DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.

Epithelial splicing regulatory proteins 1 and 2 (ESRP1/2) control the splicing pattern during epithelial to mesenchymal transition (EMT) in a physiological context and in cancer, including breast cancer (BC). Here, we report that ESRP1, but not ESRP2, is overexpressed in luminal BCs of patients with poor prognosis and correlates with estrogen receptor α (ERα) levels. Analysis of ERα genome-binding profiles in cell lines and primary breast tumors showed its binding in the proximity of ESRP1 and ESRP2 genes, whose expression is strongly decreased by ERα silencing in hormone-deprived conditions. The combined knock-down of ESRP1/2 in MCF-7 cells followed by RNA-Seq, revealed the dysregulation of 754 genes, with a widespread alteration of alternative splicing events (ASEs) of genes involved in cell signaling, metabolism, cell growth, and EMT. Functional network analysis of ASEs correlated with ESRP1/2 expression in ERα+ BCs showed RAC1 as the hub node in the protein–protein interactions altered by ESRP1/2 silencing. The comparison of ERα- and ESRP-modulated ASEs revealed 63 commonly regulated events, including 27 detected in primary BCs and endocrine-resistant cell lines. Our data support a functional implication of the ERα-ESRP1/2 axis in the onset and progression of BC by controlling the splicing patterns of related genes.

Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.

The pathophysiology of residual pulmonary vascular obstruction (RPVO) and recurrent venous thromboembolism (VTE) after unprovoked pulmonary embolism (PE) remains poorly understood. The purpose was to evaluate fibrinolytic and tissue remodeling markers as indicators of RPVO and recurrence after a first unprovoked PE. Analyses were conducted in the 18 to 70-year-old patients included in the PADIS-PE trial, with a pulmonary vascular obstruction (PVO) index ≥ 30% at PE diagnosis. After an initial six-month vitamin K antagonist treatment, patients were randomised to receive placebo or warfarin for 18 months and assessed for the absence or presence of residual pulmonary vascular obstruction (RPVO < or ≥ 5%, respectively). Quantitative assessment of fibrinolytic (D-dimer, tPA, uPA, TFPI) and tissue remodeling (TGFβ1) markers, and a tissue-factor-based turbidimetric clot lysis assay (CLA) were performed one month after warfarin discontinuation. Symptomatic recurrent VTE was monitored for 42 months after randomisation. Among the 371 patients included in PADIS-PE, 23 fulfilled clinico-radiological criteria and had an available blood sample. Six (26%) patients presented RPVO ≥ 5% and symptomatic recurrent VTE occurred in nine (39%) patients. Clot formation and lysis parameters were not associated with RPVO. TGFβ1 plasma levels were higher in patients with RPVO. Clot formation potential measured with CLA was higher in patients with recurrent VTE. No association between recurrent VTE and TGFβ1 was observed. In adult patients with a first unprovoked PE and a PVO index ≥ 30%, TGFβ1 plasma levels were associated with RPVO, whereas clot formation parameters measured with CLA were associated with VTE recurrence.

Venous thromboembolism (VTE), manifesting as deep vein thrombosis (DVT) and pulmonary embolism (PE), is a common, recurrent and potentially fatal condition. Anticoagulation remains the cornerstone of therapy, yet determining optimal treatment duration (e.g. decision to shorten or extend anticoagulant treatment) is difficult due to the uncertain balance between long-term bleeding risk and recurrence. Future advances in vascular nuclear molecular imaging could critically help support this decision-making process. Current VTE diagnostic imaging relies on structural or perfusion-based techniques to infer thrombosis from abnormal vasculature structure or filling defects. While highly effective in localising thrombi and assessing hemodynamic impact, they provide little insight into the biological activity or age of the clot. Consequently, anticoagulation strategies (duration and management) often proceed without direct clot-specific molecular information, potentially leading to suboptimal outcomes and increased risk of fatal bleeding. By contrast, nuclear VTE molecular imaging -using radiolabelled probes that selectively target key thrombus components such as fibrin or activated platelets- enables direct visualisation of the clot. Single-photon emission computed tomography (SPECT) and positron emission tomography (PET) targeted imaging of VTE, beyond enhancing diagnostic accuracy, are expected to provide valuable insights into the structure, age, and activity of the clot. In particular, integration of these modalities with molecular findings from high throughput technologies could further elucidate the cellular and molecular mechanisms driving thrombus formation and resolution. When coupled with PET's ability to assess molecular processes in vivo, such approaches may establish precision imaging biomarkers, bridging the gap between clot biology and clinical imaging, and ultimately transform VTE management from a structural or perfusion based to molecularly informed paradigm.

Introduction The pathophysiology of residual pulmonary vascular obstruction (RPVO) and recurrent venous thromboembolism (VTE) after unprovoked pulmonary embolism (PE) remains poorly understood. The purpose was to evaluate fibrinolytic and tissue remodeling markers as indicators of RPVO and recurrence after a first unprovoked PE. Methods Analyses were conducted in the 18 to 70-year-old patients included in the PADIS-PE trial, with a pulmonary vascular obstruction (PVO) index ≥30% at PE diagnosis. After an initial six-month vitamin K antagonist treatment, patients were randomised to receive placebo or warfarin for 18 months, assessed for the absence or presence of residual pulmonary vascular obstruction (RPVO < or ≥5%, respectively) and followed during two years. Quantitative assessment of fibrinolytic (D-dimer, tPA, uPA, TFPI) and tissue remodeling (TGFß1) markers, and a tissue-factor-based turbidimetric clot lysis assay (CLA) were performed one month after warfarin discontinuation. Results Among the 371 patients included in the PADIS-PE trial, 23 were eligible. Six (26%) patients presented RPVO, symptomatic recurrent VTE occurred in nine (39%) patients. Clot formation and lysis parameters were not associated with RPVO. TGFß1 plasma levels were higher in patients with RPVO. Clot formation potential measured with CLA was higher in patients with recurrent VTE. No association between recurrent VTE and TGFß1 was observed. In multivariable analysis, time to peak was associated with VTE recurrence. Conclusion In adult patients with a first unprovoked PE and a PVO index ≥30%, TGFß1 plasma level was associated with RPVO, whereas clot formation parameters measured with CLA were associated with VTE recurrence.