Genome-wide discovery of circulating cell-free DNA methylation biomarkers for colorectal cancer detection.

BACKGROUND: Colorectal polyp is known a precursor of colorectal cancer (CRC) that holds an increased risk for progression to CRC. Circulating cell-free DNA (cfDNA) methylation has shown favorable performance in the detection and monitoring the malignant progression in a variety of cancers. RESULTS: To discover cfDNA methylation markers for the diagnosis of CRC, we first performed a genome-wide analysis between eight CRC and eight polyp tissues using the Infinium HumanMethylationEPIC BeadChip. We identified 7008 DMCs, and after filtering, we validated 39 DMCs by MethylTarget sequencing in 62 CRC and 56 polyp tissues. A panel of four CpGs (cg04486886, cg06712559, cg13539460, and cg27541454) was selected as the methylation marker in tissue by LASSO and random forest models. A diagnosis prediction model was built based on the four CpGs, and the methylation diagnosis score (md-score) can effectively discriminate tissues with CRC from polyp patients (AUROC > 0.9). Finally, the cg27541454 was confirmed hypermethylated in CRC (AUC = 0.85) in the plasma validation cohort. CONCLUSIONS: Our findings suggest that the md-score could robustly detect CRC from polyp tissues, and cg27541454 may be a promising candidate noninvasive biomarker for CRC early diagnosis.

RAGE ablation attenuates glioma progression and enhances tumor immune responses by suppressing galectin-3 expression.

BACKGROUND: Malignant gliomas consist of heterogeneous cellular components that have adopted multiple overlapping escape mechanisms that overcome both targeted and immune-based therapies. The receptor for advanced glycation end products (RAGE) is a member of the immunoglobulin superfamily that is activated by diverse proinflammatory ligands present in the tumor microenvironment. Activation of RAGE by its ligands stimulates multiple signaling pathways that are important in tumor growth and invasion. However, treatment strategies that only target the interaction of RAGE with its ligands are ineffective as cancer therapies due to the abundance and diversity of exogenous RAGE ligands in gliomas. METHODS: As an alternative approach to RAGE ligand inhibition, we evaluated the genetic ablation of RAGE on the tumorigenicity of 2 syngeneic murine glioma models. RAGE expression was inhibited in the GL261 and K-Luc gliomas by shRNA and CRSPR/Cas9 techniques prior to intracranial implantation. Tumor growth, invasion, and inflammatory responses were examined by histology, survival, Nanostring, and flow cytometry. RESULTS: Intracellular RAGE ablation abrogated glioma growth and invasion by suppressing AKT and ERK1/2 activities and by downregulating MMP9 expression. Interestingly, RAGE inhibition in both glioma models enhanced tumor inflammatory responses by downregulating the expression of galectin-3 and potentiated immunotherapy responses to immune checkpoint blockade. CONCLUSIONS: We demonstrated that intracellular RAGE ablation suppresses multiple cellular pathways that are important in glioma progression, invasion, and immune escape. These findings strongly support the development of RAGE ablation as a treatment strategy for malignant gliomas.

Colorectal cancer cell intrinsic fibroblast activation protein alpha binds to Enolase1 and activates NF-κB pathway to promote metastasis.

Fibroblast activation protein alpha (FAP) is a marker of cancer-associated fibroblast, which is also expressed in cancer epithelial cells. However, the role of FAP in colorectal cancer (CRC) cells remains to be elucidated. Here we investigate the expression pattern of FAP in CRC tissues and cells to prove that FAP is upregulated in CRC cells. Loss- of and gain-of-function assays identified FAP promotes migration and invasion instead of an effect on cell proliferation. Microarray assays are adopted to identify the different expressed genes after FAP knockdown and gene set enrichment analysis (GSEA) is used to exploit the involved signaling pathway. Our works reveal FAP exerts a function dependent on NF-κB signaling pathway and FAP expression is associated with NF-κB signaling pathway in clinical samples. Our work shows FAP is secreted by CRC cells and soluble FAP could promote metastasis. To investigate the mechanism of FAP influencing the NF-κB signaling pathway, LC/MS is performed to identify the proteins interacting with FAP. We find that FAP binds to ENO1 and activates NF-κB signaling pathway dependent on ENO1. Blocking ENO1 could partially reverse the pro-metastatic effect mediated by FAP. We also provide evidences that both FAP and ENO1 are associated with CRC stages, and high levels of FAP and ENO1 predict a poor survival in CRC patients. In summary, our work could provide a novel mechanism of FAP in CRC cells and a potential strategy for treatment of metastatic CRC.

Prediction of the Prognosis Based on Chromosomal Instability-Related DNA Methylation Patterns of ELOVL2 and UBAC2 in PTCs.

