Novel diagnostic and prognostic biomarkers of colorectal cancer: Capable to overcome the heterogeneity-specific barrier and valid for global applications

Decoding the DSCC1 gene as a pan-cancer biomarker in human cancers via comprehensive multi-omics analyses

OBJECTIVES

While dysregulation of DSCC1 (DNA Replication And Sister Chromatid Cohesion 1) has been established in breast cancer and colorectal cancer, its associations with other tumors remain unclear. Therefore, this study was launched to explore the role of DSCC1 in pan-cancer.

METHODOLOGY

In this study, we investigate the biological functions of DSCC1 across 33 solid tumors, elucidating its role in promoting oncogenesis and progression in various cancers through comprehensive analysis of multi-omics data.

RESULTS

We conducted a comprehensive analysis of DSCC1 expression using RNA-seq data from TCGA and GTEx databases across 30 cancer types. Striking variations were observed, with significant overexpression of DSCC1 identified in numerous cancers. Elevated DSCC1 level was strongly associated with poorer prognosis, shorter survival, and advanced tumor stages in kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), as indicated by Kaplan-Meier curves and GEPIA2 analysis. Further investigation into the molecular mechanisms revealed reduced DNA methylation in the DSCC1 promoter region in KIRP, LIHC, and LUAD, supporting enhanced RNA transcription. Protein expression analysis via the Human Protein Atlas (HPA) corroborated mRNA expression findings, showcasing elevated DSCC1 protein in KIRP, LIHC, and LUAD tissues. Mutational analysis using cBioPortal revealed alterations in 0.4% of KIRP, 17% of LIHC, and 5% of LUAD samples, predominantly characterized by amplification. Immune cell infiltration analysis demonstrated robust positive correlations between DSCC1 expression and CD8+ T cells, CD4+ T cells, and B cells, influencing the tumor microenvironment. STRING and gene enrichment analyses unveiled DSCC1's involvement in critical pathways, emphasizing its multifaceted impact. Notably, drug sensitivity analysis highlighted a significant correlation between DSCC1 mRNA expression and responses to 78 anticancer treatments, suggesting its potential as a predictive biomarker and therapeutic target for KIRP, LIHC, and LUAD. Finally, immunohistochemistry staining of clinical samples validated computational results, confirming elevated DSCC1 protein expression.

CONCLUSION

Overall, this study provides comprehensive insights into the pivotal role of DSCC1 in KIRP, LIHC, and LUAD initiation, progression, and therapeutic responsiveness, laying the foundation for further investigations and personalized treatment strategies.

Bone morphogenetic protein 1: a prognostic indicator and potential biomarker in three cancer types

BACKGROUND

Bone morphogenetic protein 1 (BMP1) is a metalloprotease that plays a role in activating both transforming growth factor-β (TGF-β) and BMP signaling pathways. TGF-β has been identified as a factor initiating and facilitating cancer development. Consequently, we propose the hypothesis that dysregulation of BMP1 could potentially contribute to the onset and advancement of human cancers.

METHODS

In this research, we aimed to analyze BMP1 expression level and the associated clinical outcomes across various cancers using online cancer OMICS databases, advanced Bioinformatics tools, and molecular analyses.

RESULTS

The outcomes of our web server-based expression analysis indicated an up-regulation of BMP1 in a majority of the human cancers examined. External validation using clinical samples also showed higher expression of BMP1. Moreover, heightened BMP1 expression exhibited a noteworthy correlation with reduced overall survival (OS) duration in Bladder Cancer (BLCA), Kidney Renal Clear Cell Carcinoma (KIRC), and Lung Adenocarcinoma (LUAD) patients. This suggests a substantial involvement of the BMP1 gene in the development and progression of these three types of cancers. The major signaling pathways related with BMP1 enriched genes were "ECM-receptor interaction, Amoebiasis, Focal adhesion, Protein digestion and absorption, progesterone-mediated, PI3K-Akt signaling pathway, and platelet activation". Moreover, we also explored some interesting correlations among BMP1 expression and its DNA promoter methylation level, CD8+ T immune cells level, and genetic variations.

CONCLUSION

In conclusion, our study has provided some solid basis for BMP1 to be used as a reliable common biomarker for BLCA, KIRC, and LUAD patients.

