Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer

Low RPMB indicates better disease-free survival of adjuvant radiotherapy after radical surgery in thymoma

BACKGROUND

The current use of adjuvant radiotherapy in thymoma (THYM) following radical surgery is primarily based on clinical factors and is a subject of ongoing debate.

METHODS

We developed a new biomarker, promotor methylation burden of Deoxyribonucleic acid repair genes (RPMB), to identify patients who may benefit from adjuvant radiotherapy after complete resection in THYM. RPMB quantitatively measures the promoter methylation level of Deoxyribonucleic acid (DNA) repair genes.

RESULTS

The methylation profile of 124 patients and corresponding clinical data were retrieved from The Cancer Genome Atlas (TCGA) database. The methylation level of DNA repair genes (DRGs) was found to be significantly hypomethylated juxtaposed to other genes across the whole human genome (all P < 0.001). THYM patients with higher RPMB tended to be female (P = 1.114×10-12) and have a more advanced Masaoka stage (P = 0.034). Kaplan-Meier analysis showed that high RPMB could significantly predict a poor disease-free survival (DFS) in THYM patients who received adjuvant radiotherapy after complete resection (HR = 5.750, 95% CI: 1.213-27.251, P = 0.013). Furthermore, Cox regression analysis indicated that RPMB was the only prognostic factor significantly associated with DFS after adjuvant radiotherapy (P = 0.028).

CONCLUSIONS

Low RPMB may be a potential indicator to identify suitable patients who can benefit from adjuvant radiotherapy in THYM, sparing others from treatment toxicity.

Prediction of disease-free survival of N1/2 non-small cell lung cancer after adjuvant chemotherapy by the biomarker RPMB

No molecular biomarkers have been proven applicable in clinical practice to identify patients who can benefit from adjuvant chemotherapy in non-small cell lung cancer (NSCLC). In this study, we established a biomarker, RPMB, short for promotor methylation burden of DNA repair genes (DRGs), to identify the subgroup of patients who might benefit from adjuvant chemotherapy in NSCLC. Methylation profiles of 828 NSCLC primary tumors and their clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. The RPMB for each patient after radical resection was calculated and its correlation with the prognosis of NSCLC was extensively investigated. DRGs of NSCLC were much more hypomethylated than the other genes (all p＜0.001). RPMB was defined as the ratio of methylated DRGs to the total number of all the DRGs. Patients with higher RPMB values tended to be nonsmokers, had adenocarcinoma, were female and had peripheral tumors. Subgroup analysis of forest plot among different clinical factors showed that high RPMB was significantly correlated to better disease-free survival (DFS) in pathologic N-positive patients after adjuvant chemotherapy (HR = 0.404, n = 62, p = 0.034). Notably, more superior DFS was exhibited in high RPMB NSCLCs with N1 nodal stage compared with those with low RPMB values (HR = 0.348, n = 47, p = 0.043). High RPMB might be used as a potential predictor to identify suitable N-positive NSCLC patients who can benefit from adjuvant chemotherapy after radical surgery.

Fertilization, Oocyte Activation, Calcium Release and Epigenetic Remodelling: Lessons From Cancer Models

Oocyte activation deficiency (OAD) is the basis of Total Fertilisation Failure (TFF) and is attributed to mutations in the PLCζ gene—termed male factor infertility. This derives abnormal Ca²⁺ oscillations and could be the main cause of primary disruptions in the gene expression of Ca²⁺-related proteins. Epigenetic mechanisms are universally accepted as key regulators of gene expression. However, epigenetic dysregulations have not been considered as potential mechanisms of oocyte-borne OAD. Herein, we discuss changes in the DNA methylome during oogenesis and embryogenesis. We further highlight key pathways comprising the oocyte Ca²⁺ toolkit, which could be targets of epigenetic alterations, especially aberrations in DNA methylation. Considering that the vast majority of epigenetic modifications examined during fertilization revolve around alterations in DNA methylation, we aim in this article to associate Ca²⁺-specific mechanisms with these alterations. To strengthen this perspective, we bring evidence from cancer research on the intricate link between DNA methylation and Ca²⁺ signaling as cancer research has examined such questions in a lot more detail. From a therapeutic standpoint, if our hypothesis is proven to be correct, this will explain the cause of TFF in idiopathic cases and will open doors for novel therapeutic targets.

