Functional consequence of the p53 codon 72 polymorphism in colorectal cancer

Deep top-down proteomics revealed significant proteoform-level differences between metastatic and nonmetastatic colorectal cancer cells

Understanding cancer metastasis at the proteoform level is crucial for discovering previously unknown protein biomarkers for cancer diagnosis and drug development. We present the first top-down proteomics (TDP) study of a pair of isogenic human nonmetastatic and metastatic colorectal cancer (CRC) cell lines (SW480 and SW620). We identified 23,622 proteoforms of 2332 proteins from the two cell lines, representing nearly fivefold improvement in the number of proteoform identifications (IDs) compared to previous TDP datasets of human cancer cells. We revealed substantial differences between the SW480 and SW620 cell lines regarding proteoform and single amino acid variant (SAAV) profiles. Quantitative TDP unveiled differentially expressed proteoforms between the two cell lines, and the corresponding genes had diversified functions and were closely related to cancer. Our study represents a pivotal advance in TDP toward the characterization of human proteome in a proteoform-specific manner, which will transform basic and translational biomedical research.

Differential Transcriptional Regulation of Polymorphic p53 Codon 72 in Metabolic Pathways

p53 is a transcription factor that is activated under DNA damage stress and regulates the expression of proapoptotic genes including the expression of growth arrest genes to subsequently determine the fate of cells. To investigate the functional differences of polymorphic p53 codon 72, we constructed isogenic lines encoding each polymorphic p53 codon 72 based on induced pluripotent stem cells, which can endogenously express each polymorphic p53 protein only, encoding either the arginine 72 (R72) variant or proline 72 (P72) variant, respectively. We found that there was no significant functional difference between P72 and R72 cells in growth arrest or apoptosis as a representative function of p53. In the comprehensive analysis, the expression pattern of the common p53 target genes, including cell cycle arrest or apoptosis, was also increased regardless of the polymorphic p53 codon 72 status, whereas the expression pattern involved in metabolism was decreased and more significant in R72 than in P72 cells. This study noted that polymorphic p53 codon 72 differentially regulated the functional categories of metabolism and not the pathways that determine cell fate, such as growth arrest and apoptosis in cells exposed to genotoxic stress.

Diagnosis and prognostic value of C-X-C motif chemokine ligand 1 in colon adenocarcinoma based on The Cancer Genome Atlas and Guangxi cohort

Objective: The objective was to identify and validate C-X-C motif chemokine ligand 1(CXCL1) for diagnosis and prognosis in colon adenocarcinoma (COAD).

Methods: Our current study had enrolled one The Cancer Genome Atlas (TCGA) cohort and two Guangxi cohorts to identify and verify the diagnostic and prognostic values of CXCL1 in COAD. Functional enrichment was performed by gene set enrichment analysis (GSEA).

Results: In TCGA cohort, the expression of CXCL1 was significantly up-regulated in tumor tissues and decreased as the tumor stage developed. The receiver operating characteristic (ROC) curve showed that CXCL1 had a high diagnostic value for COAD. The result of Kaplan-Meier survival analysis showed that CXCL1 gene expression (P=0.045) was significantly correlated with overall survival (OS) of COAD. Results of Guangxi cohort also verified the diagnostic value of CXCL1 in COAD, and sub-group survival analyses also suggested that patients with high CXCL1 expression were related to a favorable OS (Corrected P=0.005). GSEA revealed that CXCL1 high expression phenotype was related to cytokine activity, cell apoptosis, P53 regulation pathway, and regulation of autophagy in COAD.

Conclusions: In this study, we found that CXCL1 gene might be a potential diagnostic biomarker for COAD, and might serve as a prognostic biomarker for specific subgroup of COAD.

Diagnostic and prognostic values of C‑X‑C motif chemokine ligand 3 in patients with colon cancer

The diagnostic and prognostic mechanisms of C-X-C motif chemokine ligand 3 (CXCL3) in colon cancer (CC) have not yet been reported. Therefore, the objective of the present study was to use cohorts of patients from Guangxi Medical University and the Gene Expression Omnibus (GEO) database to investigate and validate CXCL3 for the diagnosis and prognosis of CC, and to explore its prospective molecular mechanism. Reverse transcription-quantitative PCR (RT-qPCR) analysis of 38 paired tumor and non-tumor tissues, and immunohistochemistry (IHC) of 212 tumor and 46 non-tumor tissues was conducted to explore the expression of CXCL3 and its diagnostic and prognostic significance in the Guangxi Medical University CC cohort. A GEO dataset, GSE40967, was used to validate the prognostic significance of CXCL3. Gene set enrichment analysis (GSEA) was also conducted to explore the potential molecular mechanisms underlying the effects of CXCL3 in CC. The RT-qPCR results indicated that CXCL3 expression was significantly higher in cancer tissues compared with adjacent normal tissues, suggesting that it may have high diagnostic value for CC. Multivariate Cox analysis based on the IHC results suggested that there was no appreciable association between CXCL3 positivity and the overall survival (OS) time of CC. However, a stratified analysis revealed that high expression of CXCL3 was associated with considerably increased mortality in the subgroup of CC patients with tumor size <5 cm (adjusted P=0.042, adjusted HR=2.298, 95% CI=1.030–5.126) and with tumor thrombus (adjusted P=0.019, adjusted HR=5.096, 95% CI=1.306–19.886). In the GSE40967 dataset, high expression of CXCL3 was closely associated with poor OS in CC (adjusted P=0.049, adjusted HR=1.416, 95% CI=1.002–2.003). Furthermore, GSEA indicated that the high expression of CXCL3 was closely associated with DNA repair, cell cycle process, cell apoptosis process and the P53 regulation pathway. In summary, these result suggest that CXCL3 might serve as a novel biomarker in the diagnosis and prognosis of CC.

