Noninvasive DNA methylation biomarkers in colorectal cancer: A systematic review

Chronic kidney diseases and the risk of colorectal cancer: A systematic review and meta-analysis

Objective

We conducted this review to offer a comprehensive search and up-to-date overview of the currently available information about the probability risk of colorectal cancer among chronic kidney disease patients.

Method

We performed a systematic review and meta-analysis following Preferred Reporting Items for Systematic Reviews (PRISMA) and meta-analysis guidelines. We identified, reviewed, and extracted from Scopus, PubMed, EMBASE, and Komaki Databases for research publications on chronic kidney disease and colorectal cancer published between February 2016 and January 2023. We meta-analyzed the prevalence of colorectal cancer with chronic kidney disease. We ran a random effect meta-regression. Risk-of-bias assessment was evaluated using the Newcastle-Ottawa Scale. The systematic review was registered with PROSPERO (CRD42023400983).

Results

The risk of CRC in chronic kidney diseases was reported in 50 research studies, which included 4,337,966 people from 16 different countries. SIR of CRC was obtained from 14 studies and showed a significant relationship between CRC with CKD patients, with a pooled SIR of 1.33; 95% CI (1.30-1.36), with higher heterogeneity (Q = 121.82, P < 0.001, and I2 = 86.9%). Metaregression showed that there was no significant correlation between the risk of CRC and the proportion of males or age.

Conclusion

Overall, this study shows that patients with chronic kidney disease have a significantly increased risk of colorectal cancer. More studies with larger sample sizes, and robust surveillance are needed.

Comparison of performance of two Stool DNA Tests and a Faecal Immunochemical Test in Detecting Colorectal Neoplasm: a Multicentre Diagnostic Study

BACKGROUND

The most widely used non-invasive screening tests for colorectal cancer (CRC) are faecal occult blood tests. Stool DNA test was developed in recent years. However, direct comparative analyses of these tests within the same population are still sparse.

METHODS

2842 participants who visited outpatient clinics or cancer screening centres were enrolled. Stool DNA test-I (KRAS, BMP3, NDRG4, and haemoglobin immunochemical tests), stool DNA test-II (SDC2 and SFRP2 tests) and FIT alone were performed and colonoscopy was used as the gold standard among 2240 participants. 42 and 302 participants had CRC and advanced adenomas (AA), respectively.

RESULTS

The sensitivity for CRC of stool DNA test-I, -II and FIT was 90.5%, 92.9% and 81.0%, respectively. The sensitivity for advanced neoplasm (CRC plus AA) of stool DNA test-I, -II and FIT was 34.9%, 42.2% and 25.9%, respectively. The specificity of stool DNA test-I, -II and FIT was 91.4%, 93.3% and 96.8%, respectively, among those with negative results on colonoscopy. When the specificity of FIT was adjusted to match that of stool DNA tests by changing the threshold, no significant difference was seen in the sensitivities among the 3 tests for detecting CRC. For advanced neoplasm, the sensitivity of FIT was higher than DNA test-I and similar to DNA test-II under the same specificities.

CONCLUSIONS

There was no significant advantage of the two stool DNA tests compared to FIT in detecting CRC or advanced neoplasm in this study.

IMPACT

Our findings do not support extensive use of stool DNA tests instead of FIT.

Circulating methylated RUNX3 and SFRP1 genes as a noninvasive panel for early detection of colorectal cancer

OBJECTIVE

This study was conducted to assess the methylation status of runt-related transcription factor 3 (RUNX3) and secreted frizzled-related protein 1 (SFRP1) genes in paired tissue and serum samples of colorectal cancer (CRC), adenomatous, and control subjects and elucidate the association between methylation status on RUNX3 and SFRP1 mRNA expression.

METHODS

Methylation status of RUNX3 and SFRP1 in paired tissue and serum samples and RUNX3 and SFRP1 mRNA expression in tissue from 85 patients with CRC, 40 with adenoma, and 40 healthy controls were determined using methylation-specific PCR and reverse transcription PCR.

RESULTS

The frequency RUNX3 and SFRP1 genes methylation was significantly higher in both tissues and serum of CRC patients and was significantly associated with absence of its corresponding mRNA expression. The concordance between tissue and serum methylation status was 94.4% for RUNX3 and 94.3% for SFRP1. Tissue RUNX3 methylation status detected CRC with 63.53% sensitivity and 80.00% specificity, while serum RUNX3 methylation status detected CRC with 60.00% sensitivity and 82.50% specificity. Tissue SFRP1 methylation status showed a sensitivity of 82.35% and specificity of 65.00%, while serum SFRP1 methylation status showed a sensitivity of 77.65% and specificity of 70.00% in detection of CRC. RUNX3/SFRP1/carcinoembryonic antigen (CEA) panel identified CRC with sensitivity of 89.41% in tissue and 84.71% in serum.

