scholarly journals Integrative Analysis of Identifying Methylation-Driven Genes Signature Predicts Prognosis in Colorectal Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Hao Huang ◽  
Jinming Fu ◽  
Lei Zhang ◽  
Jing Xu ◽  
Dapeng Li ◽  
...  

BackgroundAberrant DNA methylation is a critical regulator of gene expression and plays a crucial role in the occurrence, progression, and prognosis of colorectal cancer (CRC). We aimed to identify methylation-driven genes by integrative epigenetic and transcriptomic analysis to predict the prognosis of CRC patients.MethodsMethylation-driven genes were selected for CRC using a MethylMix algorithm and LASSO regression screening strategy, and were further used to construct a prognostic risk-assessment model. The Cancer Genome Atlas (TCGA) database was obtained as the training set for both the screening of methylation-driven genes and the effect of genes signature on CRC prognosis. Then, the prognostic genes signature was validated in three independent expression arrays of CRC data from Gene Expression Omnibus (GEO).ResultsWe identified 143 methylation-driven genes, of which the combination of BATF, PHYHIPL, RBP1, and PNPLA4 expression levels was screened as a better prognostic model with the best area under the curve (AUC) (AUC = 0.876). Compared with patients in the low-risk group, CRC patients in the high-risk group had significantly poorer overall survival in the training set (HR = 2.184, 95% CI: 1.404–3.396, P < 0.001). Similar results were observed in the validation set. Moreover, VanderWeele’s mediation analysis indicated that the effect of methylation on prognosis was mediated by the levels of their expression (HRindirect = 1.473, P = 0.001, Proportion mediated, 69.10%).ConclusionsWe identified a four-gene prognostic signature by integrative analysis and developed a risk-assessment model that is significantly associated with patients’ survival. Methylation-driven genes might be a potential prognostic signature for CRC patients.

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xiao-Liang Xing ◽  
Zhi-Yong Yao ◽  
Chaoqun Xing ◽  
Zhi Huang ◽  
Jing Peng ◽  
...  

Abstract Background Colorectal cancer (CRC) is the second most prevalent cancer, as it accounts for approximately 10% of all annually diagnosed cancers. Studies have indicated that DNA methylation is involved in cancer genesis. The purpose of this study was to investigate the relationships among DNA methylation, gene expression and the tumor-immune microenvironment of CRC, and finally, to identify potential key genes related to immune cell infiltration in CRC. Methods In the present study, we used the ChAMP and DESeq2 packages, correlation analyses, and Cox regression analyses to identify immune-related differentially expressed genes (IR-DEGs) that were correlated with aberrant methylation and to construct a risk assessment model. Results Finally, we found that HSPA1A expression and CCRL2 expression were positively and negatively associated with the risk score of CRC, respectively. Patients in the high-risk group were more positively correlated with some types of tumor-infiltrating immune cells, whereas they were negatively correlated with other tumor-infiltrating immune cells. After the patients were regrouped according to the median risk score, we could more effectively distinguish them based on survival outcome, clinicopathological characteristics, specific tumor-immune infiltration status and highly expressed immune-related biomarkers. Conclusion This study suggested that the risk assessment model constructed by pairing immune-related differentially expressed genes correlated with aberrant DNA methylation could predict the outcome of CRC patients and might help to identify those patients who could benefit from antitumor immunotherapy.


2021 ◽  
Vol 9 ◽  
Author(s):  
Qiao-Ying Xie ◽  
Ming-Wei Wang ◽  
Zu-Ying Hu ◽  
Cheng-Jian Cao ◽  
Cong Wang ◽  
...  

