Screening of differential expressed genes from gene chip and sequencing data and evaluate its prognostic values in males with digestive system neoplasms
Original Article

Screening of differential expressed genes from gene chip and sequencing data and evaluate its prognostic values in males with digestive system neoplasms

Kai Fang1#, Caixia Hu1#, Xiufen Zhang1, Zijian Guo2, Lihua Li1

1Oncology Institute, 2Department of Oncological Surgery, The Affiliated Hospital of Jiangnan University, Wuxi 214062, China

Contributions: (I) Conception and design: K Fang, C Hu; (II) Administrative support: L Li, Z Guo; (III) Provision of study materials or patients: K Fang, L Li; (IV) Collection and assembly of data: K Fang, C Hu, X Zhang; (V) Data analysis and interpretation: K Fang, C Hu; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors.

#These authors contributed equally to this work.

Correspondence to: Lihua Li. Oncology Institute, The Affiliated Hospital of Jiangnan University, Wuxi 214062, China. Email: LLHWXSY@aliyun.com; Zijian Guo. Department of Oncological Surgery, The Affiliated Hospital of Jiangnan University, Wuxi 214062, China. Email: gzjwxsy@sina.com.

Background: Digestive system neoplasm is a common cancer in males worldwide. This study aimed to explore the commonalities in males with digestive system neoplasms (MDSN) and its clinical relevance.

Methods: A total of 46 differential expressed genes (DEGs) in MDSN were identified shared in TCGA and GEO databases.

Results: These DEGs significantly affected a variety of cell function and signaling pathways. Of which, a hub of 7 genes (CCNB1, MAD2L1, BUB1, CHEK1, MCM2, CCNA2 and CDC25B) were interacted with each other in protein level and significantly enriched in cell cycle pathway. Further methylation analysis, we found that BUB1, MAD2L1 and MCM2 were hypomethylation via m6A modification. Besides, BUB1, MAD2L1 and MCM2 were co-expressed in mRNA level and up-regulation of them led to worse prognostic in hepatocellular carcinoma, while caused a better prognostic in stomach adenocarcinoma (STAD), and had a race difference between white and Asian people in STAD. Medicine molecules, I-threonine (ID: PA451673) and enzymes (ID: PA164712734) might be efficient medicines in BUB1, MAD2L1 and MCM2 up-regulated MDSN patients.

Conclusions: Taken together, hypomethylation via m6A modification might cause BUB1, MAD2L1 and MCM2 up-regulation in MDSN. Dysregulation of BUB1, MAD2L1 and MCM2 function as contrast prognostic in liver hepatocellular carcinoma and STAD. Our study provides more accurate therapeutic targets and prognostic biomarkers for specific cancer types.

Keywords: BUB1; MAD2L1; MCM2; m6A modification; liver hepatocellular carcinoma; stomach adenocarcinoma (STAD)


Submitted Apr 09, 2019. Accepted for publication Sep 09, 2019.

doi: 10.21037/tcr.2019.09.58


Introduction

Tumors are hereditary diseases whose biological basis is genetic abnormality. Oncogenic factors lead to somatic cell gene mutations, resulting in dysfunction and disorder of gene expression, affecting the biological activity and genetic characteristics of cells, and forming tumor cells with different morphology, metabolism and function from normal cells. Genetic abnormalities of different genes lead to different tumors (1). The incidence and mortality rate of tumors in male is higher than that in female, and half of tumors in male occur in the respiratory tract and digestive tract (2). We sought to identify genes that are differential expressed in male with digestive system tumors (MDSN).

Recently, gene expression profiling and bioinformatics analysis have been widely used to identify potential biomarkers for various cancers (3,4). LncRNA CTB-193M12.5 was found associated with prognosis of lung adenocarcinoma by integrated The Cancer Genome Atlas (TCGA) analysis (5). Similarly, an in-depth understanding of the notable signaling pathway was achieved through the analysis of pan-carcinoma using TCGA data (6). Besides, approximately 895 genes and their associated pathways were identified by analyzing the Gene Expression Omnibus (GEO) datasets of 7,168 tumour samples from 16 independent cancer types (7). However, there are still limited studies on MDSN.

DNA methylation is a chemically modified form of DNA that alters hereditary properties without altering DNA sequences and is one of the earliest epigenetic regulatory mechanisms that have been discovered. DNA methylation causes changes in chromatin structure, DNA conformation, DNA stability and DNA-protein interactions, thereby controlling gene expression (8). In general, hypermethylation inhibits gene expression, while hypomethylation leads to gene over-expression. The N6-methyladenosine (m6A) modification is the most common methylation modification in transcripts and involves almost all aspects of mRNA regulation (9). Documents revealed that the modification of m6A is involved in all processes of mRNA transcription and translation, involving various cancers (10,11).