ER expression associates with poor prognosis in male lung squamous carcinoma after radical resection

Background

Clinical options for lung squamous carcinoma (LUSC) are still quite limited. Carcinogenesis is an exceedingly complicated process involving multi-level dysregulations. Therefore, only looking into one layer of genomic dysregulation is far from sufficient.

Methods

We identified differentially expressed genes with consistent upstream genetic or epigenetic dysregulations in LUSC. Random walk was adopted to identify genes significantly affected by upstream abnormalities. Expression differentiation and survival analysis were conducted for these significant genes, respectively. Prognostic power of selected gene was also tested in 102 male LUSC samples through immunohistochemistry assay.

Results

Twelve genes were successfully retrieved from biological network, including ERα (ESRS1), EGFR, AR, ATXN1, MAPK3, PRKACA, PRKCA, SMAD4, TP53, TRAF2, UBQLN4 and YWHAG, which were closely related to sex hormone signaling pathway. Survival analysis in public datasets indicated ERα was significantly associated with a poor overall survival (OS) in male LUSC. The result of our immunohistochemistry assay also demonstrated this correlation using R0 resected tumors (n = 102, HR: 2.152, 95% CI: 1.089–4.255, p = 0.024). Although disease-free survival (DFS) difference was non-significant (n = 102, p = 0.12), the tendency of distinction was straight-forward. Cox analysis indicated ERα was the only independent prognostic factor for male patients’ OS after R0 resection (HR = 2.152, p = 0.037).

Conclusion

ERα was significantly related to a poor prognosis in LUSC, especially for male patients after radical surgery, confirmed by our immunohistochemistry data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08777-6.

Electrochemically detecting DNA methylation in the EN1 gene promoter: implications for understanding ageing and disease

There is a growing need for biomarkers which predict age-onset pathology. Although this is challenging, the methylome offers significant potential. Cancer is associated with the hypermethylation of many gene promoters, among which are developmental genes. Evolutionary theory suggests developmental genes arbitrate early-late life trade-offs, causing epimutations that increase disease vulnerability. Such genes could predict age-related disease. The aim of this work was to optimise an electrochemical procedure for the future investigation of a broad range of ageing-related pathologies. An electrochemical approach, which adopted three analytical techniques, was used to investigate DNA methylation in the engrailed-1 (EN1) gene promoter. Using synthetic single-stranded DNA, one technique was able to detect DNA at concentrations as low as 10 nM, with methylation status distinguishable at concentrations >25 nM. A negative correlation could be observed between % methylation of a heterogeneous solution and the key electrochemical parameter, charge transfer resistance (Rct; r = -0.982, P<0.01). The technique was applied to the breast cancer cell line Michigan Cancer Foundation-7 (MCF-7), where a similar correlation was observed (r = -0.965, P<0.01). These results suggest electrochemistry can effectively measure DNA methylation at low concentrations of DNA. This has implications for the future detection of age-related disease.

Promoter Methylation of DNA Repair Genes Predicts Disease-free Survival of Gastric Adenocarcinoma after Adjuvant Radiotherapy

The relentless debate on postoperative adjuvant radiotherapy in gastric adenocarcinoma (GA) has been lasting for decades. In this study, a new biomarker, named promoter methylation burden of DNA repair genes (RPMB), was established to identify the subgroup of patients who might benefit from adjuvant radiotherapy. Methylation profiles of 397 GA tumor samples were downloaded from The Cancer Genome Atlas (TCGA). RPMB for a patient was defined as the ratio of methylated DNA repair genes to the number of all DNA repair genes. Subgroup analyses in term of overall survival (OS) and disease-free survival (DFS) indicated that most of the subgroups favored the high-RMPB group. Kaplan-Meier analysis showed that overall the patients with high RPMB after R0 resection had a significantly better clinical outcome regarding DFS (hazard ratio [HR] = 0.013, p = 0.042). Additionally, high-RPMB patients, who underwent adjuvant radiotherapy with both ≥T2 tumor and positive lymph nodes, showed superior DFS in comparison with the low-RPMB group (HR = 5.35 × 10⁻¹⁰, n = 26, p = 0.010). RPMB might be considered as a promising biomarker for decision-making with regard to postoperative adjuvant radiotherapy for GA patients.

