scholarly journals Construction and Analysis of a Colorectal Cancer Prognostic Model Based on N6-Methyladenosine-Related lncRNAs

2021 ◽  
Vol 9 ◽  
Author(s):  
Hanqian Zeng ◽  
Yiying Xu ◽  
Shiwen Xu ◽  
Linli Jin ◽  
Yanyan Shen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Lymph Node ◽  
High Risk ◽  
Prognostic Model ◽  
Clinical Staging ◽  
Risk Scores ◽  
Lymph Node Status ◽  
Rna Methylation ◽  
M6a Rna Methylation ◽  
Cancer Tissues

Given the relatively poor understanding of the expression and functional effects of the N6-methyladenosine (m6A) RNA methylation on colorectal cancer (CRC), we attempted to measure its prognostic value and clinical significance. We comprehensively screened 37 m6A-related prognostic long non-coding RNAs (lncRNAs) with significant differences in expression based on 21 acknowledged regulators of m6A modification and data on 473 colorectal cancer tissues and 41 para-cancer tissues obtained from the TCGA database. Accordingly, we classified 473 CRC patients into two clusters by consensus clustering on the basis of significantly different survival outcomes. We also found a potential correlation between m6A-related prognostic lncRNAs and BRAF-KRAS expression, as well as immune cell infiltration. Then, we established a prognostic model by selecting 16 m6A-related prognostic lncRNAs via LASSO Cox analysis and grouped the CRC patients into low- and high-risk groups to calculate risk scores. Then, we performed stratified sampling to validate and confirm our model by categorising the 473 samples into a training group (N = 208) and a testing group (N = 205) in a 1:1 ratio. The survival curve showed a distinct clinical outcome in the low- and high-risk subgroups. We reconfirmed the reliability and independence of the prognostic model through various measures: risk curve, heat map and univariate and multivariate Cox analyses. To ensure that the outcomes were applicable to clinical settings, we performed stratified analyses on different clinical features, such as age, lymph node status and clinical stage. CRC patients with downregulated m6A-related gene expression, lower immune score, distant metastasis, lymph node metastasis or more advanced clinical staging had higher risk scores, indicating less-desirable outcomes. Moreover, we explored the immunology of colorectal cancer cells. The risk score showed positive correlations with eosinophils, M2 macrophages and neutrophils. In summary, our effort revealed the significance of m6A RNA methylation regulators in colorectal cancer, and the prognostic model we constructed may be used as an essential reference for predicting the outcome of CRC patients.

scholarly journals Characteristic of molecular subtypes in lung adenocarcinoma based on m6A RNA methylation modification and immune microenvironment

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hao Zhou ◽  
Miaosen Zheng ◽  
Muqi Shi ◽  
Jinjie Wang ◽  
Zhanghao Huang ◽  
...  
Keyword(s):  
Survival Analysis ◽  
High Risk ◽  
Lung Adenocarcinoma ◽  
Poor Prognosis ◽  
Prognostic Model ◽  
Immune Cell ◽  
Immune Cell Infiltration ◽  
Immune Microenvironment ◽  
Rna Methylation ◽  
M6a Rna Methylation

Abstract Background Lung adenocarcinoma (LUAD) is a major subtype of lung cancer and closely associated with poor prognosis. N6-methyladenosine (m6A), one of the most predominant modifications in mRNAs, is found to participate in tumorigenesis. However, the potential function of m6A RNA methylation in the tumor immune microenvironment is still murky. Methods The gene expression profile cohort and its corresponding clinical data of LUAD patients were downloaded from TCGA database and GEO database. Based on the expression of 21 m6A regulators, we identified two distinct subgroups by consensus clustering. The single-sample gene-set enrichment analysis (ssGSEA) algorithm was conducted to quantify the relative abundance of the fraction of 28 immune cell types. The prognostic model was constructed by Lasso Cox regression. Survival analysis and receiver operating characteristic (ROC) curves were used to evaluate the prognostic model. Result Consensus classification separated the patients into two clusters (clusters 1 and 2). Those patients in cluster 1 showed a better prognosis and were related to higher immune scores and more immune cell infiltration. Subsequently, 457 differentially expressed genes (DEGs) between the two clusters were identified, and then a seven-gene prognostic model was constricted. The survival analysis showed poor prognosis in patients with high-risk score. The ROC curve confirmed the predictive accuracy of this prognostic risk signature. Besides, further analysis indicated that there were significant differences between the high-risk and low-risk groups in stages, status, clustering subtypes, and immunoscore. Low-risk group was related to higher immune score, more immune cell infiltration, and lower clinical stages. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. Ultimately, the efficacy of this prognostic model was successfully validated in several external cohorts (GSE30219, GSE50081 and GSE72094). Conclusion Our study provides a robust signature for predicting patients’ prognosis, which might be helpful for therapeutic strategies discovery of LUAD.

