Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer.

Genomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarkers. However such lists of differentially expressed genes can be highly variable for multiple reasons. As such, looking at differential expression in the context of gene sets and pathways has been more robust. Using next-generation genome sequencing data from The Cancer Genome Atlas, differential gene expression between age- and stage- matched human prostate tumors and non-malignant samples was assessed and used to craft a pathway signature of prostate cancer. Up- and down-regulated genes were assigned to pathways composed of curated groups of related genes from multiple databases. The significance of these pathways was then evaluated according to the number of differentially expressed genes found in the pathway and their position within the pathway using Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis. The "transforming growth factor-beta signaling" and "Ran regulation of mitotic spindle formation" pathways were strongly associated with prostate cancer. Several other significant pathways confirm reported findings from microarray data that suggest actin cytoskeleton regulation, cell cycle, mitogen-activated protein kinase signaling, and calcium signaling are also altered in prostate cancer. Thus we have demonstrated feasibility of pathway analysis and identified an underexplored area (Ran) for investigation in prostate cancer pathogenesis

Functional Classification of Differentially Expressed Genes in Human Prostate Cancer According to PANTHER Protein Class (A) and Biological Process Gene Ontology Terms (B).

<p>(A) “Nucleic Acid Binding” includes RNA and DNA binding, nucleases, and helicases. “Transcription Factor” includes zinc finger, helix-turn-helix, high mobility group box, basic helix-loop-helix, and basic leucine zipper transcription factors; cofactors; and nuclear hormone receptors. “Hydrolase” refers to proteases, phosphatases, esterases, lipases, deaminases, phosphodiesterases, glycosidases, deacetylases, pyrophosphatases, glucosidases, galactosidases, and amylases. “Receptor” includes protein kinase receptors, nuclear hormone receptors, cytokine receptors, ligand-gated ion channels, and G-protein coupled receptors. “Enzyme Modulator” includes G protein, kinase, phosphatase, and protease modulators. (B) “Metabolic Process” features carbohydrate, cellular amino acid, lipid, protein, and nucleobase-containing compound metabolism; and the tricarboxylic acid cycle. “Cellular Process” categories are cell-cell signaling, cell cycle, growth and proliferation, cell component movement, and cytokinesis. “Biological Regulation” includes the regulation of apoptosis, metabolism, cell cycle, translation, catalytic activity, and homeostasis. “Developmental Process” categories are system, ectoderm, mesoderm, and endoderm development; cell differentiation; death; anatomical structure morphogenesis; embryo development; sex determination; and pattern specification processes. “Localization” includes transport proteins, protein and RNA localization processes.</p

Magnitude of gene expression differences between tumor and non-malignant human prostate cancer samples.

<p>In this one-dimensional scatter plot the magnitude of gene expression changes represented by log₂ fold ratios are shown. Each point represents a gene or transcript. Significantly differentially expressed genes and transcripts are shown as solid red diamonds.</p

Alternative splicing of ALCAM enables tunable regulation of cell-cell adhesion through differential proteolysis

While many adhesion receptors are known to influence tumor progression, the mechanisms by which they dynamically regulate cell-cell adhesion remain elusive. We previously identified Activated Leukocyte Cell Adhesion Molecule (ALCAM) as a clinically relevant driver of metastasis and hypothesized that a tunable mechanism of ectodomain shedding regulates its contribution to dissemination. To test this hypothesis, we examined an under-explored ALCAM splice variant (ALCAM-Iso2) and demonstrated that loss of the membrane-proximal region of ALCAM (exon 13) increased metastasis four-fold. Mechanistic studies identified a novel MMP14-dependent membrane distal cleavage site in ALCAM-Iso2, which mediated a ten-fold increase in shedding, thereby decreasing cellular cohesion. Importantly, the loss of cohesion is not limited to the cell capable of shedding because the released extracellular domain diminished cohesion of non-shedding cells through disruption of ALCAM-ALCAM interactions. ALCAM-Iso2-dominated expression in bladder cancer tissue, compared to normal bladder, further emphasizes that ALCAM alternative splicing may contribute to clinical disease progression. The requirement for both the loss of exon 13 and the gain of metalloprotease activity suggests that ALCAM shedding and concomitant regulation of tumor cell adhesion is a locally tunable process

Exosomes, Microvesicles, and Other Extracellular Vesicles-A Keystone Symposia Report

Extracellular vesicles (EVs) are small, lipid-bilayer-bound particles released by cells that can contain important bioactive molecules, including lipids, RNAs, and proteins. Once released in the extracellular environment, EVs can act as messengers locally as well as to distant tissues to coordinate tissue homeostasis and systemic responses. There is a growing interest in not only understanding the physiology of EVs as signaling particles but also leveraging them as minimally invasive diagnostic and prognostic biomarkers (e.g., they can be found in biofluids) and drug-delivery vehicles. On October 30-November 2, 2022, researchers in the EV field convened for the Keystone symposium Exosomes, Microvesicles, and Other Extracellular Vesicles to discuss developing standardized language and methodology, new data on the basic biology of EVs and potential clinical utility, as well as novel technologies to isolate and characterize EVs