CDCA8, a mitosis-related gene, as a prospective pan-cancer biomarker: implications for survival prognosis and oncogenic immunology

BACKGROUND

Human cell division cycle-associated protein 8 (CDCA8), a critical regulator of mitosis, has been identified as a prospective prognostic biomarker in several cancer types, including breast, colon, and lung cancers. This study analyzed the diagnostic/prognostic potential and clinical implications of CDCA8 across diverse cancers.

METHODS

Bioinformatics and molecular experiments.

RESULTS

Analyzing TCGA data via TIMER2 and GEPIA2 databases revealed significant up-regulation of CDCA8 in 23 cancer types compared to normal tissues. Prognostically, elevated CDCA8 expression correlated with poorer overall survival in KIRC, LUAD, and SKCM, emphasizing its potential as a prognostic marker. UALCAN analysis demonstrated CDCA8 up-regulation based on clinical variables, such as cancer stage, race, and gender, in these cancers. Epigenetic exploration indicated reduced CDCA8 promoter methylation levels in Kidney Renal Clear Cell Carcinoma (KIRC), Lung Adenocarcinoma (LUAD), and Skin Cutaneous Melanoma (SKCM) tissues compared to normal controls. Promoter methylation and mutational analyses showcased a hypomethylation and low mutation rate for CDCA8 in these cancers. Correlation analysis revealed positive associations between CDCA8 expression and infiltrating immune cells, particularly CD8+ and CD4+ T cells. Protein-protein interaction (PPI) network analysis unveiled key interacting proteins, while gene enrichment analysis highlighted their involvement in crucial cellular processes and pathways. Additionally, exploration of CDCA8-associated drugs through DrugBank presented potential therapeutic options for KIRC, LUAD, and SKCM. In vitro validation using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) confirmed elevated CDCA8 expression in LUAD cell lines (A549 and H1299) compared to control cell lines (Beas-2B and NL-20).

CONCLUSION

This study provides concise insights into CDCA8's multifaceted role in KIRC, LUAD, and SKCM, covering expression patterns, diagnostic and prognostic relevance, epigenetic regulation, mutational landscape, immune infiltration, and therapeutic implications.

Elucidating cuproptosis-related gene SLC31A1 diagnostic and prognostic values in cancer

OBJECTIVES

Cancer remains a global health challenge, necessitating the identification of novel biomarkers and therapeutic targets. Cuproptosis, a recently recognized form of cell death linked to copper metabolism, presents a promising avenue for anticancer strategies. We investigated the clinical significance of SLC31A1, a key regulator of cuproptosis, in multiple cancer types, aiming to elucidate its potential as a diagnostic biomarker, prognostic, indicator and therapeutic target.

METHODS

We conducted a pan-cancer analysis through TIMER2.0, evaluating SLC31A1 expression across multiple cancer types. Survival analysis was performed using KM plotter. Expression validation was carried out using UALCAN and Human Protein Atlas (HPA) databases. Methylation analysis was conducted with the help of ULACAN and OncoDB. Mutational analysis was performed using cBioPortal database. Immune infiltration analysis via the TIMER2.0 and gene enrichment analysis via the Metascape were performed to gain insights into the potential mechanisms underlying SLC31A1's role in cancer. Finally, Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was employed to confirm SLC31A1 expression in clinical samples.

RESULTS

Out of analyzed cancer, SLC31A1 exhibited significant up-regulation and correlation with worse overall survival (OS) across Breast Cancer (BRCA), Cervical Squamous Cell Carcinoma (CESC), Head and Neck Squamous Cell Carcinoma (HNSC), and Esophageal Carcinoma (ESCA). Mutational and promoter methylation analyses further revealed that hypomethylation is the major cause of SLC31A1 overexpression among BRCA, CESC, HNSC, and ESCA. Immune infiltration analysis showed significant associations between SLC31A1 expression and the presence of CD8+ T cells, CD4+ T cells, and macrophages in the tumor microenvironment. Gene enrichment analysis provided valuable insights into potential molecular pathways in context to BRCA, CESC, HNSC, and ESCA. Furthermore, when SLC31A1 was analyzed using clinical samples through RT-qPCR, this gene showed promising diagnostic potential, reflected by high Area Under the Curve (AUC) values.