scholarly journals Identification of RNA-Binding Proteins with Prognostic Prediction in Colorectal Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Xiao-fen Bai ◽  
Jing-wen Liu
Keyword(s):  
Colorectal Cancer ◽  
High Risk ◽  
Prognostic Model ◽  
Binding Proteins ◽  
Rna Binding ◽  
Cox Regression ◽  
Rna Binding Proteins ◽  
Risk Group ◽  
The Cancer Genome Atlas ◽  
Risk Scores

Colorectal cancer (CRC) is one of the most common malignancies of the digestive system. Recent studies have revealed the importance of RNA-binding proteins (RBPs) in tumorigenesis, but their role in CRC remains unclear. The present study systematically analyzed the relationships between RBPs and CRC using data from The Cancer Genome Atlas. We detected 483 differentially expressed RBPs and identified a series of pathways and processes using GO (Gene Ontology) analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis. Analyzing protein–protein interactions and modules identified the edges and modules of RBPs. Univariate and multivariate Cox regression analyses were then used to construct a prognostic model that included 13 RBPs. Survival analyses indicated that the overall survival (OS) was significantly lower for CRC patients in the high-risk group than for those in the low-risk group, and that high risk scores were associated with poor OS. Finally, we constructed a nomogram that included 13 RBPs for calculating the estimated survival probabilities of CRC patients at 1, 2, and 3 years. Calibration plots indicated good conformity between the predicted and observed outcomes. This study has revealed that the expression of RBPs differs between CRC and normal tissues. A prognostic model based on 13 RBP coding genes has been developed that can provide independent prognoses of CRC.

scholarly journals Assessing the clinical utility of genetic risk scores for targeted cancer screening

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Carly A. Conran ◽  
Zhuqing Shi ◽  
William Kyle Resurreccion ◽  
Rong Na ◽  
Brian T. Helfand ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Primary Care ◽  
High Risk ◽  
Risk Score ◽  
Genetic Risk ◽  
Clinical Utility ◽  
Low Risk ◽  
Risk Scores ◽  
Average Risk ◽  
Genetic Risk Scores

Abstract Background Genome-wide association studies have identified thousands of disease-associated single nucleotide polymorphisms (SNPs). A subset of these SNPs may be additively combined to generate genetic risk scores (GRSs) that confer risk for a specific disease. Although the clinical validity of GRSs to predict risk of specific diseases has been well established, there is still a great need to determine their clinical utility by applying GRSs in primary care for cancer risk assessment and targeted intervention. Methods This clinical study involved 281 primary care patients without a personal history of breast, prostate or colorectal cancer who were 40–70 years old. DNA was obtained from a pre-existing biobank at NorthShore University HealthSystem. GRSs for colorectal cancer and breast or prostate cancer were calculated and shared with participants through their primary care provider. Additional data was gathered using questionnaires as well as electronic medical record information. A t-test or Chi-square test was applied for comparison of demographic and key clinical variables among different groups. Results The median age of the 281 participants was 58 years and the majority were female (66.6%). One hundred one (36.9%) participants received 2 low risk scores, 99 (35.2%) received 1 low risk and 1 average risk score, 37 (13.2%) received 1 low risk and 1 high risk score, 23 (8.2%) received 2 average risk scores, 21 (7.5%) received 1 average risk and 1 high risk score, and no one received 2 high risk scores. Before receiving GRSs, younger patients and women reported significantly more worry about risk of developing cancer. After receiving GRSs, those who received at least one high GRS reported significantly more worry about developing cancer. There were no significant differences found between gender, age, or GRS with regards to participants’ reported optimism about their future health neither before nor after receiving GRS results. Conclusions Genetic risk scores that quantify an individual’s risk of developing breast, prostate and colorectal cancers as compared with a race-defined population average risk have potential clinical utility as a tool for risk stratification and to guide cancer screening in a primary care setting.