CONCLUSION

Our results verified the reliability of using serum RUNX3 and SFRP1 methylation status as a noninvasive biomarker for diagnosis of CRC and that combined detection of RUNX3/SFRP1/CEA panel might be a promising strategy for early detection of CRC.

Serum Expression of β-Catenin Is a Potential Detection Marker in Patients with Colorectal Cancer

Object

To investigate the correlation between the level of serum β-catenin and the disease progression of colorectal polyp (CRP) and colorectal cancer (CRC) and find its potential diagnostic value.

Methods

A total of 327 clinical serum samples and their electronic medical records were collected. Detecting by enzyme-linked immunosorbent assay (ELISA), the correlations of serum β-catenin with tumor marker carcinoembryonic antigen (CEA) and CRC clinicopathological parameters and the receiver operating characteristic (ROC) curve were analyzed.

Results

Serum β-catenin levels in the CRP and CRC patients were significantly higher than those in the healthy control (HC) group (P < 0.05 and P < 0.001). Compared with CRP, serum β-catenin level in CRC was also increased (P < 0.05). However, there was no significant difference in gender, age, location, tumor size, Dukes staging, or metastasis (P > 0.05) between serum β-catenin and clinical parameters of CRC. There was no correlation between serum β-catenin levels and CEA in CRC patients (P = 0.14). ROC curve analysis showed that serum β-catenin possessed the maximum diagnostic efficiency in CRP (AUC = 0.73, P < 0.05) with 86.41% sensitivity and 51.56% specificity. β-Catenin combined with CEA had the highest diagnostic efficiency (AUC = 0.88, P < 0.05) with 81.88% sensitivity and 73.44% specificity. With CRC patients from CRP patients, ROC analysis of the combining detection (AUC = 0.70, P < 0.05) had the 70% sensitivity and 84.5% specificity.

Conclusion

The serum β-catenin levels are gradually increased in CRP and CRC, while there is no correlation between its levels and CRC disease process. Single serum β-catenin or combined CEA would be one of the potential candidate biomarkers for colorectal disease diagnosis.

Study of p16 promoter methylation in Egyptian colorectal cancer patients

Many tumor-suppressor genes contain CpG islands in their promoter regions which raised the necessity of investigating the role of methylation in silencing these genes. We examined p16 methylation as a potential biomarker in the peripheral blood of colorectal cancer (CRC) patients. Using methylation-specific polymerase chain reaction method, the methylation status of p16 was investigated in the tumor tissue and blood of 65 CRC patients and blood samples from 70 healthy control individuals. Also, the relationship between p16 methylation level and the clinical-pathological findings in CRC was evaluated. The frequency of blood p16 methylation in CRC cases was significantly higher than in control (P = 0.0001). The sensitivity and specificity of p16 methylation in diagnosing CRC was 55.38% and 98.5%, respectively, with 77.7% diagnostic accuracy. There was significant association between p16 methylation and age, sex, Dukes staging, lymph node involvement, and carcinoembryonic antigen levels. Our study revealed that p16 promoter methylation could be considered as both potential diagnostic and prognostic biomarker of CRC.

Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer

OBJECTIVE

Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC).

DESIGN

Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy.

RESULTS

Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4, 68.5% for GRIA4, 69.7% for ITGA4, 69.1% for MAP3K14-AS1% and 65.1% for MSC. Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival.

CONCLUSION

This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.

Risk of Colorectal Cancer in Chronic Kidney Disease: A Systematic Review and Meta-Analysis

BACKGROUND

Association between chronic kidney disease and colorectal cancer (CRC) remains unclear.

GOALS

To assess the risk of CRC in patients with various chronic kidney diseases before and after kidney transplantation.

STUDY

Electronic databases were searched for cohort studies assessing the risk of CRC in patients with chronic kidney diseases. The primary outcome was the risk of CRC among studies that reported the risk as standardized incidence rate (SIR).