CONCLUSION

Our pan-cancer study highlights the up-regulation of SLC31A1 and its correlation with worse OS in BRCA, CESC, HNSC, and ESCA. In sum, outcomes of this study showed that SLC31A1 could be a potential biomarker and novel therapeutic target of BRCA, CESC, HNSC, and ESCA.

Investigating novel biomarkers in uterine corpus endometrial carcinoma: in silico analysis and clinical specimens validation via RT-qPCR and immunohistochemistry

The rising incidence and mortality rate of Uterine Corpus Endometrial Carcinoma (UCEC) pose significant health concerns. CC and CXC chemokines have been linked to tumorigenesis and cancer progression. Recognizing the growing significance of CC and CXC chemokines' diagnostic and prognostic significance in diverse cancer types, our objective was to comprehensively analyze the diagnostic and prognostic values of hub genes from the CC and CXC chemokines in UCEC, utilizing both in silico and clinical samples and cell lines-based approaches. In silico analyses include STRING, Cytoscape, Cytohubba, The Cancer Genome Atlas (TCGA) datasets analysis via the UALCAN, GEPIA, OncoDB, and MuTarget, SurvivalGenie, MEXPRESS, cBioPoratal, TIMER, ENCORI, and DrugBank. Meanwhile, clinical samples and cell lines based analyses include Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), targeted bisulfite sequencing (bisulfite-seq) analysis, and immunohistochemistry (IHC). Through present study, we identified CCL25 (CC motif chemokine ligand 25), CXCL10 (C-X-C motif chemokine ligand 10), CXCL12 (C-X-C motif chemokine ligand 12), and CXCL16 (C-X-C motif chemokine ligand 16) as crucial hub genes among the CC and CXC chemokines. Analyzing the expression data from TCGA, we observed a significant up-regulation of CCL25, CXCL10, and CXCL16 in UCEC samples compared to controls. In contrast, we noted a significant down-regulation of CXCL12 expression in UCEC samples. On clinical UCEC samples and cell lines analysis, the significant higher expression of CCL25, CXCL10, and CXCL16 and significant lower expression of CXCL12 were also denoted in UCEC samples than the controls via RT-qPCR and IHC analyses. Moreover, in silico analysis also confirmed the abnormal promoter methylation levels of the hub genes in TCGA UCEC samples, which was later validated by the clinical samples using targeted based bisulfite-seq analysis. In addition, various additional aspects of the CCL25, CXCL10, CXCL12, and CXCL16 have also been uncovered in UCEC during the present study. Our findings offer novel insights that contribute to the clinical utility of CCL25, CXCL10, CXCL12, and CXCL16 chemokines as potential diagnostic and prognostic biomarkers in UCEC.

Bioinformatics, RNA sequencing, and targeted bisulfite sequencing analyses identify the role of PROM2 as a diagnostic and prognostic biomarker

OBJECTIVES

Prominin 2 (PROM2) gene has been reported as a molecular biomarker of human cancers; however, its role is still controversial. This study was therefore arranged to seek the role of PROM2 in different cancers with Bioinformatics and in vitro analyses.

METHODS

A combination of bioinformatics and molecular experiments.

RESULTS

Through the utilization of Bioinformatics analysis, it was observed that in 19 out of the 24 human cancers studied, there was a significant increase in the expression of PROM2 compared to the respective control samples. Additionally, the overexpression of PROM2 was linked specifically to a decrease in overall survival (OS) among breast cancer (BRCA), lung adenocarcinoma (LUAD), and uterine corpus endometrial carcinoma (UCEC) patients. Furthermore, advanced molecular investigations were conducted, encompassing RNA sequencing (RNA-seq) as well as targeted bisulfite sequencing (bisulfite-seq) assessments of PROM2. These analyses were performed across an array of lung cancer cell lines (A549, ABC-1, EBC-1, and LK-2) and a normal control lung cell line (MRC-9). Results of these analysis revealed overexpression and reduced methylation of PROM2 within lung cancer cell lines, relative to the corresponding control cell line. This suggests that PROM2 assumes a substantial function in the advancement and course of BRCA, LUAD, and UCEC cancers. Subsequent pathway analysis revealed that genes enriched by PROM2 are actively engaged in four pivotal pathways. Additionally, intriguing associations were observed between PROM2 expression, tumor purity, infiltration of CD8+ T immune cells, and genetic modifications. Moreover, we also predicted a few MicroRNAs (miRNAs), transcription factors (TFs), and potential drugs that could help to understand and better manage these cancers via designing appropriate therapies targeting PROM2.