scholarly journals Development and Validation of a Unique Gignature of Cancer Stemness-related Genes for Predicting the Overall survival of Colorectal Cancer Patients

2020 ◽  
Author(s):  
Ran Wei ◽  
Jichuan Quan ◽  
Shuofeng Li ◽  
Zhao Lu ◽  
Xu Guan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Cox Regression ◽  
The Cancer Genome Atlas ◽  
Cancer Stemness ◽  
Poor Overall Survival ◽  
Tissue Samples ◽  
Cox Regression Analysis ◽  
Rna Methylation ◽  
M6a Rna Methylation

Abstract Background: Cancer stem cells (CSCs), which are characterized by self-renewal and plasticity, are highly correlated with tumor metastasis and drug resistance. To fully understand the role of CSCs in colorectal cancer (CRC), we evaluated the stemness traits and prognostic value of stemness-related genes in CRC.Methods: In this study, the data from 616 CRC patients from The Cancer Genome Atlas (TCGA) were assessed and subtyped based on the mRNA expression-based stemness index (mRNAsi). The correlations of cancer stemness with the immune microenvironment, tumor mutational burden (TMB) and N6-methyladenosine (m6A) RNA methylation regulators were analyzed. Weighted gene co-expression network analysis (WGCNA) was performed to identify the crucial stemness-related genes and modules. Furthermore, a prognostic expression signature was constructed using Lasso-penalized Cox regression analysis. The signature was validated via multiplex immunofluorescence staining of tissue samples in an independent cohort of 48 CRC patients.Results: This study suggests that high mRNAsi scores are associated with poor overall survival in stage Ⅳ CRC patients. Moreover, the levels of TMB and m6A RNA methylation regulators were positively correlated with mRNAsi scores, and low mRNAsi scores were characterized by increased immune activity in CRC. The analysis identified 2 key modules and 34 key genes as prognosis-related candidate biomarkers. Finally, a 3-gene prognostic signature (PARPBP, KNSTRN and KIF2C) was explored together with specific clinical features to construct a nomogram, which was successfully validated in an external cohort. Conclusions: There is a unique correlation between CSCs and the prognosis of CRC patients, and the novel biomarkers related to cell stemness could accurately predict the clinical outcomes of these patients.

Outcome and immune landscape of HER2-positive invasive lobular carcinoma in the North Central Cancer Treatment Group (NCCTG) N9831 (Alliance) trial.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 535-535
Author(s):  
Saranya Chumsri ◽  
Zhuo Li ◽  
Tracy Shachner ◽  
Pooja Advani ◽  
Kostandinos Sideras ◽  
...  
Keyword(s):  
Lymph Node ◽  
High Risk ◽  
Invasive Lobular Carcinoma ◽  
Clinical Characteristics ◽  
Cox Regression ◽  
Lobular Carcinoma ◽  
Categorical Variables ◽  
Lymph Node Status ◽  
Her2 Positive ◽  
Gene Signatures