RESULTS

Fifty-four studies, including 1,208,767 patients that reported the incidence of CRC in chronic kidney diseases were identified. SIR of CRC were obtained from 17 retrospective cohort studies. Among the 3 studies (4 reports) that included chronic kidney disease patients without kidney transplantation, there was a significant increased risk of CRC (pooled SIR 1.18) (95% confidence interval, 1.01-1.37; P=0.033). High heterogeneity was seen (I=85.6%), and metaregression showed that there were positive correlations between the risk of CRC and the proportions of males, age and follow-up period. Among the 15 studies (17 reports) that included postkidney transplant patients, the pooled SIR was significantly increased at 1.40 (95% confidence interval, 1.15-1.71; P=0.00080). High heterogeneity was seen (I=88.9%), and metaregression showed that the follow-up period correlated with the risk of CRC.

CONCLUSIONS

In the present systematic review and meta-analysis, we demonstrated that patients with chronic kidney disease, regardless of a history of transplant, have a significant increased risk of CRC. A more intensive surveillance for CRC is required in this population.

Colorectal cancer: epigenetic alterations and their clinical implications

Colorectal cancer (CRC) is a heterogeneous disease with distinct molecular and clinical features, which reflects the wide range of prognostic outcomes and treatment responses observed among CRC patients worldwide. Our understanding of the CRC epigenome has been largely developed over the last decade and it is now believed that among thousands of epigenetic alterations present in each tumor, a small subgroup of these may be considered as a CRC driver event. DNA methylation profiles have been the most widely studied in CRC, which includes a subset of patients with distinct molecular and clinical features now categorized as CpG island methylator phenotype (CIMP). Major advances have been made in our capacity to detect epigenetic alterations, providing us with new potential biomarkers for diagnostic, prognostic and therapeutic purposes. This review aims to summarize our current knowledge about epigenetic alterations occurring in CRC, underlying their potential future clinical implications in terms of diagnosis, prognosis and therapeutic strategies for CRC patients.

High levels of circulating folate concentrations are associated with DNA methylation of tumor suppressor and repair genes p16, MLH1, and MGMT in elderly Chileans

BACKGROUND

Changes in DNA methylation, one of the most studied epigenetic mechanisms, are considered an initial marker for early cancer detection. We evaluated how availability of dietary factors (folates and vitamin B12) involved in one-carbon metabolism may contribute to DNA methylation changes of cancer-related genes in human subjects.

METHODS

We studied, by pyrosequencing, the methylation of tumor suppressor gene p16, DNA repair genes MLH1 and MGMT, and the repetitive element LINE-1 (as a surrogate for global DNA methylation), in blood of elderly individuals (n = 249) who had been exposed to folic acid (FA) through FA-fortified wheat flour during the last 12 years.

RESULTS

We found that serum folate and to a lesser extent, vitamin B12 concentrations, were significantly correlated with DNA methylation of p16, MLH1, and MGMT, but not with LINE-1. High serum folate concentrations (>45.3 nmol/L) were present in 31.1% of the participants. Although the methylated fraction of CpG sites in p16, MLH1, and MGMT was low (1.17-3.8%), high folate concentrations were significantly associated with methylation at the 3rd tertile of specific CpG sites in all genes with OR between 1.97 and 4.17.

CONCLUSIONS

This study shows that a public policy, like food fortification with FA that increases circulating serum folate levels, could affect methylation levels of specific genes linked to cancer risk. Our present results deserve additional studies to clarify the real impact of high FA levels for risk of cancer in a whole population chronically exposed to a fortified food such as wheat flour.

TRIAL REGISTRATION

ISRCTN 48153354 and ISRCTN 02694183.

Whole-Genome DNA Methylation Analyses Revealed Epigenetic Instability in Tumorigenic Human iPS Cell-Derived Neural Stem/Progenitor Cells