Expression Differentiation Is Not Helpful in Identifying Prognostic Genes Based on TCGA Datasets

A routine pipeline seems very common in many cancer studies that expression differentiation might be helpful in identifying prognostic molecules. There also exists a striking unanimity that molecules upregulated in cancer usually shorten survival, while downregulated ones have the opposite effect. In this study, based on the transcriptional profiles of 18 malignancies, cancer and corresponding adjacent normal tissues were used to calculate differential scores. Cox correlation coefficients of global genes were also calculated to denote survival association. The relationship between expression differentiation and survival association has been extensively studied in 18 malignancy types. Contradictory to our stereotypic research pattern, expression differentiation between cancer and adjacent normal tissues was proven irrelevant to corresponding survival correlation. Surprisingly, the more stringent cutoff we used in differentially expressed gene identification, the less prognostic information we would obtain from the collected gene groups. Moreover, the direction of dysregulated genes in cancer was irrelevant to the direction of corresponding survival correlation. Cancer-normal expression differentiation is irrelevant to genes’ survival correlation in multiple cancers and, therefore, not helpful in identifying prognostic genes. For future studies, it is more sensible to look into another alternative rather than collect differentially expressed molecules in the initial step.

Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component

BACKGROUND

Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression.

METHODS

Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes. All analyses were adjusted for the quantity of stroma in each sample, which was inferred from gene expression data.

RESULTS

High heterogeneity among samples was observed; the proportion of altered genome ranged between 0.04 and 26.6%. Recurrent CNA regions with gains were frequent in chromosomes 7p, 8q, 13q, and 20, whereas 8p, 17p, and 18 cumulated losses. A significant positive correlation was observed between the number of somatic mutations and total CNA (Spearman's r=0.42, P=0.006). Approximately 37% of genes located in CNA regions changed their level of expression and the average partial correlation (adjusted for stromal content) with copy number was 0.54 (interquartile range 0.20 to 0.81). Altered genes showed enrichment in pathways relevant for CRC. Tumours classified as CMS2 and CMS4 by the consensus molecular subtyping showed higher frequency of CNA. Losses of one small region in 1p36.33, with gene CDK11B, were associated with poor prognosis. More than 66% of the recurrent CNA were validated in the The Cancer Genome Atlas (TCGA) data when analysed with the same procedure. Furthermore, 79% of the genes with altered expression in our data were validated in the TCGA.

CONCLUSIONS

Although CNA are frequent events in microsatellite stable CRC, few focal recurrent regions were found. These aberrations have strong effects on gene expression and contribute to deregulate relevant cancer pathways. Owing to the diploid nature of stromal cells, it is important to consider the purity of tumour samples to accurately calculate CNA events in CRC.

Comprehensive investigation of a novel differentially expressed lncRNA expression profile signature to assess the survival of patients with colorectal adenocarcinoma

Growing evidence has shown that long non-coding RNAs (lncRNAs) can serve as prospective markers for survival in patients with colorectal adenocarcinoma. However, most studies have explored a limited number of lncRNAs in a small number of cases. The objective of this study is to identify a panel of lncRNA signature that could evaluate the prognosis in colorectal adenocarcinoma based on the data from The Cancer Genome Atlas (TCGA). Altogether, 371 colon adenocarcinoma (COAD) patients with complete clinical data were included in our study as the test cohort. A total of 578 differentially expressed lncRNAs (DELs) were observed, among which 20 lncRNAs closely related to overall survival (OS) in COAD patients were identified using a Cox proportional regression model. A risk score formula was developed to assess the prognostic value of the lncRNA signature in COAD with four lncRNAs (LINC01555, RP11-610P16.1, RP11-108K3.1 and LINC01207), which were identified to possess the most remarkable correlation with OS in COAD patients. COAD patients with a high-risk score had poorer OS than those with a low-risk score. The multivariate Cox regression analyses confirmed that the four-lncRNA signature could function as an independent prognostic indicator for COAD patients, which was largely mirrored in the validating cohort with rectal adenocarcinoma (READ) containing 158 cases. In addition, the correlative genes of LINC01555 and LINC01207 were enriched in the cAMP signaling and mucin type O-Glycan biosynthesis pathways. With further validation in the future, our study indicates that the four-lncRNA signature could serve as an independent biomarker for survival of colorectal adenocarcinoma.

Long non-coding RNA SNHG17 is an unfavourable prognostic factor and promotes cell proliferation by epigenetically silencing P57 in colorectal cancer

The first report of potential mechanisms of IncRNA SNHG17 in CRC, prompting the development of IncRNA-directed diagnosis and treatments.