This research employs rule mining methods to study the important roles of miRNAs in human diseases. From past experience and from reviewing the literature, rule mining is a widely used data mining ...technique for the discovery of interesting relationships in large data sets. MicroRNAs (miRNAs) are endogenous and highly conserved non-coding RNA molecules. They can inhibit and/or promote the post-transcriptional expression of target messenger RNAs (mRNAs). miRNAs thus play a pivotal role in a cell’s differentiation, proliferation, growth, mobility, and apoptosis, as well as in viral replication and proliferation. This has inspired many research works aimed at detecting miRNAs’ functions in human disease. However, with the current deluge of miRNA data, previous works have suffered from limitations in terms of handling the relationship between various molecules. Firstly, they usually identify single miRNAs as biomarkers, and always produce low sensitivity and specificity. Secondly, intensive research largely depends on the inverse expression relationships between miRNAs and mRNAs to discover miRNA-mRNA regulatory modules. Finally, the miRNA-miRNA co-regulations and miRNA self-regulations have not been well investigated. As a result, rule mining is a powerful new technology with great potential to help researchers focus on the most important miRNAs for understanding human diseases. This thesis reports our past and current research outcomes in this area. The contributions of the thesis are as follows:• A novel rule mining method is proposed to detect the significant miRNA biomarkers.• A “change to change” method is proposed to mine both positive and negative regulatory relationships from paired miRNA and mRNA expression data sets.• A progressive data refining approach is proposed to identify the lung cancer miRNA-miRNA co-regulation network.• A novel framework is proposed to detect the self-regulation miRNAs. The research was conducted through four case studies. (1) The first case study was on lung squamous cell carcinoma for accurate diagnosis of this disease through the reliable miRNA biomarkers identified by a novel rule discovery method. (2) The second case study was on paired miRNA and mRNA expression data of HCV patients to detect both positive and negative regulatory modules. (3) The third case study was on lung cancer data sets for the computational methods to identify miRNA-miRNA co-regulation networks and miRNA-miRNA co-regulatory relationships. (4) The fourth case study was on multiple data types to infer self-regulation miRNAs in humans through an integrative rule mining framework and approach. All the results have been verified by the existing literature and databases.
The innate immune response contributes to the development or attenuation of acute and chronic diseases, including cancer. Microbial DNA and mislocalized DNA from damaged host cells can activate ...different host responses that shape disease outcomes. Here, we show that mice and humans lacking a single allele of the DNA repair protein Ku70 had increased susceptibility to the development of intestinal cancer. Mechanistically, Ku70 translocates from the nucleus into the cytoplasm where it binds to cytosolic DNA and interacts with the GTPase Ras and the kinase Raf, forming a tripartite protein complex and docking at Rab5
Rab7
early-late endosomes. This Ku70-Ras-Raf signalosome activates the MEK-ERK pathways, leading to impaired activation of cell cycle proteins Cdc25A and CDK1, reducing cell proliferation and tumorigenesis. We also identified the domains of Ku70, Ras, and Raf involved in activating the Ku70 signaling pathway. Therapeutics targeting components of the Ku70 signalosome could improve the treatment outcomes in cancer.
Abstract
Neuroblastoma is the most common solid tumour during early childhood, and accounts for 15% of all childhood cancer death. One of the key features of neuroblastoma is aggressive progression ...due to tumour-driven angiogenesis. However, the mechanism through which neuroblastoma cells drive angiogenesis is unclear. Here we showed that the long noncoding RNA MALAT1 was over-expressed in human neuroblastoma cells under hypoxic condition, the condition which triggers pro-angiogenic switch and angiogenesis. In vitro angiogenesis assays demonstrated that conditioned medium from neuroblastoma cells transfected with MALAT1 siRNAs, compared with conditioned medium from neuroblastoma cells transfected with control siRNAs, induced considerably less endothelial cell migration, invasion and vascular sprouting under hypoxic condition. Affymetrix microarray differential gene expression study showed that one of the genes most significantly down-regulated by MALAT1 siRNAs in human neuroblastoma cells under hypoxic condition, was fibroblast growth factor (FGF). RT-PCR and immunoblot analyses confirmed that MALAT1 siRNAs reduced FGF mRNA and protein expression, and in vitro angiogenesis assays demonstrated that forced over-expression of FGF in neuroblastoma cells blocked MALAT1 siRNA-mediated reduction in endothelial cell migration, invasion and vascular sprouting. Taken together, our data suggest that over-expression of MALAT1 in human neuroblastoma cells plays an important role hypoxia-driven angiogenesis by up-regulating FGF mRNA expression.