Aim: Metabolic syndrome (MS) screening is essential for the early detection of the occupational population. This study aimed to screen out biomarkers related to MS and establish a risk assessment and prediction model for the routine physical examination of an occupational population.Methods: The least absolute shrinkage and selection operator (Lasso) regression algorithm of machine learning was used to screen biomarkers related to MS. Then, the accuracy of the logistic regression model was further verified based on the Lasso regression algorithm. The areas under the receiving operating characteristic curves were used to evaluate the selection accuracy of biomarkers in identifying MS subjects with risk. The screened biomarkers were used to establish a logistic regression model and calculate the odds ratio (OR) of the corresponding biomarkers. A nomogram risk prediction model was established based on the selected biomarkers, and the consistency index (C-index) and calibration curve were derived.Results: A total of 2,844 occupational workers were included, and 10 biomarkers related to MS were screened. The number of non-MS cases was 2,189 and that of MS was 655. The area under the curve (AUC) value for non-Lasso and Lasso logistic regression was 0.652 and 0.907, respectively. The established risk assessment model revealed that the main risk biomarkers were absolute basophil count (OR: 3.38, CI:1.05–6.85), platelet packed volume (OR: 2.63, CI:2.31–3.79), leukocyte count (OR: 2.01, CI:1.79–2.19), red blood cell count (OR: 1.99, CI:1.80–2.71), and alanine aminotransferase level (OR: 1.53, CI:1.12–1.98). Furthermore, favorable results with C-indexes (0.840) and calibration curves closer to ideal curves indicated the accurate predictive ability of this nomogram.Conclusions: The risk assessment model based on the Lasso logistic regression algorithm helped identify MS with high accuracy in physically examining an occupational population.


PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9621
Author(s):  
Shanliang Zhong ◽  
Huanwen Chen ◽  
Sujin Yang ◽  
Jifeng Feng ◽  
Siying Zhou

We aimed to identify prognostic signature based on autophagy-related genes (ARGs) for breast cancer patients. The datasets of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to construct multiple-ARG risk signature. In total, 32 ARGs were identified as differentially expressed between tumors and adjacent normal tissues based on TCGA. Six ARGs (IFNG, TP63, PPP1R15A, PTK6, EIF4EBP1 and NKX2-3) with non-zero coefficient were selected from the 32 ARGs using LASSO regression. The 6-ARG signature divided patients into high-and low-risk group. Survival analysis indicated that low-risk group had longer survival time than high-risk group. We further validated the 6-ARG signature using dataset from GEO and found similar results. We analyzed the associations between ARGs and breast cancer survival in TCGA and nine GEO datasets, and obtained 170 ARGs with significant associations. EIF4EBP1, FOS and FAS were the top three ARGs with highest numbers of significant associations. EIF4EBP1 may be a key ARG which had a higher expression level in patients with more malignant molecular subtypes and higher grade breast cancer. In conclusion, our 6-ARG signature was of significance in predicting of overall survival of patients with breast cancer. EIF4EBP1 may be a key ARG associated with breast cancer survival.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yunfei Dong ◽  
Tao Shang ◽  
HaiXin Ji ◽  
Xiukou Zhou ◽  
Zhi Chen

BackgroundThe pathological stage of colon cancer cannot accurately predict recurrence, and to date, no gene expression characteristics have been demonstrated to be reliable for prognostic stratification in clinical practice, perhaps because colon cancer is a heterogeneous disease. The purpose was to establish a comprehensive molecular classification and prognostic marker for colon cancer based on invasion-related expression profiling.MethodsFrom the Gene Expression Omnibus (GEO) database, we collected two microarray datasets of colon cancer samples, and another dataset was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) further underwent univariate analysis, least absolute shrinkage, selection operator (LASSO) regression analysis, and multivariate Cox survival analysis to screen prognosis-associated feature genes, which were further verified with test datasets.ResultsTwo molecular subtypes (C1 and C2) were identified based on invasion-related genes in the colon cancer samples in TCGA training dataset, and C2 had a good prognosis. Moreover, C1 was more sensitive to immunotherapy. A total of 1,514 invasion-related genes, specifically 124 downregulated genes and 1,390 upregulated genes in C1 and C2, were identified as DEGs. A four-gene prognostic signature was identified and validated, and colon cancer patients were stratified into a high-risk group and a low-risk group. Multivariate regression analyses and a nomogram indicated that the four-gene signature developed in this study was an independent predictive factor and had a relatively good predictive capability when adjusting for other clinical factors.ConclusionThis research provided novel insights into the mechanisms underlying invasion and offered a novel biomarker of a poor prognosis in colon cancer patients.


2020 ◽  
Author(s):  
Qiao-Ying Xie ◽  
Ming-Wei Wang ◽  
Zu-Ying Hu ◽  
Yan-Ming Chu ◽  
Cheng-Jian Cao ◽  
...  

