, and differential recognition of their regulatory motifs depending on the identity of the rs3736234 polymorphism, influence OLR1 exon 5 inclusion and the efficiency of Ox-LDL uptake, with potential implications for atherosclerosis and coronary disease.

Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells

Splicing of mRNA precursors can occur cotranscriptionally and it has been proposed that chromatin structure influences splice site recognition and regulation. Here we have systematically explored potential links between nucleosome positioning and alternative splicing regulation upon progesterone stimulation of breast cancer cells. We confirm preferential nucleosome positioning in exons and report four distinct profiles of nucleosome density around alternatively spliced exons, with RNA polymerase II accumulation closely following nucleosome positioning. Hormone stimulation induces switches between profile classes, correlating with a subset of alternative splicing changes. Hormone-induced exon inclusion often correlates with higher nucleosome occupancy at the exon or the preceding intronic region and with higher RNA polymerase II accumulation. In contrast, exons skipped upon hormone stimulation display low nucleosome densities even before hormone treatment, suggesting that chromatin structure primes alternative splicing regulation. Skipped exons frequently harbor binding sites for hnRNP AB, a hormone-induced splicing regulator whose knock down prevents some hormone-induced skipping events. Collectively, our results argue that a variety of chromatin architecture mechanisms can influence alternative splicing decisions.

Chromatin's thread to alternative splicing regulation

Intron removal (pre-mRNA splicing) is a necessary step for expression of most genes in higher eukaryotes. Alternative splice site selection is a prevalent mechanism that diversifies genome outputs and offers ample opportunities for gene regulation in these organisms. Pre-mRNA splicing occurs co-transcriptionally and is influenced by features in chromatin structure, including nucleosome density and epigenetic modifications. We review here the molecular mechanisms by which the reciprocal interplay between chromatin and RNA processing can contribute to alternative splicing regulation.

Radiation Genes: a database devoted to microarrays screenings revealing transcriptome alterations induced by ionizing radiation in mammalian cells

The analysis of the great extent of data generated by using DNA microarrays technologies has shown that the transcriptional response to radiation can be considerably different depending on the quality, the dose range and dose rate of radiation, as well as the timing selected for the analysis. At present, it is very difficult to integrate data obtained under several experimental conditions in different biological systems to reach overall conclusions or build regulatory models which may be tested and validated. In fact, most available data is buried in different websites, public or private, in general or local repositories or in files included in published papers; it is often in various formats, which makes a wide comparison even more difficult. The Radiation Genes Database (http://www.caspur.it/RadiationGenes) collects microarrays data from various local and public repositories or from published papers and supplementary materials. The database classifies it in terms of significant variables, such as radiation quality, dose, dose rate and sampling timing, as to provide user-friendly tools to facilitate data integration and comparison.

Low-Dose Ionizing Radiation Stimulates Transcription and Production of Endothelin by Human Vein Endothelial Cells

A transient increase of EDN1 mRNA accumulation is observed in human vein endothelial cells (HUVECs) after a low dose of ionizing radiation. The kinetics of this mRNA accumulation parallels that of other AP1-regulated transcripts, showing a sharp peak 2 h after irradiation. This accumulation is followed by a net increase of endothelin 1 and big endothelin 1 in the cytoplasm that reaches a peak 4 h after irradiation. We followed the kinetics of endothelin 1 secretion in cell culture medium and did not find a detectable increase in the rate of secretion by the irradiated cells compared to sham-irradiated cells. We conclude that in HUVEC monolayers, an increase in endothelin production does not automatically correspond to an increase in secretion. These findings suggest that endothelin is an important component in the response of endothelial cells to ionizing radiation and that it could be used as a biomarker for low-dose irradiation of endothelial tissues.

Is the Beck Depression Inventory reliable over time? An evaluation of multiple test-retest reliability in a nonclinical college student sample

The Beck Depression Inventory (BDI) is one of the most widely used measures of depression. Many studies have examined the reliability and validity of the BDI. However, we found no published studies that considered the stability of the BDI over multiple administrations (i.e., more than 3 trials), such as is common in clinical trials research and during some clinical interventions. The purpose of this study is to examine the multiple test-retest reliability of the BDI in a presumably nonclinical sample. Results show a 40% decline in BDI scores over 8 weeks, a main effect that accounts for approximately 10% of the variance. We achieved a 40% decrease in self-reported symptoms of depression due to repeated measurement alone, not due to any intervention. This change likely represents measurement error with this instrument rather than any "real" change in depression. The limitations of this study, its implications for research, and its applications to clinical practice are discussed.