Papillary thyroid carcinoma (PTC) is the most common malignant tumor of endocrine systems. Chromosomal instability (CIN) is crucial to the clinical prognoses of tumor patients. DNA methylation plays an important role in the regulation of gene expression and CIN. Based on PTC samples from The Cancer Genome Atlas database, we used multiple regression analyses to identify methylation patterns of CpG sites with the strongest correlation with gene expression. A total of 4,997 genes were obtained through combining the CpG sites, which were represented as featured DNA methylation patterns. In order to identify CIN-related epigenetic markers of PTC survival, we developed a method to characterize CIN based on DNA methylation patterns of genes using the Student's t statistics. We found that 1,239 genes were highly associated with CIN. With the use of the log-rank test, univariate Cox regression analyses, and the Kaplan-Meier method, DNA methylation patterns of UBAC2 and ELOVL2, highly correlated with CIN, provided potential prognostic values for PTC. The higher these two genes, risk scores were correlated with worse PTC patient prognoses. Moreover, the ELOVL2 risk score was significantly different in the four stages of PTC, suggesting that it was related to the progress of PTC. The DNA methylation pattern associated with CIN may therefore be a good predictor of PTC survival.

Iodine promotes thyroid cancer development via SPANXA1 through the PI3K/AKT signalling pathway.

The aim of this study was to examine the impact of iodine on the development of thyroid cancer cells and to detect the underlying mechanisms. It was observed that proliferation was promoted and apoptosis was inhibited in cells treated with iodine at a specific concentration. This treatment group was then selected for further analysis, to investigate how iodine affects the development of thyroid cancer cells. It was reported that sperm protein associated with the nucleus, X-linked, family member A1 (SPANXA1) expression in iodine-treated cells was significantly upregulated. Furthermore, downregulation of SPANXA1 inhibited cell proliferation, migration and invasion, and promoted cell apoptosis. These results suggested that SPANXA1 played an important role in iodine-treated thyroid cancer cells. Novel associations between SPANXA1 and thyroid cancer were described in the current study. In addition, SPANXA1 gene silencing resulted in the downregulation of PI3K and phosphorylated (p)AKT expression in iodine-treated thyroid cancer cells, whereas iodine treatment alone resulted in upregulated PI3K and p-AKT expression. Inhibiting PI3K further suppressed cell proliferation and contributed to apoptosis, even in the presence of SPANXA1 at high levels. As a consequence, PI3K/AKT may be one of the key signalling pathways by which iodine promotes thyroid cancer development in association with SPANXA1. In addition, our results further suggested that patients with thyroid cancer may need to avoid high-iodine intake.

Upregulation Of Protein Tyrosine Phosphatase Receptor Type C Associates To The Combination Of Hashimoto's Thyroiditis And Papillary Thyroid Carcinoma And Is Predictive Of A Poor Prognosis.

INTRODUCTION: PTC is not generally considered a lethal disease, but prone to recurrence as the prognosis. Hashimoto's thyroiditis (HT) is an important factor that affects the prognosis of papillary thyroid carcinoma (PTC). It is crucial to find biomarkers to identify the combination of HT with PTC and to predict the prognosis. METHODS: RNASeq data from the Cancer Genome Atlas (TCGA) database was used to screen differentially expressed genes (DEGs) of PTC with HT via the edgeR package of R software version 3.3.0. Also, the DEGs were applied to the DAVID web-based tool to determine the enrichment of gene functions via Gene Ontology (GO) analysis and to identify associated pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. By constructing protein interaction networks within Cytoscape software, we screened candidate genes and explored possible relationships with the clinical phenotype of PTC. Finally, additional thyroid tissue samples were collected to verify the results above. RESULTS: After analyzing the RNA-Seq data of PTC patients from the Cancer Genomic Atlas, 497 differentially expressed PTC genes were found to be associated with HT, of which protein tyrosine phosphatase receptor type C (PTPRC), KIT, and COL1A1 were associated with tumor size and lymph node metastasis (p < 0.05). Verification of these results with another 30 thyroid tissues of clinical PTC patients revealed that the expression level of PTPRC in the PTC with HT group was higher than that in the PTC without HT group (p < 0.05) and the ROC curve showed a good discrimination (area under the curve = 0.846). However, the correlation with the clinical phenotype was not statistically significant (p > 0.05). DISCUSSION: These data suggest that upregulation of PTPRC enhances the incidence of HT associated with PTC and is also predictive of a poor prognosis.

Three single nucleotide polymorphisms associated with type 2 diabetes mellitus in a Chinese population.

