Prostate cancer (PCa) is one of the leading causes of death in men worldwide. The molecular features, associated 8 with the onset and progression of the disease, are under vigorous investigation. Formalin-fixed paraffin-9 embedded (FFPE) tissues are valuable resources for large-scale studies, however, their application in proteomics 10 is limited due to protein cross-linking. In this study, the adjustment of a protocol for the proteomic analysis of 11 FFPE tissues was performed which was followed by a pilot application on FFPE PCa clinical samples to investigate 12 whether the optimized protocol can provide biologically relevant data for the investigation of PCa. For the 13 optimization, FFPE mouse tissues were processed using eight seven protein extraction protocols including 14 combinations of homogenization methods (beads, sonication, boiling) and buffers (SDS based and Urea-15 Thiourea based). The proteome extraction efficaiency was then evaluated based on protein identifications and 16 reproducibility using SDS electrophoresis and high resolution LC-MS/MS analysis. Comparison between the FFPE 17 and matched fresh frozen (FF) tissues, using an optimized protocol involving protein extraction with an SDS-18 based buffer following beads homogenization and boiling, showed a substantial overlap in protein 19 identifications (1106 common between the 1214 identified in FF and 1249 identified in FFPE) with a strong 20 correlation in relative abundances (r s =0.7820.819, p <0.001). Next, FFPE tissues (3 sections, 15μm each per 21 sample) from 10 patients with PCa corresponding to tumor (GS=6 or GS≥8) and adjacent benign regions were 22 processed with the optimized protocol. Extracted proteins were analyzed by GeLC-MS/MS followed by statistical 23 and bioinformatics analysis. Proteins significantly deregulated between PCa GS≥8 and PCa GS=6 represented 24 extracellular matrix organisation, gluconeogenesis and phosphorylation pathways. Proteins deregulated 25 between cancerous tissues and adjacent benign tissues counterparts, showed reflected increased translation, 26 peptide synthesis and protein metabolism in the former, which is consistent to with the literature. In conclusion, 27 the results support the relevance of the proteomic findings in the context of PCa and the reliability of the 28 optimized protocol for proteomics analysis of FFPE material.

The main objective of this work is to provide an update on synthetic nucleic acid analogues and nanoassemblies as tools in gene therapy. In particular, the synthesis and properties of peptide-oligonucleotide conjugates (POCs), which have high potential in research and as therapeutics, are described in detail. The exploration of POCs has already led to fruitful results in the treatment of neurological diseases, lung disorders, cancer, leukemia, viral, and bacterial infections. However, delivery and in vivo stability are the major barriers to the clinical application of POCs and other analogues that still have to be overcome. This review summarizes recent achievements in the delivery and in vivo administration of synthetic nucleic acid analogues, focusing on POCs, and compares their efficiency.

Prostate cancer (PCa) is one of the leading causes of death in the male population worldwide. Various clinical samples such as urine, blood serum, and prostatic fluid have been commonly used for the identification of PCa-associated molecular changes. Tissue, the site of oncogenesis, is increasingly gaining more attention as a study material for studies aimed at the discovery of biomarkers for predicting the disease outcome and therapeutic targets. Areas covered: This review is the output of a systematic literature search on PubMed to retrieve articles relevant to the proteomic analysis of tissues for the study of PCa. Studies performed during the last 10 years using human tissues are summarized. Expert commentary: Multiple proteomics studies were performed in the past 10 years focusing on PCa initial diagnosis and staging. Even though some reproducible findings have been reported, many studies lacked adequate validation of findings and relied on relatively lower-resolution proteomics techniques compared to the current state of the art. Incorporation of high-resolution proteomics techniques, including investigations of protein post-translational modifications (PTMs), is expected in the near future to complement other -omics and enhance current efforts toward the molecular subtyping of PCa for patient stratification.

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