High incidence of LRAT promoter hypermethylation in colorectal cancer correlates with tumor stage. Med Oncol. 2014;31:254. [PMID: 25260806 DOI: 10.1007/s12032-014-0254-7]

The diagnostic and prognostic value of C1orf174 in colorectal cancer

Introduction

Colorectal cancer (CRC) is among the lethal cancers, indicating the need for the identification of novel biomarkers for the detection of patients in earlier stages. RNA and microRNA sequencing were analyzed using bioinformatics and machine learning algorithms to identify differentially expressed genes (DEGs), followed by validation in CRC patients.

Methods

The genome-wide RNA sequencing of 631 samples, comprising 398 patients and 233 normal cases was extracted from the Cancer Genome Atlas (TCGA). The DEGs were identified using DESeq package in R. Survival analysis was evaluated using Kaplan-Meier analysis to identify prognostic biomarkers. Predictive biomarkers were determined by machine learning algorithms such as Deep learning, Decision Tree, and Support Vector Machine. The biological pathways, protein-protein interaction (PPI), the co-expression of DEGs, and the correlation between DEGs and clinical data were evaluated. Additionally, the diagnostic markers were assessed with a combioROC package. Finally, the candidate tope score gene was validated by Real-time PCR in CRC patients.

Results

The survival analysis revealed five novel prognostic genes, including KCNK13, C1orf174, CLEC18A, SRRM5, and GPR89A. Thirty-nine upregulated, 40 downregulated genes, and 20 miRNAs were detected by SVM with high accuracy and AUC. The upregulation of KRT20 and FAM118A genes and the downregulation of LRAT and PROZ genes had the highest coefficient in the advanced stage. Furthermore, our findings showed that three miRNAs (mir-19b-1, mir-326, and mir-330) upregulated in the advanced stage. C1orf174, as a novel gene, was validated using RT-PCR in CRC patients. The combineROC curve analysis indicated that the combination of C1orf174-AKAP4-DIRC1-SKIL-Scan29A4 can be considered as diagnostic markers with sensitivity, specificity, and AUC values of 0.90, 0.94, and 0.92, respectively.

Conclusion

Machine learning algorithms can be used to Identify key dysregulated genes/miRNAs involved in the pathogenesis of diseases, leading to the detection of patients in earlier stages. Our data also demonstrated the prognostic value of C1orf174 in colorectal cancer.

Identification of prognostic biomarkers related to retinoic acid metabolism in gliomas and analysis of their impact on the immune microenvironment

Glioma is a primary tumor of the central nervous system. Numerous investigations have demonstrated that retinoic acid (RA) signaling plays an important role in glioblastoma. This research aimed to develop a RA metabolism-related gene signature associated with glioma. The RA metabolism-related differentially expressed genes were obtained through differential analysis of RA metabolism-related genes in GSE4290. The univariate Cox and least absolute shrinkage and selection operator regression analysis were adopted to build a RA metabolism-related glioma prognostic signature. We further conducted immune feature estimation and functional enrichment analysis between 2 risk subgroups. Finally, the potential drug-targeting prognostic genes were predicted through the DrugBank database. A sum of 10 RA metabolism-related differentially expressed genes between normal and tumor groups were identified. Then, a RA metabolism-related prognostic signature was built based on the 7 prognostic genes (ADH4, DHRS3, DHRS9, LRAT, RDH10, RDH12, and RDH5). Glioma patients were separated into 2 risk subgroups (low-risk vs high-risk) based on the median value of the risk score. We found that monocytes were negatively correlated with DHRS9, while activated naive CD4+T cell was positively correlated with RDH10. These prognostic genes participated in some immune-related processes, such as "B cell-mediated immunity." Finally, 4 drugs targeting DHRS3, LRAT, and RDH12 were predicted, including vitamin A, nicotinamide adenine dinucleotide, ethanol, and cyclohexylformamide. The prognostic signature comprised of ADH4, DHRS3, DHRS9, LRAT, RDH10, RDH12, and RDH5 based on RA metabolism was established, which provided a theoretical basis and reference value for the research of glioma.

Endoplasmic reticulum stress as a target for retinoids in cancer treatment

Retinoids, natural and synthetic derivatives of vitamin A, have various regulatory activities including controlling cellular proliferation, differentiation, and death. Furthermore, they have been used to treat specific cancers with satisfying results. Nevertheless, retinoids have yet to be converted into effective systemic therapies for the majority of tumor types. Regulation of unfolded protein response signaling, and persistent activation of endoplasmic reticulum stress (ER-stress) are promising treatment methods for cancer. The present article reviews the current understanding of how vitamin A and its derivatives may aid to cause ER-stress-activated apoptosis, as well as therapeutic options for exploiting ER-stress for achieving beneficial goal. The therapeutic use of some retinoids discussed in this article was related to decreased disease recurrence and improved therapeutic outcomes via ER-stress activation and promotion, indicating that retinoids may play an important role in cancer treatment and prevention. More research is needed to expand the use of vitamin A derivatives in cancer therapy, either alone or in combination with unfolded protein response inducers.

Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer

BACKGROUND

Aberrant methylation is common during the initiation and progression of colorectal cancer (CRC), and detecting these changes that occur during early adenoma (ADE) formation and CRC progression has clinical value.

AIM

To identify potential DNA methylation markers specific to ADE and CRC.

METHODS

Here, we performed SeqCap targeted bisulfite sequencing and RNA-seq analysis of colorectal ADE and CRC samples to profile the epigenomic-transcriptomic landscape.

RESULTS

Comparing 22 CRC and 25 ADE samples, global methylation was higher in the former, but both showed similar methylation patterns regarding differentially methylated gene positions, chromatin signatures, and repeated elements. High-grade CRC tended to exhibit elevated methylation levels in gene promoter regions compared to those in low-grade CRC. Combined with RNA-seq gene expression data, we identified 14 methylation-regulated differentially expressed genes, of which only AGTR1 and NECAB1 methylation had prognostic significance.

CONCLUSION

Our results suggest that genome-wide alterations in DNA methylation occur during the early stages of CRC and demonstrate the methylation signatures associated with colorectal ADEs and CRC, suggesting prognostic biomarkers for CRC.

Mechanism of Phellodendron and Anemarrhena Drug Pair on the Treatment of Liver Cancer Based on Network Pharmacology and Bioinformatics

Background

This study aims to explore the key targets and signaling pathways of the traditional Chinese medicine Phellodendron and Anemarrhena drug pair (PADP) for the treatment of liver cancer.

Methods

Firstly, bioinformatics technology was used to analyze GSE62232 gene chip to obtain the differential genes of liver cancer. A network pharmacology technology was used to find the active components of PADP and their targets. Secondly, the differential genes were imported into STRING database to draw a PPI network, and network topology structure map combined with Cytoscape software. And the R language was used to identify differential gene targets and pathways through GO and KEGG pathway enrichment analysis. In addition, AutoDock Vina was used for molecular docking of core targets and core compounds. Moreover, GEPIA online analysis tool was used to perform survival analysis of the core target genes. Finally, RT-PCR was used to verify the changes of key target genes. CCK−8 assay was performed to detect cell proliferation. Flow cytometry was performed to detect the cell cycle and apoptotic. Transwell invasion assay was performed to detect cell invasion.

Results

Firstly, a total of 21,654 genes were obtained. After screening, 1019 differential genes were obtained, including 614 down-regulated genes and 405 up-regulated genes. Furthermore, after screening by ADME standards, 52 active ingredients were obtained, of which 37 were Phellodendron and 15 were Anemarrhena. And a total of 36 differential genes have been identified, including 13 up-regulated genes and 23 down-regulated genes. Moreover, through enrichment analysis, we found that PADP may treat liver cancer through multiple channels and multiple pathways including the p53 signaling pathway, IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway and so on. Secondly, the molecular docking results showed that there was certain affinity between the core compounds and core target genes. In addition, GEPIA online analysis showed that ESR1, AR, CCNB1, CDK1, AKR1C3 and CCNA2 might become potential target genes for the survival and prognosis of PADP for the treatment of liver cancer. Finally, it was found that PADP could up regulate genes ESR1 and AR, down regulate genes CCNB1, CDK1, AKR1C3, and CCNA2. PADP could promote the apoptosis of liver cancer cells, shorten the cell cycle, and inhibit the proliferation and invasion of liver cancer cells.

Conclusion

PADP may treat liver cancer through multiple targets, multiple channels, and multiple pathways, thereby suppressing cancer cells and improving the living quality of patients.

Boman B. Retinoids in Treatment of Colorectal Cancer

Retinoids are vitamin A metabolites best known for their role in embryonic development. Indeed, retinoid acid (RA) signaling plays a key role in regulating the development of the embryo body-plan by controlling embryonic stem cells (SCs). Retinoids function through their ability to induce cellular differentiation. Mutations in RA signaling pathway genes occur in most human cancers. The classic example is the chromosomal translocation involving RA receptor alpha in acute promyelocytic leukemia (APL). Because all-trans retinoic acid (ATRA) is a highly effective and often curative treatment for APL patients, determining if retinoids are efficacious for other cancer types is imperative. We review the current research on retinoids in colorectal cancer (CRC) and provide bioinformatics analyses of RA signaling. Our results show that most RA pathway genes are overexpressed and often mutated in CRC. Moreover, aberrant expression of many RA signaling proteins predicts decreased CRC patient survival. We also review aldehyde dehydrogenase (ALDH) expression in CRC because ALDH is a key enzyme in RA signaling, which regulates colonic SCs. Further investigation of RA signaling mechanisms that regulate colon SCs and how dysregulation contributes to the SC overpopulation that drives CRC growth should provide insight into strategies for designing new SC-targeted therapies for CRC.