Abstract Background: Metabolic syndrome (MS) screening is important for the early detection of occupational population. This study aimed to screen out biomarkers related to MS and establish a risk assessment and prediction model for the routine physical examination of an occupational population.Methods: The least absolute shrinkage and selection operator (Lasso) regression algorithm of machine learning was used to screen biomarkers related to MS. Then, the accuracy of the logistic regression model was further verified based on the Lasso regression algorithm. Finally, the screened biomarkers were used to establish a logistic regression model and calculate the odds ratio (OR) of the corresponding biomarkers. Results: A total of 2844 occupational workers were included, and 10 biomarkers related to MS were screened. The area under the curve (AUC) value for non-Lasso and Lasso regression was 0.652 and 0.907, respectively. The established risk assessment model revealed that the main risk factors were basophil absolute count (OR: 3.38), platelet packed volume (OR: 2.63), leukocyte count (OR: 2.01), red blood cell count (OR: 1.99), and alanine aminotransferase level (OR: 1.53). Conclusion: The risk assessment model based on the Lasso regression algorithm helped identify Metabolic syndrome with high accuracy in physically examining an occupational population.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 144-144 ◽  
Author(s):  
Ang Li ◽  
Qian V. Wu ◽  
Greg Warnick ◽  
Neil A Zakai ◽  
Edward N. Libby ◽  
...  

Abstract Introduction: Patients with newly diagnosed multiple myeloma (MM) have high risk of venous thromboembolism (VTE) when starting initial treatment that contains immunomodulatory drugs (IMID) such as lenalidomide or thalidomide. The National Comprehensive Cancer Network (NCCN) guideline recommends primary anticoagulant thromboprophylaxis for the high-risk patients. However, it is challenging to risk-stratify patients without a validated risk model. We have conducted a retrospective cohort study using the SEER-Medicare (Surveillance, Epidemiology, and End Results) database to derive a new VTE risk assessment model. Methods: We selected all patients 66 or older with newly diagnosed MM 2007 to 2013. Patients were included if they had a prescription of IMID within twelve months of diagnosis and complete enrollment for fee-for-service and prescription drug coverage. We ascertained baseline demographics and VTE risk factors from the current NCCN guideline using validated codes. The VTE outcome was defined as either one inpatient or two outpatient claims at least 30 days apart in combination with an anticoagulant prescription within 90 days. All patients were followed from the date of IMID initiation until first VTE occurrence or death and were censored for disenrollment from Medicare, discontinuation of IMID (after a grace period of 90 days), autologous transplantation, or the end of claims data (12/31/2014). Cause specific Cox regression models were used for time to VTE analysis. For variable selection, all risk factors with p-value <0.10 were considered candidates for inclusion in the final multivariable regression model. VTE history, recent surgery, and anticoagulant exposure were forced into the model, regardless of significance testing. Integer points were assigned according to the beta coefficients and subsequent risk groups were created. The model's discrimination was validated internally by the bias-corrected Harrell's c statistic and the 95% confidence interval was estimated from 200 bootstrap samples. Results: We identified 2397 MM patients on IMID that met the study criteria. The median time on IMID treatment was 116 days (IQR 28-279). The mean age of patients was 74, 49% were female, 80% were White, 13% were Black, 6.5% were Asian. Only 13% of patients had concurrent anticoagulant exposure (11% warfarin, 2% LMWH, 1% DOAC) with a median duration of 116 days (IQR 42-315 days). In the multivariable model built from candidate covariates, we identified history of VTE, recent surgery, cytotoxic (non-bortezomib) chemotherapy, higher dose dexamethasone, older age, and Black race, as important risk factors. Asian race and LMWH/DOAC use were associated with lower VTE risk (Table 1). We derived a risk assessment model that stratified patients into 2 prognostic risk groups (Table 1): 25% (n=581) in the very high-risk group (score 2 to 7), 75% (n=1816) in the standard-risk group (score -3 to 1). The incidence of VTE at 3 months and 6 months were 9.5% and 16.3% in the very high-risk group compared to 3.7% and 6.3% in the standard-risk group with a resulting hazard ratio of 2.73 (p<0.001) (Figure 1). The bias-corrected Harrell's c statistic for the product index was 0.63 (0.59-0.68). Conclusions: We have derived a VTE risk assessment model specifically for patients with MM starting IMID therapy. The HAS-RiSC score combines 7 clinical risk factors - History of VTE, Age 80+, Surgery within last 90 days, Race Black, race Asian, Steroid use, and Chemotherapy - into a simplified VTE risk assessment model that identifies a subgroup of patients at very high risk for VTE. External validation of this risk assessment model is currently in progress. Disclosures Garcia: Daiichi Sankyo: Research Funding; Incyte: Research Funding; Janssen: Consultancy, Research Funding; Pfizer: Consultancy; Retham Technologies LLC: Consultancy; Shingoi: Consultancy; Portola: Research Funding; Bristol Meyers Squibb: Consultancy; Boehringer Ingelheim: Consultancy. Lyman:Amgen: Other: Research support; Generex Biotechnology: Membership on an entity's Board of Directors or advisory committees; Halozyme; G1 Therapeutics; Coherus Biosciences: Consultancy.