In these studies, the raw gene expression data of TCGA database and GEO database were analyzed, and 46 shared differential expressed genes (DEGs) were found in MDSN tumour tissue samples compared with adjacent normal samples. Therein, a hub of 7 genes (CCNB1, MAD2L1, BUB1, CHEK1, MCM2, CCNA2 and CDC25B) were found to be enriched in cell cycle pathway and the 7 genes were found to be interacted with each other in protein level. Furthermore, MAD2L1, BUB1 and MCM2 was hypomethylation via m6A modification. Survival analysis of MAD2L1, BUB1 and MCM2 suggested that these three genes have a promising prognostic values in MDSN. Particular, in stomach adenocarcinoma (STAD), there was a race difference between white and Asian people. Medicine molecules related analysis shown that medicine molecules, I-threonine (ID: PA451673) and enzymes (ID: PA164712734) might be efficient medicines in these three genes up-regulated MDSN patients.


Methods

TCGA database

RNA sequence expression profiles of digestive system neoplasms in males were obtained from TCGA database, consists of 976 male tumour tissues and 81 normal tissues, including esophageal carcinoma (ESCA), STAD, liver hepatocellular carcinoma (LIHC), colon adenocarcinoma and rectum adenocarcinoma (COAD and READ) (Table S1).

GEO database

Microarray expression profiles of GSE41258, GSE23400, GSE3335 and GSE84402 were obtained from GEO database and consisted of 277 tumour tissues and 143 normal tissues (Table S1). Methylation expression profiles of GSE73003 were downloaded in GEO database, containing 20 paired tumour tissues and non-tumour tissues.

Table S1
Table S1 Resources of TCGA and GEO dataset
Full table

Identification of DEGs

The DEGs between tumour tissues and adjacent non-tumorous tissues in MDSN in TCGA were identified using limma package by R software 3.5.1. While the DEGs in GEO were performed by GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/). |log FC|>2 and P<0.01 was selected as significant.

Bioinformatics analysis

DAVID (https://david.ncifcrf.gov/home.jsp) was used to conducted Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. The threshold of FDR <0.05, P value<0.05 was regarded as significantly enrichment. STRING (https://string-db.org/) was performed to construct a protein-protein interaction (PPI) network for DEGs. P<0.001 and combined score >0.9 were selected as significant.

The RMBase (http://rna.sysu.edu.cn/rmbase) and m6AVar (http://m6avar.renlab.org/index.html) was used to investigate modification type of genes.

Statistic analysis and clinical relevance

Kaplan-Meier plotter was used to predict the prognostic values of genes in MDSN and the race difference between white and Asian people. Correlation analysis of genes was performed in Graphpad Prism 5 software. GEPIA (http://gepia.cancer-pku.cn/) was used for clinical relevance analysis. The data are presented as the mean ± standard deviation. P<0.05 was set as the cutoff criterion.

DEGs related medicine analysis

WebGestalt (http://www.webgestalt.org/option.php) is a functional web tool for enrichment analysis. Information in this web was collected from NCBI GEO, DrugBank, KEGG and dbSNP. In Gene Set Enrichment Analysis part, medicine molecules related DEGs were screened. P value <0.05 was regarded as significant.


Results

Identification of DEGs in MDSN

A total of 976 cancerous and 81 para-cancerous raw mRNA expression data of MDSN were downloaded from the TCGA database. R language software was used to screen DEGs in MDSN, including mRNAs and lncRNAs. In MDSN, 4 cancer types were included, ESCA, STAD, LIHC, COAD and READ. All DEGs were shown in volcano plots (Figure 1A). A total of 195 shared DEGs are common in MDSN in TCGA dataset (Figure 1B). We further screened DEGs in GEO dataset by GEO2R, 289 shared DEGs were found (Figure 1C). In TCGA and GEO database, 46 common DEGs were found in MDSN, including 29 up-regulated genes and 17 down-regulated genes (Figure 1D).

