scholarly journals Network analysis identifies DAPK3 as a potential biomarker for lymphovascular invasion and prognosis of colon adenocarcinoma

Author(s):  
Huey-Miin Chen ◽  
Justin A. MacDonald

AbstractAdenocarcinoma of the colon is the fourth most common malignancy worldwide with significant rates of mortality. Hence, the identification of novel molecular biomarkers with prognostic significance is of particular importance for improvements in treatment and patient outcome. Clinical traits and RNA-Seq data of 551 patient samples and 18,205 genes in the UCSC Toil Recompute Compendium of TCGA TARGET and GTEx datasets (restricted to |Primary_site| = colon) were obtained from the Xena platform. Weighted gene co-expression network analysis was completed, and 24 unique modules were assembled to specifically examine the association between gene networks and cancer cell invasion. One module, containing 151 genes, was significantly correlated with lymphatic invasion, a histopathological feature of higher-risk colon cancer. Search tool for the retrieval of interacting genes/proteins (STRING) and gene ontology (GO) analyses identified the module to be enriched in genes related to cytoskeletal organization and apoptotic signaling, suggesting involvement in tumor cell survival and migration along with epithelial-mesenchymal transformation. Of genes that were differentially expressed and significant for overall survival, DAPK3 (death-associated protein kinase 3) was revealed as the pseudo-hub of the module. Although DAPK3 expression was reduced in colon cancer patients, survival analysis revealed that high expression of DAPK3 was significantly correlated with greater lymphovascular invasion and poor overall survival.

2019 ◽  
Vol 34 (1) ◽  
pp. 27-32 ◽  
Author(s):  
Yan Jin ◽  
Kun Zhou ◽  
Wenjing Zhao ◽  
Rongbo Han ◽  
Xinying Huo ◽  
...  

Background: The gene metastasis-associated in colon cancer-1 (MACC1) has been reported to be overexpressed in diverse human malignancies, and an increasing amount of evidence suggests that its overexpression is associated with the development and progression of many human tumors. However, the prognostic and clinicopathological value of MACC1 in gastric cancer remains inconclusive. Therefore, we conducted this meta-analysis to investigate the effect of positive MACC1 expression on clinicopathological features and survival outcomes in gastric cancer. Methods: Medline, Web of Science, and EMBASE databases were searched for relevant articles published up to 10 April 2018. The correlation of MACC1 expression levels with overall survival and clinicopathological features was analyzed. Results: In this meta-analysis, nine studies with a total of 2103 gastric cancer patients were included. Our results showed that high expression of MACC1 was significantly related to a poor overall survival. Moreover, our meta-analysis showed that MACC1 overexpression was significantly linked to distant metastasis and vascular invasion. There were no significant correlations between positive MACC1 expression and gender, localization, tumor-node-metastasis (TNM) stage, tumor extent (T stage) and lymph node involvement (N stage) Conclusions: MACC1 expression levels can serve as a novel prognostic factor in gastric cancer patients.


2021 ◽  
Author(s):  
Fatima El agy ◽  
Sanae El bardai ◽  
Laila Bouguenouch ◽  
Nada Lahmidani ◽  
Mohammed El abkari ◽  
...  

Abstract Background: Tumor budding is now emerging as one of the robust and promising histological factors that play an important role in colon cancer. In this study, we aimed to investigate the association between tumor budding and tumor clinicopathological factors, tumor molecular signature, and patient survival for the first time in the Moroccan population. Methods: We collected data of 100 patients with operated colon adenocarcinoma. Tumor budding was assessed on HES slides, according to the International Tumor Budding Consensus Conference 2016 recommendations. The expression of MMR proteins was performed by Immunohistochemistry. KRAS and NRAS mutations testing was performed by Sanger sequencing and pyrosequençing. Results: High tumor budding grade (BUD 3) was found to be significantly associated with adverse clinicopathological features including older age (P=0.03), presence of perineural invasion (P=0.02), presence of vascular invasion (P=0.05), distant metastases (P˂0.001), advanced TNM stage (P=0.001), the occurrence of relapse (P=0.04), and the high number of deceased cases (P=0.02). Interestingly, we found that tumors with high budding were more likely to be microsatellite stable (MSS) (P=0.005) and harbor more KRAS mutations (P=0.02). In all stages, High tumor budding was correlated with poorer overall survival (P=0.04) and decreased relapse-free survival with a difference close to significance ((P=0.09). we concluded that high tumor budding was strongly associated with unfavorable clinicopathological features and special molecular biomarkers and effectively affects the overall survival of CC patients. Conclusions: Based on these findings and the ITBCC group recommendations, tumor budding should be taken into account along with other clinicopathologic factors in the risk assessment of colorectal cancer.


