Network module function enrichment analysis of lung squamous cell carcinoma and lung adenocarcinoma.

BACKGROUND: Lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) are the two major subtypes of non-small cell lung cancer that pose a serious threat to human health. However, both subtypes currently lack effective indicators for early diagnosis. METHODS: To identify tumor-specific indicators and predict cancer-related signaling pathways, LUSC and LUAD gene weighted co-expression networks were constructed. Combined with clinical data, core genes in LUSC and LUAD modules were then screened using protein-protein interaction networks and their functions and pathways were analyzed. Finally, the effect of core genes on survival of LUSC and LUAD patients was evaluated. RESULTS: We identified 12 network modules in LUSC and LUAD, respectively. LUSC modules "purple" and "green" and LUAD modules "brown" and "pink" are significantly associated with overall survival and clinical traits of tumor node metastasis, respectively. Eleven genes from LUSC and eight genes from LUAD were identified as candidate core genes, respectively. Survival analysis showed that high expression of SLIT3, ABI3BP, MYOCD, PGM5, TNXB, and DNAH9 are associated with decreased survival in LUSC patients. Furthermore, high expression of BUB1, BUB1B, TTK, and UBE2C are associated with lower patient survival. CONCLUSIONS: We found biomarker genes and biological pathways for LUSC and LUAD. These network hub genes are associated with clinical characteristics and patient outcomes and they may play important roles in LUSC and LUAD.

Shared network pattern of lung squamous carcinoma and adenocarcinoma illuminates therapeutic targets for non-small cell lung cancer.

Background: Non-small cell lung cancer (NSCLC) is a malignant tumor with high mortality. Lung squamous carcinoma (LUSC) and lung adenocarcinoma (LUAD) are the common subtypes of NSCLC. However, how LUSC and LUAD are compatible remains to be elucidated. Methods: We used a network approach to find highly interconnected genes shared with LUSC and LUAD, and we then built modules to assess the degree of preservation between them. To quantify this result, Z-scores were used to summarize the interrelationships between LUSC and LUAD. Furthermore, we correlated network hub genes with patient survival time to identify risk factors. Results: Our findings provided a look at the regulatory pattern for LUSC and LUAD. For LUSC, several genes, such as AKR1C1, AKR1C2, and AKR1C3, play key roles in regulating network modules of cell growth pathways. In addition, CCL19, CCR7, CCL21, and LY9 are enriched in LUAD network modules of T lymphocyte-related pathways. LUSC and LUAD have similar expressed gene expression patterns. Their networks share 46 hub genes with connectivity greater than 0.9. These genes are correlated with patient survival time. Among them, the expression level of COL5A2 in LUSC and LUAD is higher than that in normal tissues, which is closely related to the poor prognosis of LUSC and LUAD patients. Conclusion: LUSC and LUAD share a network pattern. COL5A2 may be a risk factor in poor prognosis in LUSC and LUAD. The common landscape of LUSC and LUAD will help better define the regulation of NSCLC candidate genes and achieve the goals of precision medicine.

Warfarin Adherence Among Patients with Atrial Fibrillation in Rural Area of Dongyang, China: A Questionnaire-Based Study.

Introduction: Adherence to warfarin is associated with improved outcome in patients with atrial fibrillation (AF), but the adherence status of patients in rural areas of China is not known. Methods: A questionnaire-based study evaluating warfarin adherence of rural residents with AF was carried out in Dongyang, China. Potentially eligible patients were screened and contacted by telephone, and their demographic characteristics were collected. Illness perception was assessed using the Brief Illness Perception Questionnaire (BIPQ), and warfarin adherence was assessed using a Chinese-version adherence scale. Univariate and multivariate analyses were conducted to identify factors associated with unsatisfactory adherence. Results: A total of 201 patients (male, n=99; mean age, 70.3±8.12 years) were included, among whom 95 (47.3%) patients showed good adherence and 63 (31.3%) poor adherence. Number of co-dispensed drugs (multivariate analysis: odds ratio [OR]=3.64, 95% confidence interval [CI] 1.35-9.81, p=0.011) and BIPQ score (OR=1.25, 95% CI 1.17-1.33, p<0.001) were identified as factors associated with good adherence. Conclusion: Medical adherence to warfarin needs to improve in rural patients with AF. Efforts that can reduce the number of co-dispensed drugs and increase illness perception may improve warfarin adherence. This study may benefit future management of warfarin administration to rural patients with AF.

