Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis

Identification of potential biomarkers for pancreatic ductal adenocarcinoma: a bioinformatics analysis

PDA is an aggressive cancer with a 5-year survival rate, which is very low. There is no effective prognosis or therapy for PDA because of the lack of target biomarkers. The objective of this article is to identify the target biomarkers for PDA using a bioinformatics approach. In this work, we have analysed the three microarray datasets from the NCBI GEO database. We used the Geo2R tool to analyse the microarray data with the Benjamini and Hochberg false discovery rate method, and the significance level cut-off was set to 0.05. We have identified 659 DEGs from the datasets. There are a total of 15 hub genes that were selected from the PPI network constructed using the STRING application. Furthermore, these 15 genes were evaluated on PDA patients using TCGA and GTEx databases in (GEPIA). The online tool DAVID was used to analyse the functional annotation information for the DEGs. The functional pathway enrichment was performed on the GO and KEGG. The hub genes were mainly enriched for cell division, chromosome segregation, protein binding and microtubule binding. Further, the gene alteration study was performed using the cBioportal tool and screened out six hub genes (ASPM, CENPF, BIRC5, TTK, DLGAP5, and TOP2A) with a high alteration rate in PDA samples. Furthermore, Kaplan-Meier survival analysis was performed on the six hub genes and identified poor-survival outcomes that may be involved in tumorigenesis and PDA development. So, this study concludes that, these six hub genes may be potential prognostic biomarkers for PDA.

Expression and function of NF-Y subunits in cancer

NF-Y is a Transcription Factor (TF) targeting the CCAAT box regulatory element. It consists of the NF-YB/NF-YC heterodimer, each containing an Histone Fold Domain (HFD), and the sequence-specific subunit NF-YA. NF-YA expression is associated with cell proliferation and absent in some post-mitotic cells. The review summarizes recent findings impacting on cancer development. The logic of the NF-Y regulome points to pro-growth, oncogenic genes in the cell-cycle, metabolism and transcriptional regulation routes. NF-YA is involved in growth/differentiation decisions upon cell-cycle re-entry after mitosis and it is widely overexpressed in tumors, the HFD subunits in some tumor types or subtypes. Overexpression of NF-Y -mostly NF-YA- is oncogenic and decreases sensitivity to anti-neoplastic drugs. The specific roles of NF-YA and NF-YC isoforms generated by alternative splicing -AS- are discussed, including the prognostic value of their levels, although the specific molecular mechanisms of activity are still to be deciphered.

Unraveling dedifferentiation and metastasis traces in pancreatic ductal adenocarcinoma ductal cells: Insights from single-cell RNA sequencing analysis of ITGB4 and C19orf33

Pancreatic Ductal Adenocarcinoma (PDAC) ranks among the most prevalent gastrointestinal malignancies, with risk factors including smoking, alcohol abuse, diabetes mellitus, obesity, age, family history, and genetic predisposition. Extensive research has focused on unraveling biomarkers and molecular intricacies associated with PDAC. Leveraging data from the Gene Expression Omnibus microarray and single-cell RNA sequencing datasets, our study identified ITGB4 and C19orf33 as potentially differentially expressed genes in PDAC samples when contrasted with non-malignant tissues. Notably, these genes exhibited a strong correlative expression pattern, primarily within ductal cells. Gene Expression Profiling Interactive Analysis corroborated our findings, further confirming the correlation between ITGB4 and C19orf33. Additionally, we conducted experiments involving two pivotal PDAC-related cell lines, MIA PaCa-2 and PANC-1, treated with oxaliplatin and 5-Fluorouracil. We also assessed the expression of these candidate genes in PDAC samples in comparison to adjacent normal tissues. Our findings revealed that C19orf33 is upregulated in PDAC samples, and treatment of PDAC cells with chemotherapeutic agents led to a correlated decrease in the expression of both ITGB4 and C19orf33. These co-expressed and correlated genes are implicated in relevant signaling pathways, suggesting shared biological activities that may contribute to the promotion of metastasis within malignant ductal cells. This study identifies ITGB4 and C19orf33 as key genes potentially shedding light on the molecular mechanisms driving tumorigenesis and metastasis in PDAC. These genes hold promise as potential diagnostic and therapeutic targets, offering valuable insights into the management of this challenging disease.