CONCLUSION

Via this study, we effectively revealed PROM2 overexpression as a potential diagnostic and prognostic biomarker of survival in BRCA, LUAD, and UCEC.

Second primary colorectal cancer in adults: a SEER analysis of incidence and outcomes

BACKGROUND

At present, there was no large epidemiological study exploring the actual incidence and survival of second primary colorectal cancer (spCRC). The different characteristics and survival of patients with spCRC and initial primary colorectal cancer (ipCRC) still need to be elucidated. In addition, the factors leading to different survival status of spCRC and ipCRC were still unclear. Our study plan to explore the annual incidence trend of spCRC as well as the factors influencing the occurrence and survival outcome of spCRC.

METHODS

This cohort study analyzed the data of 4680 spCRC patients and 330,937 initial primary colorectal cancer (ipCRC) patients. Whether patients had spCRC and whether spCRC patients survived or died were regarded as outcomes. The annual incidence of spCRC from 2004 to 2016 was analyzed by Jointpoint regression analysis. The truncation points were found, and the annual percentage change (APC) of each segment was calculated to explore the trend of spCRC change in the United States. Univariate and multivariable cox regression analyses were conducted to identify factors associated with the occurrence and prognosis of spCRC patients.

RESULTS

The total incidence of spCRC was decreased during 2000-2016 on the whole. The overall incidence of spCRC was lowered in both males and females despite 2013-2014, in the left colon, right colon, rectum and others. The incidence of spCRC was decreased in both 18-49 years' people and ≥ 50 years' people during 2000-2016, and the incidence of spCRC in the ≥ 50 years' people group was higher than those of 18-49 years. Insured (OR = 0.867 (0.778-0.966), initial primary site of other digestive (OR = 0.46, 95%CI: 0.42-0.50), rectum (OR = 0.74, 95%CI: 0.66-0.82), or right colon (OR = 0.73, 95%CI: 0.68-0.79), N 1 stage (OR = 0.87, 95%CI: 0.76-0.99), M 1 stage (OR = 0.49, 95%CI: 0.30-0.80), AJCC II stage (OR = 0.70, 95%CI: 0.60-0.82), AJCC III stage (OR = 0.69, 95%CI: 0.56-0.84), and radiation (OR = 0.69, 95%CI: 0.57-0.83) were associated with the risk of spCRC. At the end of follow-up, 2,246 spCRC patients were survived and 2,434 spCRC patients were dead. Patients with spCRC had poor survival probability than patients with ipCRC. Older age (HR = 1.02, 95%CI: 1.02-1.03), male (HR = 1.13, 95%CI: 1.04-1.23), Black (HR = 1.20, 95%CI: 1.06-1.35), uninsured (HR = 1.36, 95%CI: 1.16-1.59), Signet ring cell carcinoma (HR = 1.64, 95%CI: 1.19-2.25), T4 stage (HR = 1.63, 95%CI: 1.32-2.01), N2 stage (HR = 1.36, 95%CI: 1.08-1.72), M1 stage (HR = 4.51, 95%CI: 2.00-10.18), AJCC III (HR = 1.47, 95%CI: 1.08-1.98), and radiation (HR = 1.82, 95%CI: 1.43-2.33) were associated with increased risk of mortality in spCRC patients.

CONCLUSION

The incidence of spCRC was decreased except in people with initial primary tumor grade IV and those aged 15-39 years. The overall survival of spCRC patients was lower than ipCRC patients. Cancer patients with older age, high tumor grade, TNM stage, and AJCC stage should be caution to the occurrence of spCRC and timely interventions should be provided for spCRC patients to improve their outcomes.