Diagnostic value of WIF1 methylation for colorectal cancer: a meta-analysis

As a common antagonist of Wnt/β-catenin signaling, Wnt inhibitory factor 1 (WIF1) plays an important role in the tumor progression. The aim of our meta-analysis was to summarize the diagnostic value of WIF1 methylation in colorectal cancer (CRC). Eligible studies were retrieved by a systemic search among PubMed, Embase, CNKI, and Wanfang literature databases. The diagnostic value of WIF1 methylation for CRC was assessed by the summary receiver operating characteristics (SROC) test. Our meta-analysis of 12 studies between 1420 CRC samples and 946 control samples showed that WIF1 hypermethylation was significantly associated with CRC (P < 0.001, OR = 30.10, 95% CI = 19.48-46.50). WIF1 hypermethylation, as a diagnostic biomarker for CRC, has a pooled sensitivity of 0.40 (95% CI: 0.37-0.42), a pooled specificity of 0.95 (95% CI: 0.93-0.96), a pooled positive-likelihood ratio (PLR) of 8.65 (95% CI, 4.47-16.73), and a pooled negative-likelihood ratio (NLR) of 0.41 (95% CI, 0.30-0.55), a diagnostic odds ratio (DOR) of 26.86 (95% CI: 15.73-45.89), and an area under the curve (AUC) of 0.9115. In conclusion, our study established that WIF1 hypermethylation might be a promising diagnostic biomarker for CRC.

Methylation associated transcriptional repression of ELOVL5 in novel colorectal cancer cell lines

Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines. We generated global DNA methylation profiles with Infinium HumanMethylation450 BeadChips and analysed them in conjunction with matching gene expression profiles. Multidimensional scaling of the DNA methylation and gene expression datasets showed that BRAF mutated cell lines form a distinct group. In this group we investigated the 706 loci which we have previously identified to be hypermethylated in BRAF mutant CRC. We validated the significant findings in the The Cancer Genome Atlas colon adenocarcinoma dataset. Our analysis identified ELOVL5, FAM127B, MTERF1, ZNF606 to be subject to transcriptional downregulation through DNA hypermethylation in CRC. We further investigated ELOVL5 with qPCR and immunohistochemical staining, validating our results, but did not find a clear relation between ELOVL5 expression and tumor stage or relapse free survival. ELOVL5, FAM127B, MTERF1, ZNF606 are involved in important cellular processes such as apoptosis, lipogenesis and the downstream transcriptional effect of the MAPK-pathway. We have identified a DNA methylation profile regulating key cellular processes in CRC, resulting in a growth advantage to the tumor cells.

Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya, North East India reveals novel genes

Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.

The promoter methylomes of monochorionic twin placentas reveal intrauterine growth restriction-specific variations in the methylation patterns

Intrauterine growth restriction (IUGR) affects the foetus and has a number of pathological consequences throughout life. Recent work has indicated that variations in DNA methylation might cause placental dysfunction, which may be associated with adverse pregnancy complications. Here, we investigated the promoter methylomes of placental shares from seven monochorionic (MC) twins with selective intrauterine growth restriction (sIUGR) using the healthy twin as an ideal control. Our work demonstrated that the IUGR placental shares harboured a distinct DNA hypomethylation pattern and that the methylation variations preferentially occurred in CpG island shores or non-CpG island promoters. The differentially methylated promoters could significantly separate the IUGR placental shares from the healthy ones. Ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC‐MS/MS) further confirmed the genome‐wide DNA hypomethylation and the lower level of hydroxymethylation statuses in the IUGR placental shares. The methylation variations of the LRAT and SLC19A1 promoters, which are involved in vitamin A metabolism and folate transportation, respectively, and the EFS promoter were further validated in an additional 12 pairs of MC twins with sIUGR. Although the expressions of LRAT, SLC19A1 and EFS were not affected, we still speculated that DNA methylation and hydroxymethylation might serve a functional role during in utero foetal development.

Role of retinoids in the prevention and treatment of colorectal cancer

Vitamin A and its derivatives, retinoids, have been widely studied for their use as cancer chemotherapeutic agents. With respect to colorectal cancer (CRC), several critical mutations dysregulate pathways implicated in progression and metastasis, resulting in aberrant Wnt/β-catenin signaling, gain-of-function mutations in K-ras and phosphatidylinositol-3-kinase/Akt, cyclooxygenase-2 over-expression, reduction of peroxisome proliferator-activated receptor γ activation, and loss of p53 function. Dysregulation leads to increased cellular proliferation and invasion and decreased cell-cell interaction and differentiation. Retinoids affect these pathways by various mechanisms, many involving retinoic acid receptors (RAR). RAR bind to all-trans-retinoic acid (ATRA) to induce the transcription of genes responsible for cellular differentiation. Although most research concerning the chemotherapeutic efficacy of retinoids focuses on the ability of ATRA to decrease cancer cell proliferation, increase differentiation, or promote apoptosis; as CRC progresses, RAR expression is often lost, rendering treatment of CRCs with ATRA ineffective. Our laboratory focuses on the ability of dietary vitamin A to decrease CRC cell proliferation and invasion via RAR-independent pathways. This review discusses our research and others concerning the ability of retinoids to ameliorate the defective signaling pathways listed above and decrease tumor cell proliferation and invasion through both RAR-dependent and RAR-independent mechanisms.