Mucins as Potential Biomarkers for Early Detection of Cancer

Early detection significantly correlates with improved survival in cancer patients. So far, a limited number of biomarkers have been validated to diagnose cancers at an early stage. Considering the leading cancer types that contribute to more than 50% of deaths in the USA, we discuss the ongoing endeavors toward early detection of lung, breast, ovarian, colon, prostate, liver, and pancreatic cancers to highlight the significance of mucin glycoproteins in cancer diagnosis. As mucin deregulation is one of the earliest events in most epithelial malignancies following oncogenic transformation, these high-molecular-weight glycoproteins are considered potential candidates for biomarker development. The diagnostic potential of mucins is mainly attributed to their deregulated expression, altered glycosylation, splicing, and ability to induce autoantibodies. Secretory and shed mucins are commonly detected in patients' sera, body fluids, and tumor biopsies. For instance, CA125, also called MUC16, is one of the biomarkers implemented for the diagnosis of ovarian cancer and is currently being investigated for other malignancies. Similarly, MUC5AC, a secretory mucin, is a potential biomarker for pancreatic cancer. Moreover, anti-mucin autoantibodies and mucin-packaged exosomes have opened new avenues of biomarker development for early cancer diagnosis. In this review, we discuss the diagnostic potential of mucins in epithelial cancers and provide evidence and a rationale for developing a mucin-based biomarker panel for early cancer detection.

Implications of prognosis-associated genes in pancreatic tumor metastasis: lessons from global studies in bioinformatics

Pancreatic cancer (PC) is a highly lethal malignancy with a 5-year survival rate of 10%. The occurrence of metastasis, among other hallmarks, is the main contributor to its poor prognosis. Consequently, the elucidation of metastatic genes involved in the aggressive nature of the disease and its poor prognosis will result in the development of new treatment modalities for improved management of PC. There is a deep interest in understanding underlying disease pathology, identifying key prognostic genes, and genes associated with metastasis. Computational approaches, which have become increasingly relevant over the last decade, are commonly used to explore such interests. This review aims to address global studies that have employed global approaches to identify prognostic and metastatic genes, while highlighting their methods and limitations. A panel of 48 prognostic genes were identified across these studies, but only five, including ANLN, ARNTL2, PLAU, TOP2A, and VCAN, were validated in multiple studies and associated with metastasis. Their association with metastasis has been further explored here, and the implications of these genes in the metastatic cascade have been interpreted.

Identification of significant alteration genes, pathways and TFs induced by LPS in ARDS via bioinformatical analysis

Background and aims

Acute respiratory distress syndrome (ARDS) or acute lung injury (ALI) is one of the most common acute thoracopathy with complicated pathogenesis in ICU. The study is to explore the differentially expressed genes (DEGs) in the lung tissue and underlying altering mechanisms in ARDS.

Methods

Gene expression profiles of GSE2411 and GSE130936 were available from GEO database, both of them included in GPL339. Then, an integrated analysis of these genes was performed, including gene ontology (GO) and KEGG pathway enrichment analysis in DAVID database, protein–protein interaction (PPI) network construction evaluated by the online database STRING, Transcription Factors (TFs) forecasting based on the Cytoscape plugin iRegulon, and their expression in varied organs in The Human Protein Atlas.

Results

A total of 39 differential expressed genes were screened from the two datasets, including 39 up-regulated genes and 0 down-regulated genes. The up-regulated genes were mainly enriched in the biological process, such as immune system process, innate immune response, inflammatory response, and also involved in some signal pathways, including cytokine–cytokine receptor interaction, Salmonella infection, Legionellosis, Chemokine, and Toll-like receptor signal pathway with an integrated analysis. GBP2, IFIT2 and IFIT3 were identified as hub genes in the lung by PPI network analysis with MCODE plug-in, as well as GO and KEGG re-enrichment. All of the three hub genes were regulated by the predictive common TFs, including STAT1, E2F1, IRF1, IRF2, and IRF9.

Conclusions

This study implied that hub gene GBP2, IFIT2 and IFIT3, which might be regulated by STAT1, E2F1, IRF1, IRF2, or IRF9, played significant roles in ARDS. They could be potential diagnostic or therapeutic targets for ARDS patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06578-7.

Gene expression of cytokinesis regulators PRC1, KIF14 and CIT has no prognostic role in colorectal and pancreatic cancer