535 Background: Invasive lobular carcinoma (ILC) is a rarer form of breast cancer, accounting for 10% of the disease cases. HER2 overexpression in ILC is infrequent and limited data exist regarding clinical characteristics and outcome of HER2-positive (HER2+) ILC patients (pts) treated with adjuvant trastuzumab. Methods: Patient characteristics were compared between ILC and invasive ductal carcinoma (IDC) using Wilcoxon rank sum test for continuous variables and Chi-square test for categorical variables. Kaplan-Meier (KM) method was used to estimate the freedom from mortality and recurrence. Cox regression model was used to evaluate the association between ILC and outcomes adjusted for other characteristics. NanoString technology was used to quantify mRNA to develop immune-related gene signatures. Results: From a total of 3,304 pts, 122 (3.7%) pts had ILC. Pts with ILC were significantly older (median age 54 vs. 49 years), had larger tumors, lower grade, more ER and PR positive tumors, and more lymph node involvement (25.4% had N3 disease compared to 12.7% in IDC). Overall, with KM analysis, pts with ILC had significantly worse overall survival (OS, p = 0.005) and recurrence-free survival (RFS, p = 0.046) compared to IDC. The 15-year freedom from recurrence was merely 57.67% in ILC compared to 72.68% in IDC. A significant number of hormone receptor-positive (HR+) ILC pts developed late recurrence with cumulative event rates increasing from 23% at 5 years to 42% at 15 years. Nevertheless, in multivariate Cox regression analysis adjusting for other clinical characteristics, including age, tumor size, grade, ER/PR, and lymph node status, lobular histology was not significantly associated with worse outcome for OS (HR = 1.19, 95%CI 0.67-2.1, p = 0.55) and RFS (HR = 1.5, 95%CI 0.9-2.5, p = 0.12), as compared with IDC. However, ILC pts appeared to have similar degree of benefit from trastuzumab, with RFS HR = 0.58 compared to HR = 0.67 in the entire population. For immune landscape, there was no significant difference in gene signatures related to CD45, CD8, B cells, or cytotoxic cells. However, ILC had more enrichment in mast cell gene signature and fewer macrophage, NK CD56dim, and regulatory T cell signatures compared to IDC (p < 0.05). Conclusions: HER2+ ILC has distinct clinical characteristics and immune landscape compared to IDC. ILC pts appeared to have worse outcome compared to IDC likely because ILC pts often presented with more locally advanced disease. However, similar benefit of trastuzumab was observed in ILC pts. Due to high risk of late relapse in HR+ HER2+ ILC, extended adjuvant endocrine therapy should be considered in this group of high-risk pts. Clinical trial information: NCT00005970.

Prognostic Value of m6A RNA Methylation Modulators and Potential Clinical Application in Pancreatic Cancer

2020 ◽  
Author(s):  
Lianzi Wang ◽  
Huimin Li ◽  
Tao Li ◽  
Huihui Wang ◽  
Xuemei Li ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
High Risk ◽  
Pancreatic Adenocarcinoma ◽  
Risk Score ◽  
Prognostic Indicator ◽  
Gene Set Enrichment Analysis ◽  
Wilcoxon Test ◽  
Rna Methylation ◽  
Incidence And Mortality ◽  
M6a Rna Methylation

Abstract Background m6A is the most prevalent and abundant form of mRNA modification and plays a dual role in cancer development. The high incidence and mortality of pancreatic cancer are critical obstacles worldwide. In this study, we investigated the function of m6A RNA methylation modulators in pancreatic cancer. Methods Expression of 13 m6A RNA methylation modulators and clinical data from patients with pancreatic adenocarcinoma were obtained from TCGA database. Differences in the expression of 13 m6A RNA methylation modulators between tumour (n = 178) and healthy (n = 4) samples were compared by Wilcoxon test. LASSO Cox regression was used to select m6A RNA methylation modulators for analysis of the relationship between expression and clinical characteristics by univariate and multivariate regression. The pathways of the m6A RNA methylation modulators were examined by gene set enrichment analysis (GSEA) and we found enrichment in chemokine, ribosome, and mTOR signalling pathways. Results WTAP had a low expression in tumour samples compared with healthy samples. Furthermore, our analyses revealed that the m6A RNA methylation modulators YTHDF1, ALKBH5, METTL3, METTL14, and KIAA1429 correlated with high-risk patients, resulting in an elevated risk score and a lower overall survival. High-risk score correlated with clinical characteristic and was an independent prognostic indicator for pancreatic adenocarcinoma. The pathways involved were identified by GSEA to explore the potential mechanism of action. Conclusion Modulators involved in m6A RNA methylation were associated with the development of pancreatic cancer. A risk score based on the expression of YTHDF1, ALKBH5, METTL3, METTL14, and KIAA1429 may be an independent prognostic indicator.

scholarly journals Prognostic Impact of the Number of Examined Lymph Nodes in Stage II Colorectal Adenocarcinoma: A Retrospective Study

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Purun Lei ◽  
Ying Ruan ◽  
Jianpei Liu ◽  
Qixian Zhang ◽  
Xiao Tang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Lymph Node ◽  
Lymph Nodes ◽  
Stage Ii ◽  
Lymph Node Status ◽  
Stage Migration ◽  
Prognostic Impact ◽  
Disease Specific Survival ◽  
Stage Ii Colorectal Cancer ◽  
Disease Specific