Potential role of chimeric genes in pathway-related gene co-expression modules.

BACKGROUND: Gene fusion has epigenetic modification functions. The novel proteins encoded by gene fusion products play a role in cancer development. Therefore, a better understanding of the novel protein products may provide insights into the pathogenesis of tumors. However, the characteristics of chimeric genes are rarely studied. Here, we used weighted co-expression network analysis to investigate the biological roles and underlying mechanisms of chimeric genes. METHODS: Download the pig transcriptome data, we screened chimeric genes and parental genes from 688 sequences and 153 samples, predict their domains, and analyze their associations. We constructed a co-expression network of chimeric genes in pigs and conducted Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the generated modules using DAVID to identify key networks and modules related to chimeric genes. RESULTS: Our findings showed that most of the protein domains of chimeric genes were derived from fused pre-genes. Chimeric genes were enriched in modules involved in the negative regulation of cell proliferation and protein localization to centrosomes. In addition, the chimeric genes were related to the growth factor-ß superfamily, which regulates cell growth and differentiation. Furthermore, in helper T cells, chimeric genes regulate the specific recognition of T cell receptors, implying that chimeric genes play a key role in the regulation pathway of T cells. Chimeric genes can produce new domains, and some chimeric genes are a key role involved in pathway-related function. CONCLUSIONS: Most chimeric genes show binding activity. Domains of chimeric genes are derived from several combinations of parent genes. Chimeric genes play a key role in the regulation of several cellular pathways. Our findings may provide new directions to explore the roles of chimeric genes in tumors.

Biological activities of siRNA-loaded lanthanum phosphate nanoparticles on colorectal cancer.

Lanthanum can reduce absorption of phosphate by forming lanthanum phosphate complexes after oral administration of lanthanum carbonate tablets (FOSRENOL®) in patients. Based on the pH-responsive interaction of phosphate and lanthanum ions, the chitosan coated siRNA-loaded lanthanum phosphate nanoparticles (CS/LaP/siRNA NPs) were prepared for improving cancer treatment, in which polysaccharide chitosan was used as the outer shell to control the excessive growth of lanthanum phosphate complexes, and enable intestinal mucoadhesion. The CS/LaP/siEGFR NPs exhibited significant biological activities in human colorectal cancer HT-29 cells by the synergistic effects of siEGFRs and lanthanum ions, such as downregulation of EGFR and upregulation of miR-34a. Furthermore, significant tumor growth inhibition was observed in both transgenic C57BL/6-ApcMinC/Nju cancer mouse model and AOM/DSS chemically induced orthotopic colorectal cancer mouse model after intestinal instillation administration of CS/LaP/siEGFR NPs. Therefore, the lanthanum-based siRNA delivery system would provide a potential and efficient strategy for the treatment of colorectal cancers.

A novel pectin from Polygala tenuifolia blocks Aß42 aggregation and production by enhancing insulin-degradation enzyme and neprilysin.

More and more evidences show that pectin polysaccharide may have impact on Aß42, one important molecule implicated in Alzhemer's disease pathology. We speculate special structural motif of pectin might have better bioactivity on Aß42. To address this hypothesis, we reported structure and impact of a novel pectin RP02-1 with the molecular weight of 116.0 kDa from roots of Polygala tenuifolia on Aß42 aggregation and production and the underlying mechanism. Its structure is characterized as a backbone of alternate 1, 2, 4-linked α-Rhap and 1, 4-linked α-GalpA, with branches of terminal (T) -, 1, 3-,1, 4-, 1, 6- and 1, 3, 6-linked ß-Galp, T-, 1, 5- and 1, 3, 5-linked α-Araf substituted at C-4 of 1, 2, 4-linked α-Rhap. Bioactivity study shows that this pectin may significantly block the aggregation of Aß42. We further show that RP02-1 suppresses Aß42 production with no apparent cytotoxicity in both CHO/APPBACE1 and HEK293-APPsw cells. Mechanism study demonstrates that RP02-1 may enhance the expression of insulin-degradation enzyme (IDE) and neprilysin (NEP), which are the main enzymes involved in Aß degradation. These results suggest that RP02-1 may be a candidate leading compound for anti-Alzheimer's disease new drug development by attenuating Aß42 production and inhibiting Aß42 aggregation.