Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that-in the case of the interdependent tumor cell morphology and adapted immune response-reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.

Splicing machinery is impaired in rheumatoid arthritis, associated with disease activity and modulated by anti-TNF therapy

OBJECTIVES

To characterise splicing machinery (SM) alterations in leucocytes of patients with rheumatoid arthritis (RA), and to assess its influence on their clinical profile and therapeutic response.

METHODS

Leucocyte subtypes from 129 patients with RA and 29 healthy donors (HD) were purified, and 45 selected SM elements (SME) were evaluated by quantitative PCR-array based on microfluidic technology (Fluidigm). Modulation by anti-tumour necrosis factor (TNF) therapy and underlying regulatory mechanisms were assessed.

RESULTS

An altered expression of several SME was found in RA leucocytes. Eight elements (SNRNP70, SNRNP200, U2AF2, RNU4ATAC, RBM3, RBM17, KHDRBS1 and SRSF10) were equally altered in all leucocytes subtypes. Logistic regressions revealed that this signature might: discriminate RA and HD, and anti-citrullinated protein antibodies (ACPAs) positivity; classify high-disease activity (disease activity score-28 (DAS28) >5.1); recognise radiological involvement; and identify patients showing atheroma plaques. Furthermore, this signature was altered in RA synovial fluid and ankle joints of K/BxN-arthritic mice. An available RNA-seq data set enabled to validate data and identified distinctive splicing events and splicing variants among patients with RA expressing high and low SME levels. 3 and 6 months anti-TNF therapy reversed their expression in parallel to the reduction of the inflammatory profile. In vitro, ACPAs modulated SME, at least partially, by Fc Receptor (FcR)-dependent mechanisms. Key inflammatory cytokines further altered SME. Lastly, induced SNRNP70-overexpression and KHDRBS1-overexpression reversed inflammation in lymphocytes, NETosis in neutrophils and adhesion in RA monocytes and influenced activity of RA synovial fibroblasts.

CONCLUSIONS

Overall, we have characterised for the first time a signature comprising eight dysregulated SME in RA leucocytes from both peripheral blood and synovial fluid, linked to disease pathophysiology, modulated by ACPAs and reversed by anti-TNF therapy.

SUN-LB056 The Pharmacological Blockade of the Splicing Factor SF3B1 Exerts Antitumor Actions in Different Endocrine-Related Cancers

The intrinsic heterogeneity of endocrine-related cancers (ERCs) hampers the identification and development of global and effective therapeutic treatments for these pathologies. However, the dysregulation of the splicing process has been postulated as a new common hallmark shared by most cancer types, since it is associated with the appearance of splicing variants with oncogenic potential (e.g. CD44v6, BCL-xs, AR-v7, SST5TMD4, In1-ghrelin). Yet, the putative alteration, pathophysiological role and potential therapeutic utility of the elements involved in the control of the splicing process [i.e. spliceosome components (SCs) and splicing factors (SFs)] remain still unknown. For this reason, we have analysed the expression levels of a representative set of SCs (n=18) and SFs (n=27) in different cohorts of ERCs [i.e. growth hormone secreting pituitary tumors (n=96); non-functioning pituitary tumors (n=23); pancreatic neuroendocrine tumors (n=20); prostate cancer (n=126); and in four in silico cohorts of liver cancer (HCC; n=445, n=115, n=75, n=45)]. Our results showed that the SF3b subunit 1 (SF3B1) gene, which encodes a protein necessary for spliceosome assembly, was consistently overexpressed in all the ERCs evaluated in this study. Interestingly, SF3B1 expression was positively correlated and associated with clinical and molecular aggressiveness features (e.g. histopathological grade, presence of metastasis, expression of oncogenic splicing variants, etc.) in these ERCs. In vitro analyses revealed that the specific blockade of SF3B1 activity, using the pladienolide-B compound, exhibited potent and relevant antitumor effects (reducing cell proliferation, migration, tumorospheres and colonies formation, hormone release and inducing apoptosis) in the vast majority of representative models of ERC cells tested herein (primary ERCs cell cultures and cell lines such as BON-1, QGP-1, LNCaP, 22Rv1, PC-3, HepG2, Hep3b or SNU-387). Remarkably, the antitumor effects of pladienolide-B treatment were further validated in vivo in that we found a significant reduction of tumor volume after 9-days of local treatment of pladienolide-B in a xenograft model of ERC. Moreover, we found that pladienolide-B treatment modulated an ample repertoire of molecular events, such as inhibition of major oncogenic signalling pathways (e.g. PI3K/AKT and JNK), modulation of the expression of key tumour markers (e.g. MKI67/CDK6/CDKN2A) and oncogenic splicing variants (e.g. AR-v7/In1-ghrelin), and regulation of the expression pattern of key components of mRNA homeostasis-associated machineries (spliceosome and SURF/EJC). In conclusion, these results indicate that SF3B1 is consistently overexpressed in different ERCs and associated to malignant features and that its pharmacological blockade with pladienolide-B could represent a novel, global and effective therapeutic approach for ERCs Unless otherwise noted, all abstracts presented at ENDO are embargoed until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. Abstracts presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.