2021 ◽  
Vol 66 (8) ◽  
pp. 459-464
Author(s):  
A. A. Nikolaev ◽  
I. V. Babkina ◽  
Elena Sergeevna Gershtein ◽  
A. A. Alferov ◽  
V. V. Delektorskaya ◽  
...  

The analysis of long-term results of treatment of 88 primary patients with colon adenocarcinoma at various stages of tumor process is presented, taking into account the TNM system criteria, and serum IGF-1, IGF-2, IGFBP-1, IGFBP-2, IGFBP-3, VEGF, and MMP-7 levels. The overall survival rate assessed by Kaplan-Meier method and Cox multivariate regression model was used as the criterion of prognosis. It was established that IGF-1, IGFBP-2 and VEGF serum levels along with the stage of colorectal cancer might be considered as statistically significant independent predictors of overall survival in patients.


BMJ Open ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. e037614
Author(s):  
Xin Chen ◽  
Jing Li ◽  
Xunlei Zhang ◽  
Yushan Liu ◽  
Jindong Wu ◽  
...  

ObjectiveOur study aimed to evaluate the prognostic and clinicopathological significance of pretreatment mean platelet volume (MPV) on cancer by using meta-analysis of published studies.DesignMeta-analysis.Data sourcesRelevant studies available before 22 December 2019 were identified by searching MEDLINE, EMBASE.Eligibility criteriaAll published studies that assessed the prognostic and clinicopathological significance of pretreatment MPV on cancer were included.Data extraction and synthesisStudies were identified and extracted by two reviewers independently. The HR/OR and its 95% CIs of survival outcomes and clinicopathological parameters were calculated.ResultsA total of 38 eligible studies (41 subsets) with 9894 patients with cancer were included in the final meta-analysis. MPV level was not significantly associated with both overall survival (HR 0.98, 95% CI 0.84 to 1.14) and disease-free survival (HR 1.22, 95% CI 0.86 to 1.73) of patients with cancer. Neither advanced nor mixed-stage tumour patients showed significant association between MPV and overall survival (HR 1.36, 95% CI 0.96 to 1.94, HR 0.90, 95% CI 0.74 to 1.09). However, high MPV had the strongest relationship with poor overall survival (HR 2.01; 95% CI 1.08 to 3.41) in gastric cancer, followed by pancreatic cancer (HR 1.54; 95% CI 1.31 to 1.82). Whereas in the subgroup using receiver operating characteristic curve method to define cut-off values, low MPV was significantly related to poor overall survival (HR 0.78, 95% CI 0.64 to 0.95). In addition, MPV had no significant association with age (OR 0.96, 95% CI 0.90 to 1.02), sex (OR 1.04, 95% CI 1.00 to 1.09), depth of cancer invasion (OR 0.90, 95% CI 0.77 to 1.04) and tumour stage (OR 0.91, 95% CI 0.78 to 1.07).ConclusionsPretreatment MPV level is of no clearly prognostic significance in cancers and no significant association with clinicopathological parameters of patients with cancers.


