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Squamous cell carcinomas (SCCs) are among the most frequent solid tumors in humans. SCCs, related or not to the human papillomavirus, share common molecular features. Immunotherapies, and specifically immune checkpoint inhibitors, have been shown to improve overall survival in multiple cancer types, including SCCs. However, only a minority of patients experience a durable response with immunotherapy. Epigenetic modulation plays a major role in escaping tumor immunosurveillance and confers resistance to immune checkpoint inhibitors. Preclinical evidence suggests that modulating the epigenome might improve the efficacy of immunotherapy. We herein review the preclinical and the clinical rationale for combining immunotherapy with an epidrug, and detail the design of PEVOsq, a basket clinical trial combining pembrolizumab with vorinostat, a histone deacetylase inhibitor, in patients with SCCs of different locations. Sequential blood and tumor sampling will be collected in order to identify predictive and pharmacodynamics biomarkers of efficacy of the combination. We also present how clinical and biological data will be managed with the aim to enable the development of a prospective integrative platform to allow secure and controlled access to the project data as well as further exploitations., Highlights • Squamous cell carcinomas (SCCs) of different locations share molecular features. • Immunotherapy improves overall survival in several cancers including SCCs. • Epigenetic modulation plays a major role in resistance to immunotherapy. • PEVOsq evaluates pembrolizumab/vorinostat combination in SCCs of several locations. • An integrative platform ensures secured optimal management of generated data.

Introduction MiRNAs are short non coding RNAs involved in post-transcriptional regulation of gene expression that can acquire oncogenic properties in consequence of overexpression or mutations. Tumour genomes undergo global demethylation that triggers genetic instability and activates transcription of sequences normally silenced by methylation. These include the overexpression of tumour specific miRNAs that can deregulate various processes in the malignant cell. Therefore, the aim of the study was to identify aberrantly activated miRNAs in classical Hodgkin lymphoma (cHL). Material and methods We have screened NGS small RNA reads (HiSeq 4000 (Illumina); single-end 50 bp seq) of cHL cell lines (n=7) and compared them to non-HL cell lines (n=10) and germinal centre B cell pools (GCB)(n=10) to find yet undescribed miRNAs. High quality reads validated using FastQC and CAP-miRSeq software mapping to the reference genome (GRCh37) (using Bowtie software) not reported as miRNAs before were identified. In order to find miRNAs expressed exclusively in cHL we have moreover compared the sequences in respect to sequence-derived gene expression data from 143 malignant lymphomas generated by the ICGC MMML-Seq consortium (www.icgc.org). Last, the expression of novel miRNAs seemingly specific for cHL was validated by real-time qPCR using custom designed molecular probes (Thermo Fisher Scientific). Results and discussions Seven novel miRNAs expressed in at least 3/7 cHL cell lines but neither in the non-HL cell lines nor in the GCB cells and observed with a frequency In silico analyses of potential target mRNAs has shown enrichment in gene ontologies including regulation of signalling (p Conclusion Our data provide evidence for aberrant activation of miRNAs in neoplastic cells probably not expressed under physiologic conditions in the same cell type. The identified miRNA #7 and potentially the currently tested 5 further candidates contribute to the unique cHL miRNAome.

Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. Nevertheless, the lack in publicly available sequence information is severely limiting advances in CHO cell biology, including the exploration of microRNAs (miRNA) as tools for CHO cell characterization and engineering. In an effort to identify and annotate both conserved and novel CHO miRNAs in the absence of a Chinese hamster genome, we deep-sequenced small RNA fractions of 6 biotechnologically relevant cell lines and mapped the resulting reads to an artificial reference sequence consisting of all known miRNA hairpins. Read alignment patterns and read count ratios of 5′ and 3′ mature miRNAs were obtained and used for an independent classification into miR/miR* and 5p/3p miRNA pairs and discrimination of miRNAs from other non-coding RNAs, resulting in the annotation of 387 mature CHO miRNAs. The quantitative content of next-generation sequencing data was analyzed and confirmed using qPCR, to find that miRNAs are markers of cell status. Finally, cDNA sequencing of 26 validated targets of miR-17-92 suggests conserved functions for miRNAs in CHO cells, which together with the now publicly available sequence information sets the stage for developing novel RNAi tools for CHO cell engineering.