Cloning of novel transcripts of the human guanine-nucleotide-exchange factor Mss4: in situ chromosomal mapping and expression in pancreatic cancer

Identification of the Novel Tumor Suppressor Role of FOCAD/miR-491-5p to Inhibit Cancer Stemness, Drug Resistance and Metastasis via Regulating RABIF/MMP Signaling in Triple Negative Breast Cancer

Triple negative breast cancer (TNBC) possesses poor prognosis mainly due to development of chemoresistance and lack of effective endocrine or targeted therapies. MiR-491-5p has been found to play a tumor suppressor role in many cancers including breast cancer. However, the precise role of miR-491-5p in TNBC has never been elucidated. In this study, we reported the novel tumor suppressor function of FOCAD/miR-491-5p in TNBC. High expression of miR-491-5p was found to be associated with better overall survival in breast cancer patients. We found that miR-491-5p could be an intronic microRNA processed form FOCAD gene. We are the first to demonstrate that both miR-491-5p and FOCAD function as tumor suppressors to inhibit cancer stemness, epithelial-mesenchymal transition, drug resistance, cell migration/invasion, and pulmonary metastasis etc. in TNBC. MiR-491-5p was first reported to directly target Rab interacting factor (RABIF) to downregulate RABIF-mediated TNBC cancer stemness, drug resistance, cell invasion, and pulmonary metastasis via matrix metalloproteinase (MMP) signaling. High expression of RABIF was found to be correlated with poor clinical outcomes of breast cancer and TNBC patients. Our data indicated that miR-491-5p and RABIF are potential prognostic biomarkers and targeting the novel FOCAD/miR-491-5p/RABIF/MMP signaling pathway could serve as a promising strategy in TNBC treatment.

Structural Insights into the Regulation Mechanism of Small GTPases by GEFs

Small GTPases are key regulators of cellular events, and their dysfunction causes many types of cancer. They serve as molecular switches by cycling between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. GTPases are deactivated by GTPase-activating proteins (GAPs) and are activated by guanine-nucleotide exchange factors (GEFs). The intrinsic GTP hydrolysis activity of small GTPases is generally low and is accelerated by GAPs. GEFs promote GDP dissociation from small GTPases to allow for GTP binding, which results in a conformational change of two highly flexible segments, called switch I and switch II, that enables binding of the gamma phosphate and allows small GTPases to interact with downstream effectors. For several decades, crystal structures of many GEFs and GAPs have been reported and have shown tremendous structural diversity. In this review, we focus on the latest structural studies of GEFs. Detailed pictures of the variety of GEF mechanisms at atomic resolution can provide insights into new approaches for drug discovery.

A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data

Accurate identification of the cancer types is essential to cancer diagnoses and treatments. Since cancer tissue and normal tissue have different gene expression, gene expression data can be used as an efficient feature source for cancer classification. However, accurate cancer classification directly using original gene expression profiles remains challenging due to the intrinsic high-dimension feature and the small size of the data samples. We proposed a new self-training subspace clustering algorithm under low-rank representation, called SSC-LRR, for cancer classification on gene expression data. Low-rank representation (LRR) is first applied to extract discriminative features from the high-dimensional gene expression data; the self-training subspace clustering (SSC) method is then used to generate the cancer classification predictions. The SSC-LRR was tested on two separate benchmark datasets in control with four state-of-the-art classification methods. It generated cancer classification predictions with an overall accuracy 89.7 percent and a general correlation 0.920, which are 18.9 and 24.4 percent higher than that of the best control method respectively. In addition, several genes (RNF114, HLA-DRB5, USP9Y, and PTPN20) were identified by SSC-LRR as new cancer identifiers that deserve further clinical investigation. Overall, the study demonstrated a new sensitive avenue to recognize cancer classifications from large-scale gene expression data.

Nucleotide exchange via local protein unfolding--structure of Rab8 in complex with MSS4

Rab GTPases function as essential regulators of vesicle transport in eukaryotic cells. MSS4 was shown to stimulate nucleotide exchange on Rab proteins associated with the exocytic pathway and to have nucleotide-free-Rab chaperone activity. A detailed kinetic analysis of MSS4 interaction with Rab8 showed that MSS4 is a relatively slow exchange factor that forms a long-lived nucleotide-free complex with RabGTPase. In contrast to other characterized exchange factor-GTPase complexes, MSS4:Rab8 complex binds GTP faster than GDP, but still ca. 3 orders of magnitude more slowly than comparable complexes. The crystal structure of the nucleotide-free MSS4:Rab8 complex revealed that MSS4 binds to the Switch I and interswitch regions of Rab8, forming an intermolecular beta-sheet. Complex formation results in dramatic structural changes of the Rab8 molecule, leading to unfolding of the nucleotide-binding site and surrounding structural elements, facilitating nucleotide release and slowing its rebinding. Coupling of nucleotide exchange activity to a cycle of GTPase unfolding and refolding represents a novel nucleotide exchange mechanism.

Investigations into the electrooxidation of guanosine-5'-triphosphate at the pyrolytic graphite electrode

The electrochemical oxidation of guanosine-5'-triphosphate has been investigated in phosphate-containing electrolytes in the pH range 1.5-10.9 at a pyrolytic graphite electrode by cyclic sweep voltammetry, spectral studies, bulk electrolysis and related techniques. In this pH range, the oxidation occurred in a single well-defined peak (Ia). The peak potential of oxidation peaks (Ep) was found to be dependent on pH, concentration and sweep rate. The kinetics of the UV-absorbing intermediates was followed spectrophotometrically and the decay of the intermediate occurred in a pseudo-first-order reaction. The first-order rate constants for the disappearance of the UV-absorbing intermediate have also been calculated. The products of the electrode reaction were characterized by HPLC and GC/MS. A tentative mechanism for the formation of the products has also been suggested.

Comparative genomic hybridization analysis of hepatoblastomas

Prior cytogenetic analyses of hepatoblastomas have shown the most common recurring abnormalities to be trisomy for chromosomes 2 and 20, and a recurrent translocation involving chromosomes 1 and 4 identified in a minority of cases. Four cases have shown double minute chromosomes, which provide cytogenetic evidence for gene amplification, although no particular genes or genetic regions have been shown to be amplified. To further investigate the cytogenetic changes involved in the pathogenesis and progression of hepatoblastoma, this study analyzes 10 tumors by comparative genomic hybridization. Regions of relative gain or loss were found in nine tumors. The most common recurrent abnormalities were gain of the long arm of chromosome 1 (six tumors), gain of chromosomes 2 (seven tumors), 17 (four tumors), and 20 (three tumors), and loss of chromosomes 4 and 11 (two tumors each). Four cases showed restricted regions of high-level gain at 1q32 or 2q24, regions that have previously been reported to be amplified in other tumors, but not in hepatoblastomas. A specific amplified gene has yet to be identified at these loci, although candidate genes have been proposed and may offer targets for future studies. Genes Chromosomes Cancer 27:196-201, 2000.