2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e14583-e14583
Author(s):  
Qin Wang ◽  
Wei Luan ◽  
M. Isabel Fiel ◽  
Sima Blank ◽  
Ki Won Kim ◽  
...  

e14583 Background: Little is known about the prognostic significance of total intrahepatic HBV DNA (ihHBV DNA) and cccDNA, a stable episome that accumulates in the nuclei and serves as the template for viral replication. This study aims to quantitate ihHBV DNA and cccDNA in the non-neoplastic liver and to assess their impact on prognosis in HBV-HCC patients. Methods: 111 patients, many on HBV antivirals, who underwent liver resection for HBV-HCC from 1991 to 2008 were assessed by real time PCR for ihHBV DNA, cccDNA, and albumin. Liver fibrosis and necroinflammation was assessed using the modified Ishak method. Independent variables associated with survival were analyzed using multivariate Cox regression model, with a median follow up for survivors of 52 months. Results: Serum HBV DNA was detectable in only 42% of patients, but 106 patients (95%) had detectable ihHBV DNA (median: 0.018copy/hepatocyte); and 89 patients (80%) had detectable cccDNA (0.00058 copy/hepatocyte). Median cccDNA/ihHBV DNA ratio was 0.019. ihHBV DNA correlated with histologic activity index (p = 0.04) and serum ALT (p = 0.004). Patients in the lowest quartile of cccDNA/ihHBV DNA ratio (<0.0032) trended towards poor overall 5-year survival by univariate analysis (p = 0.09), with higher mortality at 2 years (89% vs. 45%, p = 0.03). In multivariate analysis, AFP > 20, Ishak fibrosis stage 6 (established cirrhosis), cccDNA/ihHBV DNA < 0.0032, and large tumor diameter were independently associated with poor overall survival (Table). Conclusions: ihHBV DNA levels were associated with severity of liver necroinflammation and injury. ihHBV DNA and cccDNA levels were not associated with survival; rather, low proportion of total HBV DNA in the form of cccDNA was independently associated with poor overall survival. Thus, viral behavior at the time of liver resection influences clinical outcome for HBV-HCC patients. [Table: see text]


Tumor Biology ◽  
2017 ◽  
Vol 39 (3) ◽  
pp. 101042831769501 ◽  
Author(s):  
Piotr Ciesielski ◽  
Paweł Jóźwiak ◽  
Katarzyna Wójcik-Krowiranda ◽  
Ewa Forma ◽  
Łukasz Cwonda ◽  
...  

Ten-eleven translocation proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine, and 5-carboxylcytosine that play a significant role in DNA demethylation. Deregulation of TET genes expression and changes in the level of 5-hmC are thought to be associated with the onset and progression of several types of cancer, but there are no such data related to endometrial cancer. The aim of the work was to investigate the messenger RNA expression levels of TET1, TET2, and TET3 in relation to clinicopathological characteristics of endometrial cancer as well as the correlation between expression of TET genes and the level of 5-hmC/5-mC. The prognostic significance of TETs expression for overall survival was established. We found that TET1 and TET2 messenger RNA expression was lower and TET3 was higher in cancers compared to normal tissues. Positive correlation between 5-hmC and the relative expression of TET1 and TET2 was found, but no correlation was observed in the case of TET3. Decreased expression of TET1 and TET2 was significantly associated with increased lymph node metastasis and International Federation of Gynecology and Obstetrics stage. Kaplan–Meier analysis indicated that low TET1 expression predicted poor overall survival (p = 0.038). Multivariate analysis identified the TET1 expression in endometrial cancer as an independent prognostic factor. Our results suggest that decreased expression of TET1 correlates with tumor progression and may serve as a potential prognostic biomarker in endometrial cancer.


2021 ◽  
Author(s):  
Zhongze Cui ◽  
Shuang He ◽  
Feifei Wen ◽  
Xiaoyang Xu ◽  
Yangyang Li ◽  
...  

