ABSTRACT
Bone metastatic (BM) prostate cancer (PCa) belongs to the most lethal form of PCa, and therapeutic options are limited. Molecular profiling of metastases contributes to the understanding of mechanisms defining the bone metastatic niche. Our aim was to explore the transcriptional profile of PCa BM and to identify genes that drive progression. Paraffin-embedded tissues of 28 primary PCa and 30 BM were submitted to RNA extraction and analyzed by RNA sequencing using the Nanostring nCounter gene expression platform. A total of 770 cancer-related genes were measured using the Nanostring™ PanCancer progression panel. Gene Ontology (GO), KEGG, Reactome, STRING, Metascape, PANTHER, and Pubmed were used for data integration and gene annotation. We identified 116 differentially expressed genes (DEG) in BM compared to primaries. The most significant DEGs include CD36, FOXC2, CHAD, SPP1, MMPs, IBSP, and PTX3, which are more highly expressed in BM, and ACTG2, MYH11, CNN1, FGF2, SPOCK3, and CHRDL1, which have a lower expression. DEGs functionally relate to extracellular matrix (ECM) proteoglycans, ECM-receptors, cell-substrate adhesion, cell motility as well as receptor tyrosine kinase signaling and response to growth factors. Data integration and gene annotation of 116 DEGs were used to build a gene platform which we termed "Manually Annotated and Curated Nanostring-data Platform". In summary, our results highlight the significance of certain genes in PCa BM to which essential pro-metastatic functions could be ascribed. Data from this study provide a comprehensive platform of genes that are related to PCa BM and provide evidence for further investigations.
Subject(s)
Bone Neoplasms , Prostatic Neoplasms , Male , Humans , Prostatic Neoplasms/metabolism , Prostate/pathology , Gene Ontology , Bone Neoplasms/genetics , Bone Neoplasms/secondary , Gene Expression , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Computational Biology/methods , Tumor Microenvironment/geneticsABSTRACT
With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.
Subject(s)
Bone and Bones/metabolism , Gene Expression Profiling/methods , RNA, Messenger/isolation & purification , Transcriptome , Bone and Bones/pathology , Decalcification Technique , Formaldehyde/chemistry , Humans , Paraffin Embedding , RNA, Messenger/metabolismABSTRACT
The first total synthesis of pericoannosin A (1) containing 15 steps in the longest linear sequence with an overall yield of 5.5% is reported. The hybrid peptide-polyketide was isolated from the endophytic fungus Periconia sp. F-31 and bears a unique tricyclic core structure. The key steps are a glycolate aldol reaction and a Diels-Alder reaction utilizing an Evans auxiliary for controlling the stereochemistry. Furthermore, a late-stage equilibration was employed.