Background. Evaluation of lymph node status is critical in colorectal carcinoma (CRC) treatment. However, as patients with node involvement may be incorrectly classified into earlier stages if the examined lymph node (ELN) number is too small and escape adjuvant therapy, especially for stage II CRC. The aims of this study were to assess the impact of the ELN on the survival of patients with stage II colorectal cancer and to determine the optimal number. Methods. Data from the US Surveillance, Epidemiology, and End Results (SEER) database on stage II resected CRC (1988-2013) were extracted for mathematical modeling as ELN was available since 1988. Relationship between ELN count and stage migration and disease-specific survival was analyzed by using multivariable models. The series of the mean positive LNs, odds ratios (ORs), and hazard ratios (HRs) were fitted with a LOWESS (Locally Weighted Scatterplot Smoothing) smoother, and the structural break points were determined by the Chow test. An independent cohort of cases from 2014 was retrieved for validation in 5-year disease-specific survival (DSS). Results. An increased ELN count was associated with a higher possibility of metastasis LN detection (OR 1.010, CI 1.009-1.011, p<0.001) and better DSS in LN negative patients (OR 0.976, CI 0.975-0.977, p<0.001). The cut-off point analysis showed a threshold ELN count of 21 nodes (HR 0.692, CI 0.667-0.719, p<0.001) and was validated with significantly better DSS in the SEER 2009 cohort CRC (OR 0.657, CI 0.522-0.827, p<0.001). The cut-off value of the ELN count in site-specific surgeries was analyzed as 20 nodes in the right hemicolectomy (HR 0.674, CI 0.638-0.713, p<0.001), 19 nodes in left hemicolectomy (HR 0.691, CI 0.639-0.749, p<0.001), and 20 nodes in rectal resection patients (HR 0.671, CI 0.604-0.746, p<0.001), respectively. Conclusions. A higher number of ELNs are associated with more-accurate node staging and better prognosis in stage II CRCs. We recommend that at least 21 lymph nodes be examined for accurate diagnosis of stage II colorectal cancer.

Efficacy and tolerability of adjuvant therapy in ≥70-year-old patients with T3N0M0 colorectal cancer: An observational study

2019 ◽  
Vol 26 (3) ◽  
pp. 619-631
Author(s):  
Abdullah Sakin ◽  
Nurgul Yasar ◽  
Suleyman Sahin ◽  
Serdar Arici ◽  
Saban Secmeler ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Lymph Node ◽  
High Risk ◽  
Adjuvant Chemotherapy ◽  
Risk Group ◽  
Disease Free Survival ◽  
Old Patients ◽  
Free Survival ◽  
Disease Free

Background This study aimed to retrospectively investigate the efficacy and tolerability of adjuvant chemotherapy in ≥70-year-old patients with stage IIA (T3N0M0) colorectal cancer. Methods Lymphovascular invasion, perineural invasion, margin positivity, dissected lymph node count of <12, and presence of perforation/obstruction were accepted as risk factors. Those patients with at least one risk factor were regarded as having high risk. Results The study included 168 patients, among which 95 (56.5%) were male and 73 (43.5%) were female. The median age of patients was 73 years (range: 70–94). One hundred one (60.1%) patients were identified to have high risk. Eighty-one (87%) patients received 5-flourouracil+leucovorin and 12 (13%) patients received capecitabine regimens as adjuvant chemotherapy. The patients receiving capecitabine regimen had significantly higher rates of dose reduction at initiation and during the treatment. Among low-risk group, there was no statistically significant difference between patients with and without adjuvant chemotherapy in terms of disease-free survival or overall survival (p = 0.528 and p = 0.217, respectively). In high-risk group, patients receiving adjuvant chemotherapy significantly differed from those not receiving adjuvant chemotherapy in terms of median disease-free survival and overall survival (p = 0.009 and p < 0.001, respectively). While the grade, lymph node status, and adjuvant chemotherapy were identified as the most significant independent factors for disease-free survival, the most significant factors for overall survival were the age, Eastern Cooperative Oncology Group performance status, adjuvant chemotherapy, and recurrence. Conclusion The findings of our study showed improved disease-free survival and overall survival in high-risk ≥70-year-old patients who received adjuvant chemotherapy due to T3N0M0 colorectal cancer. We believe that 5-flourouracil+leucovorin or capecitabine regimens should be recommended for these older high-risk patients who could receive adjuvant chemotherapy regardless of age.

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