Figure 1 DEGs of MDSN in TCGA and GEO database. (A) Volcano plots were shown the DEGs in esophageal carcinoma (ESCA), stomach adenocarcinoma (STAD), liver hepatocellular carcinoma (LIHC) and colon adenocarcinoma and rectum adenocarcinoma (COAD and READ); (B) Venn diagrams were shown the shared DEGs in TCGA; (C) Venn diagrams were shown the shared DEGs in GEO dataset; (D) Venn diagrams were shown the DEGs shared in TCGA and GEO. P<0.001, logFC ≥2 was regarded as significant. DEGs, differential expressed genes.

Bioinformatics analysis of 46 DEGs in MDSN

GO and KEGG analysis was conducted on DAVID's website tool and it was found that these 46 DEGs significantly affected GO function and KEGG signaling pathways (Figure 2). In GO terms, as to molecular function, the DEGs were significantly enriched in DNA clamp loader activity, cell cycle, ATPase activity, single-stranded DNA-dependent ATPase activity, microtubule motor activity, etc. About cellular component, DNA replication factor C complex, ATP binding, microtubule, proteinaceous extracellular matrix, condensed chromosome kinetochore, etc., were significantly enriched with these DEGs. In addition, the most enriched GO terms in biological process were DNA unwinding involved in DNA replication, positive regulation of DNA-directed DNA polymerase activity, G2/M transition of mitotic cell cycle, positive regulation of mitotic cell cycle, positive regulation of apoptotic process, etc. In KEGG pathway terms, DEGs were enriched in cell cycle, DNA replication and mismatch repair. Cell cycle is the most DEGs enrichment pathway and a hub of 7 genes (CCNB1, MAD2L1, BUB1, CHEK1, MCM2, CCNA2 and CDC25B) were included.

Figure 2 GO function and KEGG pathway analysis of 46 shared DEGs of MDSN in TCGA and GEO. P<0.001 was regarded as significant enrichment. Red bar represent KEGG pathway. Green bar represent molecular function. Yellow bar represent cellular component. Blue bar represent biological process. GO, Gene ontology; DEGs, differential expressed genes.

Then, PPI network of STRING result was constructed to predict the interaction between these 46 DEGs. A total of 153 protein interaction nodes were shown in the PPI network, among them CCNB1, MAD2L1, BUB1, CHEK1, MCM2, CCNA2 and CDC25B were found to be interaction with each other in protein level (Figure 3A). The connected nodes in the network are at required interaction score >0.9. The top 20 combined score genes were selected (Figure 3B) and CCNB1, MAD2L1, BUB1, CHEK1, MCM2 and CCNA2 were included in the top 20 genes. Combined with KEGG and PPI analysis, we selected the cell cycle pathway for further study.

Figure 3 PPI network of 46 shared DEGs and m6A modification of MCM2, BUB1 and MAD2L1. (A) Interaction of 46 DEGs in protein level; (B) top 20 combined genes; (C) m6A modification of MCM2, BUB1 and MAD2L1 in m6AVar and RMBase websites. Combined score >0.9 was selected as significant. PPI, protein-protein interaction; DEGs, differential expressed genes.

Methylation status analysis of cell cycle pathway related 7 genes

We downloaded the raw mRNA methylation expression data from the GEO database, and R language was used to found differential expressed CpG methylation sites. In GSE73003, a total of 13,660 CpG methylation sites were found differential expressed, of which MAD2L1, BUB1 and MCM2 was hypomethylation. Further investigation in RMBase and m6AVar, we found that MAD2L1, BUB1 and MCM2 was hypomethylation via m6A modification (Figure 3C).

Survival analysis and clinical relevance

After verifying BUB1, MAD2L1 and MCM2 were up-regulation in MDSN than adjacent normal tissues (Figure S1). We predicted the prognostic value of BUB1, MAD2L1 and MCM2 in Kaplan-Meier plotter. Over-expression of BUB1, MAD2L1 and MCM2 significantly lead to a worse prognostic in liver hepatocellular carcinoma (Figure 4A), while causing a better prognostic in STAD (Figure 4B). Due to the number limited of males patient, BUB1, MAD2L1 and MCM2 tends to be better prognostic in rectum adenocarcinoma, however the difference is not statistically significant.

Figure S1 MAD2L1, BUB1 and MCM2 high expression in tumour tissues than normal tissues in UALCAN database.
Figure 4 Survival and co-expression analysis of BUB1, MAD2L1 and MCM2 in Kaplan-Meier plotters for hepatocellular carcinoma and gastric adenocarcinoma. (A) Up-regulation of BUB1, MAD2L1 and MCM2 significantly leads to a worse prognosis for hepatocellular carcinoma; (B) up-regulation of BUB1, MAD2L1 and MCM2 significantly leads to a better prognosis for gastric adenocarcinoma; (C,D) BUB1, MAD2L1 and MCM2 are co-expressed at the mRNA level.

