Rule mining on microRNA expression profiles for human disease understanding

University of Technology Sydney. Faculty of Engineering and Information Technology.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

An electrophysiological signature for proactive interference resolution in working memory

We used event-related potentials (ERPs) to study the temporal dynamics of proactive interference in working memory. Participants performed a Sternberg item-recognition task to determine whether a probe was in a target memory set. Familiar negative probes were found to be more difficult to reject than less familiar ones. A fronto-central N2 component peaking around 300 ms post-probe-onset differentiated among target probes, familiar and less familiar non-target probes. The study identifies N2 as the ERP signature for proactive interference resolution. It also indicates that the resolution process occurs in the same time window as target/non-target discrimination and provides the first piece of electrophysiological evidence supporting a recent interference resolution model based on localization data [Jonides, J., Nee, D.E., 2006. Brain mechanisms of proactive interference in working memory. Neuroscience 139, 181–193]

Increased chromatin accessibility facilitates intron retention in specific cell differentiation states

Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (RNA-seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role of chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing

Macrophage development and activation involve coordinated intron retention in key inflammatory regulators

Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response

Amine-Mediated Transimination and Aromatization-Triggered Domino Reaction in the Synthesis of Polyfunctionalized 4‑Aminoquinolines

Dearomatization provides numerous possibilities for the development of new transformative modes of aromatic compounds. A conceptually novel metal-free multicomponent domino reaction of the dearomatized products of 2-alkynylanilines is developed. The reaction involves the secondary amine-mediated transimination with α-amino nitriles and subsequent aromatization-triggered cascade rearrangement, nucleophilic cyclization, and retro-Strecker reaction. This process provided a new practical method for the rapid synthesis of polyfunctionalized 4-aminoquinolines from readily available starting materials

Resveratrol, an antioxidant, protects spinal cord injury in rats by suppressing MAPK pathway

Resveratrol, a polyphenol found in various plants, including grapes, plums and peanuts has shown various medIRInal properties, including antioxidant, protection of cardiovascular disease and cancer risk. However, the effects of resveratrol on spinal cord reperfusion injury have not been investigated. Hence, the present study was designed to evaluate the effect of resveratrol on nitric oxide synthase (iNOS)/p38MAPK signaling pathway and to elucidate its regulating effect on the protection of spinal cord injury. Spinal cord ischemia–reperfusion injury (IRI) was performed by the infrarenal abdominal aorta with mini aneurysm clip model. The expressions of iNOS and p38MAPK and the levels of biochemical parameters, including nitrite/nitrate, malondialdehyde (MDA), advanced oxidation products (AOPP), reduced glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT) were measured in control and experimental groups. IRI-induced rats treated with 10 mg/kg resveratrol protected spinal cord from ischemia injury as supported by improved biological parameters measured in spinal cord tissue homogenates. The resveratrol treatment significantly decreased the levels of plasma nitrite/nitrate, iNOS mRNA and protein expressions and phosphorylation of p38MAPK in IRI-induced rats. Further, IRI-produced free radicals were reduced by resveratrol treatment by increasing enzymatic and non-enzymatic antioxidant levels such as GSH, SOD and CAT. Taken together, administration of resveratrol protects the damage caused by spinal cord ischemia with potential mechanism of suppressing the activation of iNOS/p38MAPK pathway and subsequent reduction of oxidative stress due to IRI

A multiomics dataset for the study of RNA modifications in human macrophage differentiation and polarisation

Abstract RNA modifications have emerged as central regulators of gene expression programs. Amongst RNA modifications are N6-methyladenosine (m6A) and RNA 5-hydroxymethylcytosine (5hmC). While m6A is established as a versatile regulator of RNA metabolism, the functions of RNA 5hmC are unclear. Despite some evidence linking RNA modifications to immunity, their implications in gene expression control in macrophage development and functions remain unclear. Here we present a multi-omics dataset capturing different layers of the gene expression programs driving macrophage differentiation and polarisation. We obtained mRNA-Seq, m6A-IP-Seq, 5hmC-IP-Seq, Polyribo-Seq and LC-MS/MS data from monocytes and resting-, pro- and anti-inflammatory-like macrophages. We present technical validation showing high quality and correlation between samples for all datasets, and evidence of biological consistency of modelled macrophages at the transcriptomic, epitranscriptomic, translational and proteomic levels. This multi-omics dataset provides a resource for the study of RNA m6A and 5hmC in the context of macrophage biology and spans the gene expression process from transcripts to proteins

Janus kinase 2 polymorphisms are associated with risk in patients with gastric cancer in a Chinese population.

AIM: To evaluate the impact of the Janus kinase 2 single nucleotide polymorphisms (SNPs) on gastric cancer risk. METHODS: In this hospital-based, case-control study, the genotypes were identified by polymerase chain reaction-restriction fragment length polymorphism protocols in 661 individuals (359 gastric cancer patients and 302 age and sex matched cancer-free controls). RESULTS: Both the frequency of A allele in rs2230724 and G allele in rs1887427 were more frequent in patients with gastric cancer (P = 0.013 and 0.001, respectively). Compared with the common genotype, subjects with the (AG+AA) genotypes of rs2230724 and the (AG+GG) genotypes of rs1887427 had a 59% and 98% increased risk of developing gastric cancer, respectively (P = 0.010, adjusted OR = 1.59, 95% CI = 1.12-2.27; P56 years), males, nonsmokers and urban subjects, while the association between the risk and the rare genotypes of rs1887427 persisted in subgroups of younger individuals (≤56 years), males, nonsmokers and both of rural and urban subjects. CONCLUSION: The JAK2 gene rs2230724 and rs1887427 polymorphisms are associated with an increased risk of gastric cancer in a Chinese Han population