GNB1 promotes hepatocellular carcinoma progression by targeting BAG2 to activate P38/MAPK signaling

G-proteins are intracellular partners of G-protein-coupled receptors. As a member of the G-protein family, GNB1 has been shown to play a pro-cancer role in lung cancer and breast cancer. However, the biological function and detailed mechanisms of GNB1 in hepatocellular carcinoma progression are unclear. In this study, we investigated the effects of GNB1 and its possible mechanism of action in hepatocellular carcinoma (HCC). The clinical significance of GNB1 was evaluated in a large cohort of HCC patients, showing that GNB1 was overexpressed in HCC compared to adjacent normal liver tissues, and increased GNB1 expression was associated with poor prognosis. We also demonstrated that GNB1 enhances cell proliferation, colony formation, and cell migration and invasion in vitro and promotes the epithelial-to-mesenchymal transition process in HCC cells. Tumor xenograft model assay confirmed the oncogenic role of GNB1 in tumorigenicity in nude mice. Activation of P38 signaling was found in the GNB1 overexpressed HCC cells. Further intervention of P38 confirmed it as an important signaling pathway for the oncogenic role of GNB1 in HCC. Moreover, co-immunoprecipitation followed by liquid chromatograph-mass spectrometry identified that GNB1 exerted oncogenic functions via the interaction of BAG2 and activated P38 signaling pathway. Together, our results reveal that GNB1 plays a pivotal oncogenic role in HCC by promoting the P38 pathway via cooperating with BAG2. GNB1 may serve as a prognostic biomarker for patients with HCC.

Bioinformatics screening of colorectal-cancer causing molecular signatures through gene expression profiles to discover therapeutic targets and candidate agents

BACKGROUND

Detection of appropriate receptor proteins and drug agents are equally important in the case of drug discovery and development for any disease. In this study, an attempt was made to explore colorectal cancer (CRC) causing molecular signatures as receptors and drug agents as inhibitors by using integrated statistics and bioinformatics approaches.

METHODS

To identify the important genes that are involved in the initiation and progression of CRC, four microarray datasets (GSE9348, GSE110224, GSE23878, and GSE35279) and an RNA_Seq profiles (GSE50760) were downloaded from the Gene Expression Omnibus database. The datasets were analyzed by a statistical r-package of LIMMA to identify common differentially expressed genes (cDEGs). The key genes (KGs) of cDEGs were detected by using the five topological measures in the protein-protein interaction network analysis. Then we performed in-silico validation for CRC-causing KGs by using different web-tools and independent databases. We also disclosed the transcriptional and post-transcriptional regulatory factors of KGs by interaction network analysis of KGs with transcription factors (TFs) and micro-RNAs. Finally, we suggested our proposed KGs-guided computationally more effective candidate drug molecules compared to other published drugs by cross-validation with the state-of-the-art alternatives of top-ranked independent receptor proteins.

RESULTS

We identified 50 common differentially expressed genes (cDEGs) from five gene expression profile datasets, where 31 cDEGs were downregulated, and the rest 19 were up-regulated. Then we identified 11 cDEGs (CXCL8, CEMIP, MMP7, CA4, ADH1C, GUCA2A, GUCA2B, ZG16, CLCA4, MS4A12 and CLDN1) as the KGs. Different pertinent bioinformatic analyses (box plot, survival probability curves, DNA methylation, correlation with immune infiltration levels, diseases-KGs interaction, GO and KEGG pathways) based on independent databases directly or indirectly showed that these KGs are significantly associated with CRC progression. We also detected four TFs proteins (FOXC1, YY1, GATA2 and NFKB) and eight microRNAs (hsa-mir-16-5p, hsa-mir-195-5p, hsa-mir-203a-3p, hsa-mir-34a-5p, hsa-mir-107, hsa-mir-27a-3p, hsa-mir-429, and hsa-mir-335-5p) as the key transcriptional and post-transcriptional regulators of KGs. Finally, our proposed 15 molecular signatures including 11 KGs and 4 key TFs-proteins guided 9 small molecules (Cyclosporin A, Manzamine A, Cardidigin, Staurosporine, Benzo[A]Pyrene, Sitosterol, Nocardiopsis Sp, Troglitazone, and Riccardin D) were recommended as the top-ranked candidate therapeutic agents for the treatment against CRC.