Although human induced pluripotent stem cell (hiPSC) derivatives are considered promising cellular resources for regenerative medicine, their tumorigenicity potentially limits their clinical application in hiPSC technologies. We previously demonstrated that oncogenic hiPSC-derived neural stem/progenitor cells (hiPSC-NS/PCs) produced tumor-like tissues that were distinct from teratomas. To gain insight into the mechanisms underlying the regulation of tumorigenicity in hiPSC-NS/PCs, we performed an integrated analysis using the Infinium HumanMethylation450 BeadChip array and the HumanHT-12 v4.0 Expression BeadChip array to compare the comprehensive DNA methylation and gene expression profiles of tumorigenic hiPSC-NS/PCs (253G1-NS/PCs) and non-tumorigenic cells (201B7-NS/PCs). Although the DNA methylation profiles of 253G1-hiPSCs and 201B7-hiPSCs were similar regardless of passage number, the methylation status of the global DNA methylation profiles of 253G1-NS/PCs and 201B7-NS/PCs differed; the genomic regions surrounding the transcriptional start site of the CAT and PSMD5 genes were hypermethylated in 253G1-NS/PCs but not in 201B7-NS/PCs. Interestingly, the aberrant DNA methylation profile was more pronounced in 253G1-NS/PCs that had been passaged more than 15 times. In addition, we identified aberrations in DNA methylation at the RBP1 gene locus; the DNA methylation frequency in RBP1 changed as 253G1-NS/PCs were sequentially passaged. These results indicate that different NS/PC clones have different DNA methylomes and that DNA methylation patterns are unstable as cells are passaged. Therefore, DNA methylation profiles should be included in the criteria used to evaluate the tumorigenicity of hiPSC-NS/PCs in the clinical setting. Stem Cells 2017;35:1316-1327.

Evaluation of Methylation Biomarkers for Detection of Circulating Tumor DNA and Application to Colorectal Cancer

Solid tumors shed DNA into circulation, and there is growing evidence that the detection of circulating tumor DNA (ctDNA) has broad clinical utility, including monitoring of disease, prognosis, response to chemotherapy and tracking tumor heterogeneity. The appearance of ctDNA in the circulating cell-free DNA (ccfDNA) isolated from plasma or serum is commonly detected by identifying tumor-specific features such as insertions, deletions, mutations and/or aberrant methylation. Methylation is a normal cell regulatory event, and since the majority of ccfDNA is derived from white blood cells (WBC), it is important that tumour-specific DNA methylation markers show rare to no methylation events in WBC DNA. We have used a novel approach for assessment of low levels of DNA methylation in WBC DNA. DNA methylation in 29 previously identified regions (residing in 17 genes) was analyzed in WBC DNA and eight differentially-methylated regions (DMRs) were taken through to testing in clinical samples using methylation specific PCR assays. DMRs residing in four genes, BCAT1, GRASP, IKZF1 and IRF4, exhibited low positivity, 3.5% to 7%, in the plasma of colonoscopy-confirmed healthy subjects, with the sensitivity for detection of ctDNA in colonoscopy-confirmed patients with colorectal cancer being 65%, 54.5%, 67.6% and 59% respectively.

A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer

We investigated the potential role of apple phenolic compounds in human pathologies by integrating chemical characterization of phenolic compounds in three apple varieties, computational approaches to identify potential protein targets of the compounds, bioinformatics analyses on data from public archive of gene expression data, and functional analyses to hypothesize the effects of the selected compounds in molecular pathways. Starting by the analytic characterization of phenolic compounds in three apple varieties, i.e. Annurca, Red Delicious, and Golden Delicious, we used computational approaches to verify by reverse docking the potential protein targets of the identified compounds. Direct docking validation of the potential protein-ligand interactions has generated a short list of human proteins potentially bound by the apple phenolic compounds. By considering the known chemo-preventive role of apple antioxidants' extracts against some human pathologies, we performed a functional analysis by comparison with experimental gene expression data and interaction networks, obtained from public repositories. The results suggest the hypothesis that chemo-preventive effects of apple extracts in human pathologies, in particular for colorectal cancer, may be the interference with the activity of nucleotide metabolism and methylation enzymes, similarly to some classes of anticancer drugs.

Promoter methylation and expression of CDH1 and susceptibility and prognosis of eyelid squamous cell carcinoma

Eyelid skin tumors are the most frequent type of cancer in ophthalmology. And, eyelid squamous cell carcinoma (SCC) accounts for a large part of it. CDH1 encodes E-cadherin, a glycoprotein that plays an important part in cell-cell interaction. Loss of CDH1 function was suspected to be associated with tumorigenesis. Methylation of CDH1 promotors can alter the expression of its protein and is also considered as a contributor to various cancers. In this study, CDH1 methylation and expression profile as well as prognosis of 38 cases of eyelid SCC and the corresponding adjacent tissues were analyzed to clarify the role of CDH1 methylation in SCC carcinogenesis and prognosis. Methylation was detected by PCR, and CDH1 expression was evaluated by immunohistochemistry. We observed that CDH1 methylation is significantly correlated with decreased CDH1 protein expression in eyelid SCC patients. Patients with methylation and low expression of CDH1 are significantly associated with advanced and aggressive phenotypes. Therefore, CDH1 methylation and CDH1 expression are both independent prognostic factors for prognosis of eyelid SCC patients.