Colorectal cancer is one of the most common cancers and pancreatic cancer is among the most fatal and difficult to treat. New prognostic biomarkers are urgently needed to improve the treatment of colorectal and pancreatic cancer. Protein regulating cytokinesis 1 (PRC1), kinesin family member 14 (KIF14) and citron Rho-interacting serine/threonine kinase (CIT) serve important roles in cytokinesis, are strongly associated with cancer progression and have prognostic potential. The present study aimed to investigate the prognostic relevance of the PRC1, KIF14 and CIT genes in colorectal and pancreatic cancer. PRC1, KIF14 and CIT transcript expression was assessed by reverse transcription-quantitative PCR in tumors and paired distant unaffected mucosa from 67 patients with colorectal cancer and tumors and paired non-neoplastic control tissues from 48 patients with pancreatic cancer. The extent of transcript dysregulation between tumor and control tissues and between groups of patients divided by main clinical characteristics, namely patients' age and sex, disease stage, localization and grade, was determined. Finally, the associations of transcript levels in tumors with disease-free interval and overall survival time were evaluated. PRC1, KIF14 and CIT transcripts were upregulated in tumors compared with control tissues. PRC1, KIF14 and CIT levels strongly correlated to each other in both colorectal and pancreatic tumor and control tissues after correction for multiple testing. However, no significant associations were found among the transcript levels of PRC1, KIF14 and CIT and disease-free interval or overall survival time. In summary, the present study demonstrated mutual correlation of PRC1, KIF14 and CIT cytokinesis regulators with no clear prognostic value in pancreatic and colorectal cancers. Hence, according to the results of the present study, transcript levels of these genes cannot be clinically exploited as prognostic biomarkers in colorectal or pancreatic cancer patients.

ITGA2, LAMB3, and LAMC2 may be the potential therapeutic targets in pancreatic ductal adenocarcinoma: an integrated bioinformatics analysis

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer with an abysmal prognosis rate over the last few decades. Early diagnosis and prevention could effectively combat this malignancy. Therefore, it is crucial to discover potential biomarkers to identify asymptomatic premalignant or early malignant tumors of PDAC. Gene expression analysis is a powerful technique to identify candidate biomarkers involved in disease progression. In the present study, five independent gene expression datasets, including 321 PDAC tissues and 208 adjacent non-cancerous tissue samples, were subjected to statistical and bioinformatics analysis. A total of 20 differentially expressed genes (DEGs) were identified in PDAC tissues compared to non-cancerous tissue samples. Gene ontology and pathway enrichment analysis showed that DEGs were mainly enriched in extracellular matrix (ECM), cell adhesion, ECM-receptor interaction, and focal adhesion signaling. The protein-protein interaction network was constructed, and the hub genes were evaluated. Collagen type XII alpha 1 chain (COL12A1), fibronectin 1 (FN1), integrin subunit alpha 2 (ITGA2), laminin subunit beta 3 (LAMB3), laminin subunit gamma 2 (LAMC2), thrombospondin 2 (THBS2), and versican (VCAN) were identified as hub genes. The correlation analysis revealed that identified hub genes were significantly interconnected. Wherein COL12A1, FN1, ITGA2, LAMB3, LAMC2, and THBS2 were significantly associated with PDAC pathological stages. The Kaplan-Meier survival plots revealed that ITGA2, LAMB3, and LAMC2 expression were inversely correlated with a prolonged patient survival period. Furthermore, the Human Protein Atlas database was used to validate the expression and cellular origins of hub genes encoded proteins. The protein expression of hub genes was higher in pancreatic cancer tissue than in normal pancreatic tissue samples, wherein ITGA2, LAMB3, and LAMC2 were exclusively expressed in pancreatic cancer cells. Pancreatic cancer cell-specific expression of these three proteins may play pleiotropic roles in cancer progression. Our results collectively suggest that ITGA2, LAMB3, and LAMC2 could provide deep insights into pancreatic carcinogenesis molecular mechanisms and provide attractive therapeutic targets.

Expression of Genomic Instability-Related Molecules: Cyclin F, RRM2 and SPDL1 and Their Prognostic Significance in Pancreatic Adenocarcinoma

In the present study, we aimed to assess the selected components of cell cycle machinery, checkpoint, DNA repair, and synthesis, namely RRM2, cyclin F, and SPDL1 in pancreatic adenocarcinomas (PAC) by in-house immunohistochemistry (IHC) and bioinformatic analysis of public datasets, in terms of expression, correlation with clinicopathological parameters, and patient survival. Sixty eight patients with pancreatic ductal adenocarcinoma (PDAC) were included in our cohort study, and IHC was performed on tissue macroarrays. RNA-Seq-based transcriptome data for 177 PACs were retrieved from the Cancer Genome Atlas (TCGA). We found cyclin F, RRM2, and SPDL1 to be overexpressed at both protein and mRNA levels in tumor tissues compared to respective controls. Based on TCGA dataset, we have demonstrated that CCNF, RRM2, and SPDL1 are potent independent prognostic markers for poor overall survival, both by themselves and even more in combination with each other. Furthermore, high CCNF mRNA expression was associated with features of cancer progression. By contrast, overexpression of cyclin F or SPDL1 proteins denoted a good prognosis in PDAC patients; however, in the case of the former protein, the results did not reach statistical significance. Specifically, high levels of SPDL1 protein emerged as the most powerful independent prognostic factor associated with a better outcome. If validated, the CCNF/RRM2/SPDL1 three-gene panel developed in this study, as well as SPDL1 protein, may provide significant clinical implications for the prognosis prediction of PAC patients.