CONCLUSION

The findings of this study recommended that our proposed target proteins and agents might be considered as the potential diagnostic, prognostic and therapeutic signatures for CRC.

The prediction of tumor and normal tissues based on the DNA methylation values of ten key sites

Abnormal DNA methylation can alter the gene expression to promote or inhibit tumorigenesis in colon adenocarcinoma (COAD). However, the finding important genes and key sites of abnormal DNA methylation which result in the occurrence of COAD is still an eventful task. Here, we studied the effects of DNA methylation in the 12 types of genomic features on the changes of gene expression in COAD, the 10 important COAD-related genes and the key abnormal DNA methylation sites were identified. The effects of important genes on the prognosis were verified by survival analysis. Moreover, it was shown that the important genes were participated in cancer pathways and were hub genes in a co-expression network. Based on the DNA methylation levels in the ten sites, the least diversity increment algorithm for predicting tumor tissues and normal tissues in seventeen cancer types are proposed. The better results are obtained in jackknife test. For example, the predictive accuracies are 94.17 %, 91.28 %, 89.04 % and 88.89 %, respectively, for COAD, rectum adenocarcinoma, pancreatic adenocarcinoma and cholangiocarcinoma. Finally, by computing enrichment score of infiltrating immunocytes and the activity of immune pathways, we found that the genes are highly correlated with immune microenvironment.

Integrated Analysis of Necroptosis-Related Genes for Prognosis, Immune Microenvironment Infiltration, and Drug Sensitivity in Colon Cancer

Background

Necroptosis, is intimately linked to tumor development and prognosis and has been considered as a target for anticancer therapy. However, the role of necroptosis-related genes (NRGs) in colon cancer is unclear.

Methods

In the present study, we screened 76 NRGs from previous studies and described the landscape of transcriptomic and genetic variation of NRGs in colon cancer (CC) patient samples. Molecular subtypes of necroptosis in colon cancer were identified by clustering analysis, and these molecular subtypes were linked to patient prognosis and TME cell infiltration characteristics. Then, the NRS-score for predicting overall survival (OS) was built based on the TCGA database and validated in the GSE39582 cohort for its predictive power in CC patients. Besides, the ESTIMATE and CIBERSORT algorithms were applied to explore the relationship between NRS-score and tumor immune microenvironment.

Results

We identified two molecular subtypes associated with necroptosis in CC, which have diverse prognosis and immune microenvironment characteristics. Based on the differentially expressed genes between the two molecular subtypes, we further developed a necroptosis risk score signature, referred to as NRS-score. High NRS-score was associated with poor prognosis in CC through immunosuppressive microenvironment and immune escape mechanisms. The nomogram based on NRS-score showed excellent ability to predict prognosis. In addition, NRS-score presented a positive correlation with tumor mutational burden (TMB) and immune checkpoint blockade (ICB) expression and was closely correlated with multiple anticancer agent susceptibility.

Conclusion

This work revealed a close relationship between necroptosis and the prognosis and immune microenvironment of colon cancer. The NRS-score based on the 8-gene signature may be used to predict the sensitivity of immunotherapy and chemotherapy in colon cancer patients, and provides a foundation for future studies targeting necroptosis and its immune microenvironment.

Systematic literature review and network meta-analysis of pembrolizumab versus other interventions for previously untreated, unresectable or metastatic, microsatellite instability-high or mismatch repair-deficient colorectal cancer

Aim: To compare pembrolizumab with competing interventions for previously untreated, unresectable or metastatic microsatellite instability-high or mismatch repair-deficient colorectal cancer. Method: Trials were identified via a systematic literature review and synthesized using a Bayesian network meta-analysis with time-varying hazard ratios (HRs). Results: Using intention-to-treat data, HRs for overall survival were generally in favor of pembrolizumab but not statistically significant; however, statistical significance was reached versus all comparators by month 16 when accounting for crossover. Estimated HRs for progression-free survival significantly favored pembrolizumab versus all comparators by month 12. Pembrolizumab was also superior to all comparators in terms of grade ≥3 adverse events. Conclusion: These analyses suggest that pembrolizumab is a highly efficacious and safe treatment in this population.