2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Xiaonan Zhao ◽  
Zhenzi Bai ◽  
Chenghua Li ◽  
Chuanlun Sheng ◽  
Hongyan Li

Studies have demonstrated the prognosis potential of long noncoding RNAs (lncRNAs) for hepatocellular carcinoma (HCC), but specific lncRNAs for hepatitis B virus- (HBV-) related HCC have rarely been reported. This study was aimed at identifying a lncRNA prognostic signature for HBV-HCC and exploring their underlying functions. The sequencing dataset was collected from The Cancer Genome Atlas database as the training set, while the microarray dataset was obtained from the European Bioinformatics Institute database (E-TABM-36) as the validation set. Univariate and multivariate Cox regression analyses identified that eight lncRNAs (TSPEAR-AS1, LINC00511, LINC01136, MKLN1-AS, LINC00506, KRTAP5-AS1, ZNF252P-AS1, and THUMPD3-AS1) were significantly associated with overall survival (OS). These eight lncRNAs were used to construct a risk score model. The Kaplan-Meier survival curve results showed that this risk score can significantly differentiate the OS between the high-risk group and the low-risk group. Receiver operating characteristic curve analysis demonstrated that this risk score exhibited good prediction effectiveness (area under the curve AUC=0.990 for the training set; AUC=0.903 for the validation set). Furthermore, this lncRNA risk score was identified as an independent prognostic factor in the multivariate analysis after adjusting other clinical characteristics. The crucial coexpression (LINC00511-CABYR, THUMPD3-AS1-TRIP13, LINC01136-SFN, LINC00506-ANLN, and KRTAP5-AS1/TSPEAR-AS1/MKLN1-AS/ZNF252P-AS1-MC1R) or competing endogenous RNA (THUMPD3-AS1-hsa-miR-450a-TRIP13) interaction axes were identified to reveal the possible functions of lncRNAs. These genes were enriched into cell cycle-related biological processes or pathways. In conclusion, our study identified a novel eight-lncRNA prognosis signature for HBV-HCC patients and these lncRNAs may be potential therapeutic targets.


PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8877
Author(s):  
Xiaorui Fu ◽  
Jinzhong Duanmu ◽  
Taiyuan Li ◽  
Qunguang Jiang

Background Colon adenocarcinoma (COAD) is the most common colon cancer exhibiting high mortality. Due to their association with cancer progression, long noncoding RNAs (lncRNAs) are now being used as prognostic biomarkers. In the present study, we used relevant clinical information and expression profiles of lncRNAs originating from The Cancer Genome Atlas database, aiming to construct a prognostic lncRNA signature to estimate the prognosis of patients. Methods The samples were randomly spilt into training and validation cohorts. In the training cohort, prognosis-related lncRNAs were selected from differentially expressed lncRNAs using the univariate Cox analysis. Furthermore, the least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox analysis were employed for identifying prognostic lncRNAs. The prognostic signature was constructed by these lncRNAs. Results The prognostic model was able to calculate each COAD patient’s risk score and split the patients into groups of low and high risks. Compared to the low-risk group, the high-risk group had significant poor prognosis. Next, the prognostic signature was validated in the validation, as well as all cohorts. The receiver operating characteristic (ROC) curve and c-index were determined in all cohorts. Moreover, these prognostic lncRNA signatures were combined with clinicopathological risk factors to construct a nomogram for predicting the prognosis of COAD in the clinic. Finally, seven lncRNAs (CTC-273B12.10, AC009404.2, AC073283.7, RP11-167H9.4, AC007879.7, RP4-816N1.7, and RP11-400N13.2) were identified and validated by different cohorts. The Kyoto Encyclopedia of Genes and Genomes analysis of the mRNAs co-expressed with the seven prognostic lncRNAs suggested four significantly upregulated pathways, which were AGE-RAGE, focal adhesion, ECM-receptor interaction, and PI3K/Akt signaling pathways. Conclusion Thus, our study verified that the seven lncRNAs mentioned can be used as biomarkers to predict the prognosis of COAD patients and design personalized treatments.