Abstract Background: Colon adenocarcinoma (COAD) is one of the most common malignancies worldwide. Although a large number of studies have elucidated the aetiology of colorectal cancer, the exact mechanism of colorectal cancer development remains to be determined.To identify key modules and prognostic genes that may be involved in the occurrence and development of COAD, weighted gene coexpression network analysis (WGCNA) and differential expression analysis were performed on datasets GSE41657 and GSE74602 from the Gene Expression Omnibus (GEO) database to screen for prognostic differentially expressed genes. Gene expression profiles and clinical information were collected from The Cancer Genome Atlas (TCGA) database for verification.Results: Through WGCNA and DEGs analysis, 439 genes in key functional modules were obtained, and 26 prognostic related genes were finally obtained through prognostic analysis: (1) We screened 5 genes(RPP40, DUSP18, PPRC1, MFSD11 and PDCD11) that have not been studied in COAD.(2)We obtained the most critical module in the occurrence and development of colon cancer and obtained one prognosis-related gene, NUP85, from the most critical module.The relationship between it and tumor immune microenvironment was verified.(3) A prognostic model comprising four coexpressed differential genes was constructed; TIMP1, PMM2, E2F3 and MORC2 were selected as the key prognosis-related genes.Conclusions: (1)As new biomarkers,prognostic genes RPP40, DUSP18, PPRC1, MFSD11 and PDCD11 may be potential therapeutic targets for COAD, and provide new ideas for future research on the mechanism of COAD. (2)NUP85 may be an immune-related gene which was negatively correlated with CD4+ T cell and M2 macrophagesthat plays an important role in inhibiting the occurrence and development of colorectal adenocarcinoma. (3)A Cox proportional risk model based on gene expression can be used to predict the prognosis and survival time of patients with colon cancer.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2012-2012
Author(s):  
Bounleut Phanavanh ◽  
Priyangi Malaviarachchi ◽  
Adam Rosenthal ◽  
Yogesh Jethava ◽  
Bart Barlogie ◽  
...  

Abstract Prolonged survival of myeloma patients on Total Therapy regimens including IMIDS and novel agents has been associated with increased incidence of treatment-related myelodysplastic syndrome and acute leukemia (t-MDS/AL). MDS cytogenetic abnormalities (MDS-CAs) are often observed prior to t-MDS/AL development. Among 1,080 patients on TT2 and TT3 protocols, MDS-CA occurred in 11% and t-MDS/AML in 3%. Risk features of MDS-CA included TT3b treatment, age ³65 yr, male sex, elevated B2M, and MM relapse. Lower doses of CD34 HSCs applied with first transplants raised the probability of MDS-CAs, and lower CD34 HSCs dosing was an independent contributor to MDS-CAs and clinical t-MDS (Usmani et al., 2013). Although patients with MDS-CAs do not always develop t-MDS/AML, the phenomenon, also recognized in other tumors, requires understanding and development of preventive measures. We analyzed gene expression profiling (GEP) of bone marrow core biopsies at diagnosis from patients enrolled in our TT2 (n=88) and TT3 (n=263; training set) trials to identify genes associated with time to MDS-CA. Univariate Cox regression identified BCL11A as the only gene with expression associated with the time to development of MDS-CA (q <0.1). Incidence of MDS-CA for MM patients enrolled in TT2 and TT3 is 11% (Usmani et al., 2013); 3-year estimate of patients with low BCL11A expression is 8% vs. 3.9% for those with higher expression (Figure 1). Univariate analysis of baseline variables linked shorter time to MDS-CA with Age ≥ 65 yr, B2M > 5.5 mg/L, GEP70-defined high risk and low BCL11A expression, while female sex was linked with longer time to MDS-CA development. In multivariate analysis, females retained independent prognostic significance for time to MDS-CA (HR-0.41, p 0.006), as did B2M > 5.5 mg/L (HR-1.95, p=0.038) and BCL11A expression <10.323 (HR-3.24, p <0.001). In addition to its role in normal hematopoietic development (Yu et.al., 2012), BCL11A is a central transcription factor in normal erythropoiesis (Xu et.al. 2012), and differences in its expression may reflect abnormal erythropoiesis. Indeed, lower Hb levels before HSC mobilization was associated with MDS-CA development in MM patients (Papanikolaou et al., 2013) while BCL11A expression is lower in core biopsies from MM patients than in those from healthy donors. BCL11A expression correlated with a set of genes associated with erythropoiesis (r>0.55) (e.g., GYPA, TFRC, RHAG, TRIM10, ANK1, SPTA1). BM cell fractions from MM patients were purified using MACS and FACS and BCL11A expression was analyzed by qRT-PCR demonstrating that BCL11A is highly expressed in CD19+ B cells and CD235a+ erythroid cells, intermediately expressed in CD34+ HSPCs, and absent in CD3+ T cells and CD15+ myeloid cells. BCL11A expression in paired biopsies and CD138-selected PCs does not correlate, further demonstrating that BCL11A expression originates in the MM microenvironment. As suppression of hematopoiesis is common to MDS and MM, we determined whether loss of BCL11A was associated with survival independent of MDS-CA status. Lower BCL11A expression in bone biopsies was associated with poor overall survival of patients on the TT2 protocol (p=0.0182) and TT3 protocol (p=0.0015). Taken together, these data demonstrate that low BCL11A expression in newly diagnosed MM is an independent predictor of early MDS-CA development, and is associated with altered hematopoiesis and poor overall survival, and may be a biomarker of t-MDS/AML risk. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ranliang Cui ◽  
Chaomin Wang ◽  
Tiantian Li ◽  
Jialei Hua ◽  
Ting Zhao ◽  
...  

