Deciphering the complexity of human noncoding promoter-proximal transcriptome: different scales of transcriptional control : from a single gene to the whole epigenome

Long noncoding RNAs (lncRNAs) have gained increasing interest in molecular studies, their active participation in important biological functions has emerged and their direct involvement in genomic reprogramming during development and diseases, including cancer, has been demonstrated. Several studies have shown their active contribution in transcriptional control and they are emerging as relevant players in the epigenetic machinery, with key roles in nuclear functional organization. High- throughput sequencing approaches have revealed frequent noncoding transcription in promoter-proximal regions, defining the need of disclosing the complexity of mechanisms underlying regulatory elements. In our work, we uncover a complex network based on a promoter-associated noncoding RNA (paRNA), which coordinates a microRNA and epigenetic effectors able to modulate the transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin (CDH1) silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. After demonstrating the role of paRNA-based epigenetic networks and how its deregulation may contribute to cancer and other diseases, we extended this model to a genome-wide perspective, generating a comprehensive catalogue of promoter-associated RNA and a synoptic analysis of their features, functions and interactome. Integrating data from multiple cell types and experimental platforms we identified thousands of paRNA in the human genome, transcribed in both sense and antisense orientation, mostly non-polyadenylated and retained in nuclei. Their case and context specific relation with adjacent genes confirmed that paRNA execute their functions interacting with a variety of network components, regulating epigenetics at multiple levels. Positive transcriptional regulators, epigenetic effectors and chromatin marks are enriched in paRNA-positive promoters. Furthermore, paRNA-positive promoters exhibit chromatin signatures of active promoters and enhancers, denoting a dual function. paRNA-positive promoters also reside preferentially at chromatin loop boundaries, suggesting that an involvement in anchor site recognition and establishment of chromatin loops. Importantly, these features were independent of the transcriptional state of neighbouring genes. Thus, paRNA may act as cis-regulatory modules with an impact on local recruitment of transcription factors, epigenetic state and chromatin loop organization. Providing a comprehensive analysis of the promoter-proximal transcriptome and its interactome, this study offers novel insights into the roles of paRNA in epigenetic processes and human diseases, making them promising targets for drug discovery

Prostate Osteoblast-Like Cells: A Reliable Prognostic Marker of Bone Metastasis in Prostate Cancer Patients

The main aim of this study was to investigate the putative association among the presence of prostate cancer cells, defined as prostate osteoblast-like cells (POLCs), and showing the expression of typical morphological and molecular characteristics of osteoblasts, the development of bone metastasis within 5 years of diagnosis, and the uptake of 18F-choline evaluated by PET/CT analysis. To this end, prostate biopsies (n = 110) were collected comprising 44 benign lesions and 66 malignant lesions. Malignant lesions were further subdivided into two groups: biopsies from patients that had clinical evidence of bone metastasis (BM+, n = 23) and biopsies from patients that did not have clinical evidence of bone metastasis within 5 years (BM−, n = 43). Paraffin serial sections were obtained from each specimen to perform histological classifications and immunohistochemical (IHC) analysis. Small fragments of tissue were used to perform ultrastructural and microanalytical investigations. IHC demonstrated the expression of markers of epithelial-to-mesenchymal transition (VIM), bone mineralization, and osteoblastic differentiation (BMP-2, PTX-3, RUNX2, RANKL, and VDR) in prostate lesions characterized by the presence of calcium-phosphate microcalcifications and high metastatic potential. Ultrastructural studies revealed the presence of prostate cancer cells with osteoblast phenotype close to microcalcifications. Noteworthy, PET/CT analysis showed higher uptake of 18F-choline in BM+ lesions with high positivity (≥300/500 cells) for RUNX2 and/or RANKL immunostaining. Although these data require further investigations about the molecular mechanisms of POLCs generation and role in bone metastasis, our study can open new and interesting prospective in the management of prostate cancer patients. The presence of POLCs along with prostate microcalcifications may become negative prognostic markers of the occurrence of bone metastases

Evidence for WW/WZ vector boson scattering in the decay channel ℓν\ell\nuqq produced in association with two jets in proton-proton collisions at s\sqrt{s} = 13 TeV

Evidence is reported for electroweak (EW) vector boson scattering in the decay channel $\ell\nu$qq of two weak vector bosons WV (V = W or Z), produced in association with two parton jets. The search uses a data set of proton-proton collisions at 13 TeV collected with the CMS detector during 2016-2018 with an integrated luminosity of 138 fb$^{-1}$. Events are selected requiring one lepton (electron or muon), moderate missing transverse momentum, two jets with a large pseudorapidity separation and a large dijet invariant mass, and a signature consistent with the hadronic decay of a W/Z boson. The cross section is computed in a fiducial phase space defined at parton level requiring all parton transverse momenta $p_\mathrm{T} \gt$ 10 GeV and at least one pair of outgoing partons with invariant mass $m_\mathrm{qq}\gt$ 100 GeV. The measured and expected EW WV production cross sections are 1.90$^{+0.53}_{-0.46}$ pb and 2.23$^{+0.08}_{-0.11}$ (scale) $\pm$ 0.05(PDF) pb, respectively, where PDF is the parton distribution function. The observed EW signal strength is $m_\mathrm{EW}$ = 0.85 $pm$ 0.12 (stat)$^{+0.19}_{-0.17}$ (syst), corresponding to a signal significance of 4.4 standard deviations with 5.1 expected. This is the first evidence of vector boson scattering in the $\ell\nu$qq decay channel at LHC. The simultaneous measurement of the EW and quantum chromodynamics associated diboson production agrees with the standard model prediction

Evidence for WW/WZ vector boson scattering in the decay channel ℓν\ell\nuqq produced in association with two jets in proton-proton collisions at s=\sqrt{s} = 13 TeV

Evidence is reported for electroweak (EW) vector boson scattering in the decay channel $\ell\nu$qq of two weak vector bosons WV (V = W or Z), produced in association with two parton jets. The search uses a data set of proton-proton collisions at 13 TeV collected with the CMS detector during 2016-2018 with an integrated luminosity of 138 fb$^{-1}$. Events are selected requiring one lepton (electron or muon), moderate missing transverse momentum, two jets with a large pseudorapidity separation and a large dijet invariant mass, and a signature consistent with the hadronic decay of a W/Z boson. The cross section is computed in a fiducial phase space defined at parton level requiring all parton transverse momenta $p_\mathrm{T}$$\gt$ 10 GeV and at least one pair of outgoing partons with invariant mass $m_\mathrm{qq}$$\gt$ 100 GeV. The measured and expected EW WV production cross sections are 1.90 $^{+0.53}_{-0.46}$ pb and 2.23 $^{+0.08}_{-0.11}$ (scale) $\pm$ 0.05 (PDF) pb, respectively, where PDF is the parton distribution function. The observed EW signal strength is $m_\mathrm{EW}$ = 0.85 $\pm$ 0.12 (stat) $^{+0.19}_{-0.17}$ (syst), corresponding to a signal significance of 4.4 standard deviations with 5.1 expected, and it is measured keeping the quantum chromodynamics (QCD) associated diboson production fixed to the standard model prediction. This is the first evidence of vector boson scattering in the $\ell\nu$qq decay channel at LHC. The simultaneous measurement of the EW and QCD associated diboson production agrees with the standard model prediction