For ESCA, there is no significantly prognostic value of BUB1, MAD2L1 and MCM2 (Figure S2). Further co-expression analysis were performed, we found that BUB1, MAD2L1 and MCM2 co-expression with each other in mRNA level (Figure 4C,D). The co-expression and interaction (Figure 3A) of BUB1, MAD2L1 and MCM2 might increase the prognostic value in liver hepatocellular carcinoma and STAD. Further, clinical relevance analysis was performed in Kaplan-Meier plotter and GEPIA. For survival analysis of different race, high expression of BUB1, MAD2L1 and MCM2 leading a poorer prognostic in hepatocellular carcinoma in both Asian and white people (Figure 5A,B). In STAD, up-regulation of BUB1, MAD2L1 and MCM2 causing a better prognostic in Asian (Figure 5C); so did MCM2 in white people, while BUB1 and MAD2L1 has no significant prognostic value (Figure 5D). Besides, in GEPIA, we found that BUB1, MAD2L1 and MCM2 expression elevated in stage I to stage III, while down-regulated in stage IV (Figure 5E).

Figure S2 Survival analysis of MAD2L1, BUB1 and MCM2 in rectum adenocarcinoma and esophageal carcinoma. (A) BUB1, MAD2L1 and MCM2 tend to have better prognosis in rectal adenocarcinoma, but no statistically significant difference has been found; (B) BUB1, MAD2L1 and MCM2 have no significant prognostic value in esophageal cancer.
Figure 5 Clinical significance of BUB1, MAD2L1 and MCM2 in hepatocellular carcinoma and gastric adenocarcinoma. (A,B) For different race of Asian and white people, high expression of BUB1, MAD2L1 and MCM2 leading a poorer prognostic in hepatocellular carcinoma in both Asian (A) and white (B) people. (C) The up-regulation of BUB1, MAD2L1 and MCM2 in gastric adenocarcinoma has significantly improved prognosis in Asian, but only MCM2 has a better prognosis for gastric adenocarcinoma in whites (D), and BUB1 and MAD2L1 have no significant prognostic value. (E) BUB1, MAD2L1 and MCM2 expression elevated in stage I to stage III, while down-regulated in stage IV.

Medicine molecules related to BUB1, MAD2L1 and MCM2

Based on the above studies, molecule drugs of BUB1, MAD2L1 and MCM2 was identified in WebGestalt (Table 1). It shown that both I-threonine (ID: PA451673) and enzymes (ID: PA164312734) are closely related to BUB1, MAD2L1 and MCM2. For BUB1 and MAD2L1, they are significantly enriched with taxanes (ID: PA150481189), paclitaxel (ID: PA450761), calcium (ID: PA164712582) and I-serine (ID: PA451330). However, tumor detection (ID: PA164713367) and dactinomycin (ID: PA151917012) were only correlated with MCM2, while cisplatin (ID: PA449014) and vinblastine (ID: PA451877) were correlated with MAD2L1, respectively.

Table 1
Table 1 Related medicine molecules to BUB1, MAD2L1 and MCM2
Full table

Discussion

Colorectal cancer is the third most common cancer diagnosed in men worldwide, while liver, stomach and esophageal cancers are the fourth, fifth and ninth cancers, respectively. Liver cancer is the second leading cause of death, while gastric, colorectal and esophageal cancers rank third, fourth and sixth globally (2). These four types of cancers all belonged to digestive system neoplasms. So we committed to identifying the commonality in MDSN and give an insight to its mechanism.

TCGA database contains a variety of original expression data of tumors, including mRNA expression data, methylation data, gene mutation data, and related clinical data (12). Increasing literature report that through the analysis of the TCGA database, a large number of new research directions emerge. Previous researchers analyzed the TCGA database to determine a targeted treatment trial and a roadmap for stratifying gastric adenocarcinoma patients (13). Through systematic analysis of the TCGA database, biomarkers and transgenes were identified to point to relevant cellular processes and new therapeutic targets (14). With the development of scientific research and detection technology, the GEO database has become an important data tool to make up for the defects of the TCGA database. GEO has more accurate expression data, more precise experimental conditions, and further advancing the development of bioinformatics analysis. The combination of TCGA and GEO will provide more accurate and reliable clinical guidance for scientific research (15). We downloaded raw gene expression profiles from the TCGA database and GEO database, then DEGs analysis was performed, and 46 shared DEGs were found in the MDSN. Combined with bioinformatics analysis, we found that these 46 DEGs significantly enriched in GO and KEGG pathways. Of which, a hub of 7 genes (CCNB1, MAD2L1, BUB1, CHEK1, MCM2, CCNA2 and CDC25B) were interacted with each other in protein level and significantly enriched in cell cycle pathway. We hypothesized that the dysregulation of the downstream cell cycle pathway may play an important role in the tumorigenesis and development of MDSN.