Abstract Background The incidence and mortality of invasive breast cancer (IBC) are increasing annually. Hence, it is urgently needed to determine reliable biomarkers for not only monitoring curative effects, but evaluating prognosis. In present study, we aim to determine the potential role of Carboxypeptidase N1 (CPN1) in IBC tissues on chemotherapeutic efficacy and poor prognosis. Methods The expression level of CPN1 in IBC tissue samples (n = 123) was quantified by tissue microarray technique and immunohistochemical staining. Moreover, sera of IBC patients (n = 34) that underwent three to five consecutive chemotherapy sessions were collected. The patients were randomly stratified into a training (n = 15) as well as a validation group (n = 19). The expression of serum CA153 and CPN1 was quantified by electrochemiluminescence and ELISA assay, respectively. Results By univariate and multivariate Cox regression analysis, we show that CPN1 expression in IBC tissues, as an independent risk factor, is related to a poor overall survival (OS) and progression-free survival (PFS) (P < 0.05). Analysis of the data revealed that CPN1 over-expression could be consistently linked to adverse clinicopathological features such as lymph node metastasis and the pathological stage (pTNM) (P < 0.05). The serum CPN1 level trajectory of individual patients generally decreased during chemotherapy. In line with these findings were changes in the follow-up ultrasonography and a consistent decrease in serum CPN1 levels. The comparison of the area under the receiver operating curves (ROC) revealed that CPN1 has a better surveillance value than CA153 in the training (AUCCPN1 = 0.834 vs. AUCCA153 = 0.724) as well as the validation set (AUCCPN1 = 0.860 vs. AUCCA153 = 0.720) when comparing cycle2 versus cycle3. Conclusions CPN1 is a suitable potential biomarker for chemotherapeutic surveillance purposes as well as being an appropriate prognostic indicator which would support an improved chemotherapy regimen.


2021 ◽  
Author(s):  
Yang-yang Liu ◽  
Xiang-biao He

Abstract Background: Colon adenocarcinoma (COAD), a type of colon cancer, is among the most common malignant diseases afflicting people globally. Heat shock protein family, including HSPA8, are involved in tumor progression in numerous human cancers, however the association between HSPA8 and COAD has not been explored.Methods: RNA sequencing data and clinical characteristics from TCGA and GTEx, as well as protein data from CPTAC were obtained for analysis of HSPA8 expression in COAD. Furthermore, functional enrichment analysis of HSPA8-related differentially expressed genes (DEGs) was performed via GO/KEGG, immune infiltration analysis, and protein-protein interaction (PPI) network. In addition, the clinical significance of HSPA8 was analyzed by Kaplan-Meier Cox regression and prognosis assessment. R package was employed to analyze incorporated studies.Results: Compared with normal samples, the expression of HSPA8 increased remarkably in various tumors, including COAD, Moreover, high HSPA8 expression was associated with good prognosis in COAD, as well as subgroups with male, T2-T4 stage, no lymphatic and perineural invasion. (P < 0.05). High HSPA8 was a prognostic factor in Cox regression analysis. The diagnostic efficacy of HSPA8 in COAD analyzed by ROC (AUC: 0.889). Furthermore, a total of 3321 DEGs were identified between the high- and the low-expression group, of which 9 genes were up-regulated and 3312 genes were down-regulated.Conclusions: High HSPA8 expression is a potential biomarker for favorable outcomes in COAD. the results might provide clues and guidance for developing novel diagnosis, targeted therapy and prognosis of HSPA8 in COAD.


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