2010 ◽  
Vol 151 (34) ◽  
pp. 1365-1374 ◽  
Author(s):  
Marianna Dávid ◽  
Hajna Losonczy ◽  
Miklós Udvardy ◽  
Zoltán Boda ◽  
György Blaskó ◽  
...  

A kórházban kezelt sebészeti és belgyógyászati betegekben jelentős a vénásthromboembolia-rizikó. Profilaxis nélkül, a műtét típusától függően, a sebészeti beavatkozások kapcsán a betegek 15–60%-ában alakul ki mélyvénás trombózis vagy tüdőembólia, és az utóbbi ma is vezető kórházi halálok. Bár a vénás thromboemboliát leggyakrabban a közelmúltban végzett műtéttel vagy traumával hozzák kapcsolatba, a szimptómás thromboemboliás események 50–70%-a és a fatális tüdőembóliák 70–80%-a nem a sebészeti betegekben alakul ki. Nemzetközi és hazai felmérések alapján a nagy kockázattal rendelkező sebészeti betegek többsége megkapja a szükséges trombózisprofilaxist. Azonban profilaxis nélkül marad a rizikóval rendelkező belgyógyászati betegek jelentős része, a konszenzuson alapuló nemzetközi és hazai irányelvi ajánlások ellenére. A belgyógyászati betegek körében növelni kell a profilaxisban részesülők arányát és el kell érni, hogy trombózisrizikó esetén a betegek megkapják a hatásos megelőzést. A beteg trombóziskockázatának felmérése fontos eszköze a vénás thromboembolia által veszélyeztetett betegek felderítésének, megkönnyíti a döntést a profilaxis elrendeléséről és javítja az irányelvi ajánlások betartását. A trombózisveszély megállapításakor, ha nem ellenjavallt, profilaxist kell alkalmazni. „A thromboemboliák kockázatának csökkentése és kezelése” című, 4. magyar antithromboticus irányelv felhívja a figyelmet a vénástrombózis-rizikó felmérésének szükségességére, és elsőként tartalmazza a kórházban fekvő belgyógyászati és sebészeti betegek kockázati kérdőívét. Ismertetjük a kockázatbecslő kérdőíveket és áttekintjük a kérdőívekben szereplő rizikófaktorokra vonatkozó bizonyítékokon alapuló adatokat.


Author(s):  
C.K. Lakshminarayan ◽  
S. Pabbisetty ◽  
O. Adams ◽  
F. Pires ◽  
M. Thomas ◽  
...  

Abstract This paper deals with the basic concepts of Signature Analysis and the application of statistical models for its implementation. It develops a scheme for computing sample sizes when the failures are random. It also introduces statistical models that comprehend correlations among failures that fail due to the same failure mechanism. The idea of correlation is important because semiconductor chips are processed in batches. Also any risk assessment model should comprehend correlations over time. The statistical models developed will provide the required sample sizes for the Failure Analysis lab to state "We are A% confident that B% of future parts will fail due to the same signature." The paper provides tables and graphs for the evaluation of such a risk assessment. The implementation of Signature Analysis will achieve the dual objective of improved customer satisfaction and reduced cycle time. This paper will also highlight it's applicability as well as the essential elements that need to be in place for it to be effective. Different examples have been illustrated of how the concept is being used by Failure Analysis Operations (FA) and Customer Quality and Reliability Engineering groups.


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