DNA methylation changes in promoter and genomic regions produce cancer phenotypes by affecting gene transcription (16). Previous studies have shown that DNA methylation of its promoter significantly down-regulated miR-486-5p and promoted cell proliferation and invasion in rectal cancer by activating the PLAGL2/IGF2/beta-catenin signaling pathway (17). Compared with radiation-sensitive cells in squamous cell carcinoma of the head and neck, DNA methylation increased in radiation-resistant cells, so as to further understand the DNA methylation status as a biomarker of radiation-resistant cells (18). We downloaded DNA methylation expression data from the GEO database to investigate differential methylated CPG sites and found that MAD2L1, BUB1and MCM2 was hypomethylation in DMSN tumour tissues. Among the more than 100 chemical modifications that may occur in various types of RNA molecules, m6A is the most abundant internal chemical modification of mRNA, which has the greatest influence on its dynamic regulation (19-21). Ubiquitous m6A modification plays a fundamental regulatory role in gene expression. Besides, studies have shown that binding proteins selectively recognize dynamic m6A modifications to regulate mRNA translation status and longevity (22). Changes in m6A modification are observed to be involved in multiple cellular processes, which might have impacts on several human diseases (23). In order to study the m6A modification state of MAD2L1, BUB1 and MCM2, RMbase and m6AVar were used for analysis, and it was found that MAD2L1, BUB1 and MCM2 were hypomethylated by m6A modification. Therefore, we speculate that the up-regulation of MAD2L1, BUB1 and MCM2 in MDSN may be the result of m6A-modified hypomethylation.

Shi et al. reported (24) that MAD2L1 was up-regulated in cancer tissue, elevated expression of MAD2L1 increased the risk of cancer recurrence and caused a worse survival in lung adenocarcinoma. Up-regulated MAD2L1 enhanced the proliferation, invasion and migration of hepatocellular carcinoma cells and inhibited apoptosis and cell cycle arrest (25). As for BUB1, it is elevated expressed in non-small cell lung cancer and has a poor prognosis (26) similar to prostate cancer (27). However, in gastric adenocarcinoma, elevated BUB1 expression can predict prognosis well (28). In terms of MCM2, high expression of MCM2 leading a worse prognostic in hepatocellular carcinoma (29), while causing a better prognostic in cervical cancer (30). Although MAD2L1, BUB1 and MCM2 up-regulation in various cancers, they play opposite prognostic in different cancer. In this study, we revealed that up-regulation of MAD2L1, BUB1 and MCM2 lead to a worse prognostic in liver hepatocellular carcinoma, while causing a better prognostic in STAD, which provide a exact prognostic for clinical biomarkers. Not only that, we further estimate the survival rates in white and Asian people, we found in hepatocellular carcinoma, elevated MAD2L1, BUB1 and MCM2 function as the poorer prognostic in both races. However, in STAD, elevated MAD2L1, BUB1 and MCM2 signify a better prognostic only in Asian patients but not in white persons.

Chemotherapy resistance is one of the major obstacle in cancer treatment (31-34). We investigated the MAD2L1, BUB1 and MCM2 related anti-cancer drugs and found I-threonine, enzymes, taxanes, paclitaxel, calcium, I-serine, cisplatin and vinblastine are closely related to BUB1, MAD2L1 and MCM2. It is speculated that increased expression of BUB1, MAD2L1 and MCM2 can provide guidance for the use of these drug molecules.


Acknowledgments

Funding: This work was supported by Grants from the National Natural Science Foundation of China (81472485) and the Project of the Wuxi Health and Family Planning Commission (YGZXM14038).


Footnote

Conflicts of Interest: The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.


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Cite this article as: Fang K, Hu C, Zhang X, Guo Z, Li L. Screening of differential expressed genes from gene chip and sequencing data and evaluate its prognostic values in males with digestive system neoplasms. Transl Cancer Res 2019;8(6):2339-2349. doi: 10.21037/tcr.2019.09.58