An Indian study recently observed three new loci: rs9552911 in the SGCG, rs1593304 near PLXNA4 and rs4858889 in SCAP associated with type 2 diabetes mellitus (T2DM) in a south Asian population. The present study aimed to validate these findings in a Chinese population. We genotyped the above three single-nucleotide polymorphisms (SNPs), rs9552911, rs1593304, and rs4858889, in a group of 1,972 Chinese individuals, comprising of 966 type 2 diabetic patients and 976 controls. Anthropometric variables and biochemical traits were measured in all the participants. The association analyses of genotype-disease and genotype-traits were estimated. The genotype frequency of rs9552911 differed statistically between the cases and controls (P=0.017). The difference was also evident between the cases and controls in non-obese participants (P=0.033). In addition, the SNP rs9552911 was associated with weight (P=0.033), total cholesterol (P=0.006) and low-density lipoprotein-cholesterol (P=0.007). The SNP rs1593304 was associated with ß-cell function estimated by the homeostatic model assessment of ß-cell function (P=0.041). However, there was no significant association between rs4858889 and T2DM. In conclusion, the results show that the SNP rs9552911 was associated with T2DM, possibly by affecting body mass index and lipid metabolism. The SNP rs1593304 may impair ß-cell function.

The Gas6 gene rs8191974 and Ap3s2 gene rs2028299 are associated with type 2 diabetes in the northern Chinese Han population.

Previous studies in other countries have shown that single nucleotide polymorphisms (SNPs) in the growth arrest-specific gene 6 (Gas6; rs8191974) and adapter-related protein complex 3 subunit sigma-2 (Ap3s2; rs2028299) were associated with an increasedrisk for type 2 diabetes mellitus (T2DM). However, the association of these loci with T2DM has not been examined in Chinese populations. We performed a replication study to investigate the association of these susceptibility loci with T2DM in the Chinese population.We genotyped 1968 Chinese participants (996 with T2DM and 972controls) for rs8191974 in Gas6 and rs2028299 near Ap3s2, and examined their association with T2DM using a logistic regression analysis. We also analyzed the correlation of genotypes and clinical phenotypes. The distribution of the T allele of SNP rs8191974 in the Gas6 gene was significantly different between T2DM cases and controls when compared with the C allele (P<0.05, OR: 0.80, 95% CI: 0.69-0.94). The occurrence of the CT genotype and the dominant model was also significantly less frequent in the T2DM cases vs. controls when compared with the CC genotype (CT vs. CC: P<0.05, OR: 0.75, 95% CI:0.62-0.90; TT+CT vs. CC: P<0.05, OR:0.75, 95% CI:0.63-0.90). In SNP rs2028299, the allele C showed no statistically significant differencein distribution between the control and T2DM groups when compared with allele A. However, in male populations, the dominant model was statistically more frequent when compared with genotype AA (CC+CA vs. AA: P<0.05, OR:1.29, 95% CI:1.02-1.64), and in obesity-stratified analysis, we also observed a significant difference in the distribution of the dominant model between the T2DM cases and controls in subjects with BMI≥24 kg/m2 and BMI<28kg/m2 (CC+CA vs. AA: P<0.05, OR: 6.33, 95% CI:4.17-9.61). In conclusion, our study shows that SNPsrs8191974 and rs2028299 are significantly associated with T2DM in the Chinese population.

Association of ADIPOQ variants with type 2 diabetes mellitus susceptibility in ethnic Han Chinese from northeast China.

AIMS/INTRODUCTION: To investigate the association between two single nucleotide polymorphisms (SNPs; rs3774261 and rs822393) in the ADIPOQ gene and type 2 diabetes mellitus in Han Chinese from northeast China. MATERIALS AND METHODS: The present study comprised 993 type 2 diabetes mellitus patients and 966 unrelated controls from northeastern China. Two SNPs were sequenced using SNPscan. The distribution of genotype frequencies of the two SNPs in ADIPOQ between cases and controls, and in subgroups stratified based on body mass index, were compared using logistic regression analysis. Linear regression was used to analyze the association between each SNP and clinical indicators. RESULTS: The GG genotype of rs3774261 increased the risk of type 2 diabetes mellitus compared with the AA genotype in participants with a body mass index <24 (P = 0.021; odds ratio 1.636, 95% CI 1.708-2.484). Rs822393 was correlated with glycosylated hemoglobin (P = 0.043) in controls. Rs3774261 had an association with diastolic blood pressure (P = 0.017) in controls, and in controls with a body mass index <24; rs3774261 also had an association with both systolic blood pressure (P = 0.025) and diastolic blood pressure (P = 0.043). CONCLUSIONS: The present results confirm the association between ADIPOQ variants and type 2 diabetes mellitus in northeastern China. However, additional larger replication studies are required to validate these findings.