Association of polymorphism TP53 Arg72Pro with radon-induced lung cancer in the Kazakh population

Lung cancer is a problem of great concern and one of the commonest cancer diseases worldwide and in the Republic of Kazakhstan in particular. Radon exposure is classified as the second most important cause of lung cancer. According to the experts, the contribution of natural sources to the average annual radiation dose of the Kazakh population currently stands at 80 %, including 50 % from radon. However, the effect of radon on human health in the Republic of Kazakhstan is almost unknown. The tumor suppressor gene TP53 is a key mediator of the DNA damage response cascade following cell exposure to ionizing radiation. The common polymorphism TP53 Arg72Pro (rs1042522) is a risk factor for lung cancer in the Asian population, but until now no genetic association studies have been done in the Kazakh population. No information on the synergistic carcinogenic effect of radon exposure and polymorphism TP53 Arg72Pro (rs1042522) is available either. This paper presents the results of the study of association between alteration in the TP53 gene and radon-induced lung cancer risk in the Kazakh population. Genetic association was assessed in a case-control study including 44 radon-exposed patients with lung cancer, 41 patients with lung cancer without radon exposure and 42 age/sex-matched healthy controls. We found that polymorphism TP53 Arg72Pro (rs1042522) was associated with lung cancer risk in the Kazakh population (OR = 6.95, 95 % CI = 2.41–20.05). Individuals with the Arg72Pro genotype also showed a significantly higher risk of radon-induced lung cancer (OR = 8.6, 95 % CI = 2.6–28.59).

Upregulation of the alternative splicing factor NOVA2 in colorectal cancer vasculature

Background

Tumor-specific isoforms generated by alternative splicing (AS) are demonstrated to contribute to tumor progression and can represent potential biomarkers. NOVA2 is an AS factor that in physiological conditions regulates endothelial cells' (ECs) polarity and vessel lumen maturation, likely by mediating AS of apical-basal polarity regulators. However, NOVA2 expression in tumor ECs and its regulation have never been investigated.

Methods

To elucidate this, 40 colorectal cancer patients were enrolled and NOVA2 expression was investigated by immunohistochemistry in samples bearing both the normal mucosa and the tumor tissue.

Results

NOVA2 was found expressed in ECs of tumor vasculature and, importantly, it was upregulated in tumor ECs with respect to normal mucosa ECs in all cases (P<0.001). The same samples analyzed by immunohistochemistry for the expression HIF1α, a marker of hypoxia, showed a positive and significant association with NOVA2 levels (P=0.045). Of note, NOVA2 was upregulated by hypoxia also in an in vitro ECs model.

Conclusion

Our results provide, for the first time, evidence of NOVA2 expression and upregulation in tumor ECs and highlight hypoxia as a potential regulatory factor. These findings open a completely new perspective to study tumor vasculature and to uncover NOVA2 as a potential source of biomarkers and therapeutic targets based on AS isoforms.

Long noncoding RNA CCAT1 polymorphisms are associated with the risk of colorectal cancer

Colorectal cancer associated transcript 1 (CCAT1) is a novel long noncoding RNA, whose overexpression is evident in both early phase of tumorigenesis and later disease stages in colorectal cancer (CRC). No study has explored the relationship between CCAT1 polymorphisms and CRC risk. In the present study, a case-control study was conducted to investigate the association between CCAT1 polymorphisms and CRC risk in Chinese population. We identified that CCAT1 rs67085638 polymorphism was associated with an increased risk of CRC (OR = 1.72, 95%CI = 1.14-2.58, P = 0.009 in heterozygote codominant model; OR = 1.67, 95%CI = 1.13-2.47, P = 0.010 in dominant model). Moreover, CCAT1 rs7013433 polymorphism was associated with late clinical stage (OR = 1.82, 95%CI = 1.16-2.86, P = 0.009 in heterozygote codominant model; OR = 1.72, 95%CI = 1.13-2.63, P = 0.012 in dominant model). Our finding proposed a link between CCAT1 polymorphisms with CRC risk as well as different clinical stages.