Research on radiotherapy related genes and prognostic target identification of rectal cancer based on multi-omics

Abstract

Background: Radiosensitivity of rectal cancer is related to the radiotherapy efficacy and prognosis of patients with rectal cancer, and the genes and molecular mechanisms related to radiosensitivity of rectal cancer have not been clarified. We explored the radiosensitivity related genes of rectal cancer at a multi omics level.

Methods: mRNA expression data and rectum adenocarcinoma (READ) data were obtained from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus Database (GEO) (GSE150082, GSE60331, GSE46862, GSE46862). Differentially expressed genes between radiotherapy sensitive group and radiotherapy insensitive group were screened. GO analysis and KEGG pathway analysis were performed for differentially expressed genes. Among the differentially expressed genes, five core genes associated with rectal cancer prognosis were selected using random survival forest analysis. For these five core genes, drug sensitivity analysis, immune cell infiltration analysis, TISIDB database immune gene correlation analysis, GSEA enrichment analysis, construction of Nomogram prediction model, transcriptional regulatory network analysis, and qRT-PCR validation was performed on human rectal adenocarcinoma tissue.

Results: We found that 600 up-regulated genes and 553 down-regulated genes were significantly different between radiotherapy sensitive group and radiotherapy insensitive group in rectal cancer. Five key genes, TOP2A, MATR3, APOL6, JOSD1, and HOXC6, were finally screened by random survival forest analysis. These five key genes were associated with different immune cell infiltration, immune-related genes, and chemosensitivity. A comprehensive transcriptional regulatory network was constructed based on these five core genes. qRT-PCR revealed that MATR3 expression was different in rectal cancer tissues and adjacent non-cancerous tissues, while APOL6, HOXC6, JOSD1, and TOP2A expression was not different.

Conclusion: Five radiosensitivity-related genes related to the prognosis of rectal cancer: TOP2A, MATR3, APOL6, JOSD1, HOXC6, are involved in multiple processes such as immune cell infiltration, immune-related genes, chemosensitivity, signaling pathways and transcriptional regulatory networks and may be potential biomarkers for radiotherapy of rectal cancer.

Keywords: Differentially expressed genes; Multi-omics; Prognosis; Radiosensitivity; Rectal cancer.

Fig. 1

Characteristics and differences of radiosensitive genes in rectal cancer. A, B Sample expression profile. C Volcanic distribution plot of differential genes

Fig. 2

Functional enrichment of differential genes and construction of protein interaction networks. A Associated signaling pathways enriched in differential gene GO. B Associated signaling pathways enriched by differential gene KEGG

Fig. 3

Random survival forest analysis identified 5 core genes

Fig. 4

Relationship between key genes of radiotherapy sensitivity and immune infiltration in rectal cancer. A Percentage of immune cells. B Pearson correlation of immune cells.C Comparison of immune cell content between Read group and normal group

Fig. 5

Correlation between radiosensitive key genes and immune cell content in rectal cancer. A Correlation of APOL6 with immune cell content. B Correlation of HOXC6 with immune cell content. C Correlation between JOSD1 and immune cell content. D Correlation of MATR3 with immune cell content. E Correlation of TOP2A with immune cell content

Fig. 6

Relationship between key radiosensitive genes and immunomodulatory genes in rectal cancer. A Association of core genes with chemokines. B Correlation of core genes with immunosuppressive agents. C Association of core genes with immune agonists. D Association of core genes with MHC.E Association of core genes with MHC receptors

Fig. 7

Relationship between key genes of radiosensitivity and drug sensitivity in rectal cancer. A Association of core genes with Bleomycin chemosensitivity. B Association of core genes with Camptothecin chemosensitivity. C Correlation of core genes with Cisplatin chemosensitivity. D Association of core genes with Doxorubicin chemosensitivity. E Association of core genes with Gemcitabine chemosensitivity. F Correlation of core genes with Mitomycin.C chemosensitivity

Fig. 8

Relationship between key radiosensitive genes and microsatellite instability (MSI) in rectal cancer. A Association of APOL6 with MSI. B Correlation of HOXC6 with MSI. C Correlation of JOSD1 with MSI. D Correlation of MATR3 with MSI. E Correlation of TOP2A with MSI

Fig. 9

Study on specific signaling mechanism of key genes related to radiosensitivity in rectal cancer (APOL6 and HOXC6). A GO enriched pathway of APOL6 gene. B KEGG enriched pathway of APOL6 gene. C GO enriched pathway of HOXC6 gene. D KEGG enriched pathway of HOXC6 gene

Fig. 10

Study on specific signaling mechanism of key genes related to radiosensitivity in rectal cancer (JOSD1, MATR3 and TOP2A). A GO enriched pathway of JOSD1 gene. B KEGG enriched pathways for JOSD1 gene. C GO enriched pathway of MATR3 gene. D KEGG enriched pathway of MATR3 gene. E TOP2A gene GO enriched pathway. F TOP2A gene KEGG enriched pathway

Fig. 11

Nomogram for prediction of the outcome of patients with rectal cancer. A Nomogram was constructed based on the expression of APOL6, MATR3, JOSD1,TOP2A,HOXC6 and the clinical parameters. B Calibration curves of nomogram for predicting OS at 1-year and 3-year in the TCGA rectal cancer dataset. C ROC curves of the nomogram prediction model. D Decision curve analysis for nomogram

Fig. 12

Relationship between key genes of radiosensitivity in rectal cancer and clinical indicators(APOL6 and HOXC6). A Association of APOL6 gene expression with age. B Correlation between APOL6 gene expression and tumor stage. C Correlation between APOL6 gene expression and M stage. D Correlation between APOL6 gene expression and N stage. E Association of APOL6 gene expression with survival status. F Correlation between HOXC6 gene expression and tumor stage. G Correlation between HOXC6 gene expression and T stage. H Correlation between HOXC6 gene expression and N stage

Fig. 13

Relationship between key genes of radiosensitivity in rectal cancer and clinical indicators (JOSD1, MATR3 and TOP2A). A Correlation between JOSD1 gene expression and M stage. B Correlation between JOSD1 gene expression and survival status. C Correlation between MATR3 gene expression and age. D Correlation between MATR3 gene expression and survival status. E Correlation of TOP2A gene expression with age. F Correlation between TOP2A gene expression and survival status

Fig. 14

Transcriptional regulatory network of 5 core genes

Fig. 15

Results of qRT-PCR detection of key radiosensitive genes in rectal cancer tissues. A Relative expression difference of APOL6 in cancer and adjacent non-cancerous tissues. B Relative expression difference of MATR3 in cancer and adjacent non-cancerous tissues. C Relative expression difference of HOXC6 in cancer and adjacent non-cancerous tissues. D Relative expression difference of JOSD1 in cancer and adjacent non-cancerous tissues. E Relative expression difference of TOP2A in cancer and adjacent non-cancerous tissues