Citation Format: Andrew E. Tee, Peiyan Liu, Jesper Maag, Renhua Song, Jinyan Li, Belamy B. Cheung, Michelle Haber, Murray D. Norris, Glenn M. Marshall, Marcel Dinger, Tao Liu. The long noncoding RNA MALAT1 promotes hypoxia-driven angiogenesis by upregulating pro-angiogenic gene expression in neuroblastoma cells. abstract. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 146. doi:10.1158/1538-7445.AM2015-146
Background & Aims: The liver has complex interconnecting blood vessel and biliary networks; however, how the vascular and biliary network form and regulate each other and liver function are not ...well-understood. We aimed to examine the role of Heg in mammalian liver development and functional maintenance. Methods: Global (Heg-/-) or liver endothelial cell (EC)-specific deletion of Heg (Lyve1-Cre;Hegfl/fl ) mice were used to study the in vivo function of Heg in the liver. Carbon-ink anterograde and retrograde injection were used to visualize the 3-dimensional patterning of liver portal and biliary networks, respectively. RNA sequencing, histology, and molecular and biochemical assays were used to assess liver gene expression, protein distribution, liver injury response, and function. Results: Heg deficiency in liver ECs led to a sparse liver vascular and biliary network. This network paucity does not compromise liver function under baseline conditions but did alter liver zonation. Molecular analysis revealed that endothelial Heg deficiency decreased expression of Wnt ligands/agonists including Wnt2, Wnt9b, and Rspo3 in ECs, which limits Axin2 mediated canonical Wnt signaling and the expression of cytochrome P450 enzymes in hepatocytes. Under chemical-induced stressed conditions, Heg-deficiency in liver ECs protected mice from drug-induced liver injuries. Conclusion: Our study found that endothelial Heg is essential for the 3-D patterning of the liver vascular and indirectly regulates biliary networks and proper liver zonation via its regulation of Wnt ligand production in liver endothelial cells. The endothelial Heg-initiated changes of the liver metabolic zonation and metabolic enzyme expression in hepatocytes was functionally relevant to xenobiotic metabolism and drug induced liver toxicity.
Virilizer-like m
A methyltransferase-associated protein (VIRMA) maintains the stability of the m
A writer complex. Although VIRMA is critical for RNA m
A deposition, the impact of aberrant VIRMA ...expression in human diseases remains unclear. We show that VIRMA is amplified and overexpressed in 15-20% of breast cancers. Of the two known VIRMA isoforms, the nuclear-enriched full-length but not the cytoplasmic-localised N-terminal VIRMA promotes m
A-dependent breast tumourigenesis in vitro and in vivo. Mechanistically, we reveal that VIRMA overexpression upregulates the m
A-modified long non-coding RNA, NEAT1, which contributes to breast cancer cell growth. We also show that VIRMA overexpression enriches m
A on transcripts that regulate the unfolded protein response (UPR) pathway but does not promote their translation to activate the UPR under optimal growth conditions. Under stressful conditions that are often present in tumour microenvironments, VIRMA-overexpressing cells display enhanced UPR and increased susceptibility to death. Our study identifies oncogenic VIRMA overexpression as a vulnerability that may be exploited for cancer therapy.
TRPP2 channel protein belongs to the superfamily of transient receptor potential (TRP) channels and is widely expressed in various tissues, including smooth muscle in digestive gut. Accumulating ...evidence has demonstrated that TRPP2 can mediate Ca
2+
release from Ca
2+
stores. However, the functional role of TRPP2 in gallbladder smooth muscle contraction still remains unclear. In this study, we used Ca
2+
imaging and tension measurements to test agonist-induced intracellular Ca
2+
concentration increase and smooth muscle contraction of guinea pig gallbladder, respectively. When TRPP2 protein was knocked down in gallbladder muscle strips from guinea pig, carbachol (CCh)-evoked Ca
2+
release and extracellular Ca
2+
influx were reduced significantly, and gallbladder contractions induced by endothelin 1 and cholecystokinin were suppressed markedly as well. CCh-induced gallbladder contraction was markedly suppressed by pretreatment with U73122, which inhibits phospholipase C to terminate inositol 1,4,5-trisphosphate receptor (IP
3
) production, and 2-aminoethoxydiphenyl borate (2APB), which inhibits IP
3
recepor (IP
3
R) to abolish IP3R-mediated Ca
2+
release. To confirm the role of Ca
2+
release in CCh-induced gallbladder contraction, we used thapsigargin (TG)-to deplete Ca
2+
stores via inhibiting sarco/endoplasmic reticulum Ca
2+
-ATPase and eliminate the role of store-operated Ca
2+
entry on the CCh-induced gallbladder contraction. Preincubation with 2 μmol L
-1
TG significantly decreased the CCh-induced gallbladder contraction. In addition, pretreatments with U73122, 2APB or TG abolished the difference of the CCh-induced gallbladder contraction between TRPP2 knockdown and control groups. We conclude that TRPP2 mediates Ca
2+
release from intracellular Ca
2+
stores, and has an essential role in agonist-induced gallbladder muscle contraction.
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