Validation of CSN1S1 transcriptional expression, promoter methylation, and prognostic power in breast cancer using independent datasets

Abstract

Breast cancer ranked second among most frequent cancer in the world playing a significant role in mortality rate. Having prior knowledge on differentially expressed genes in breast cell carcinoma elucidated important indications to understand the molecular mechanism underneath breast carcinogenesis. In this study we have investigated the distinguished CSN1S1 expression in human breast cancer. We have analyzed CSN1S1 mRNA expression between cancer and normal tissues using TCGA datasets. Moreover, analysis including promoter methylation, mutations, prognosis, co-expression, gene ontology, and pathways of CSN1S1 were performed by the TCGA Wanderer, UCSC Xena, cBioPortal, PrognoScan, UALCAN, and Enricher server. We have observed low mRNA expression and high promoter methylation of CSN1S1 in cancer tissues compared to normal tissues. Furthermore, we have also identified low mRNA expression in clinicopathological patients, as well as 9 deleterious mutations with highly co-expressed protein MRC1, and significantly related signaling pathways. We have found a positive correlation between the lower expression of CSN1S1 and patients surviving with breast cancer. Here we have concluded that CSN1S1 acts as a biomarker for the surveillance and prognosis of breast cancer, and also works as a novel therapeutic target at the molecular and pathway levels.

Keywords: Biomarker; Breast cancer; CSN1S1; Mutational analysis; Transcriptional expression.

Fig. 1

The analysis of mRNA expression of CSN1S1 in human breast cancer in various cancer types (A) This dataset indicate CSN1S1 mRNA under regulation (blue colour) and overexpression (red colour) in cancer along with normal tissues utilizing from Oncomine server. The threshold values were defaults. (B) The breast invasive carcinoma expression of CSN1S1 across TCGA cancers (with tumor and normal samples) has been obtained from ‘Pan-cancer view’ in UALCAN webpage. (C) The CSN1S1 in human breast cancer expression patterns of cancer were utilizing from the GENT2 database. In this figure, blue colour represents healthy cells and red colour represents cancer cells. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

CSN1S1 mRNA expression in breast cancer: (A) Decreased expression of CSN1S1 was observed in normal and cancer tissues datasets with (I) invasive breast carcinoma, (II) invasive lobular breast carcinoma, (III) intra ductal cribriform breast adenocarcinoma breast carcinoma, and (IV) male breast carcinoma, by using Oncomine web portal. (B) Graph shows the CSN1S1 expression in breast invasive carcinoma and non-infected tissues based on Sample types which was derived from UALCAN platform. (C) The given proteins of CSN1S1 of human breast cancer were analyzed from the webpage of Human Protein Atlas.

Fig. 3

Clinic pathological analysis of CSN1S1 in breast cancer: in figure A, B, C, D, F, G and H the red colour represents negative and blue represents positive result. A) Estrogen receptor status (ER) (B) HER2 status and (C) PR status, (D) Nodal status, (E) Histological subtype, and (F–H) basal like or TNBC. These were obtained from bc-GenExMiner online portal. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

The methylation status of CSN1S1 in human breast cancer: The methylation status of probe cg09096383 (A) indicates healthy tissues and (B) tumor tissues, datasets generated from TCGA Wanderer (http://maplab.imppc.org/wanderer/). (C) The CSN1S1 heat map expression and its DNA methylation status were obtained from UCSC Xena.

Fig. 5

CSN1S1 in human breast cancer mutation and copy number alteration datasets were derived from cBioPortal: (A) Graph depicts nine mutations including three duplicate mutations in patients with multiple samples. (B) The bar diagram represents CSN1S1 mutation frequencies in breast cancer. Green represents mutation, purple represents fusion, red represents amplification and blue represents deep deletion. (C) The graph shows the correlation between expression of CSN1S1 and copy number alterations in breast cancer of TCGA. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6

Co-expression and correlation of CSN1S1 with various genes in breast cancer: (A) the expression of CSN1S1 with the pattern of input genes in breast invasive carcinoma obtained from UALCAN database. (B) Co-expression of CSN1S1 with MRC1 were found with heat map analysis using the UCSC Xena database. (C) Co-expression of mRNA between CSN1S1 and MRC1 in breast cancer generated from UCSC Xena web. (D) Correlation analysis between CSN1S1 and MRC1 obtained from GEPIA 2 web.

Fig. 7

We used the Enricher web to profile the co-expressed genes with the CSN1S1 in breast cancer. (A) The bar graphs illustrate pathway analysis (REACTOME pathways 2016). (B) This graph shows the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways 2019. (C) This represents NCI-Nature 2016 which terms in proteomic analysis. (D) The data represents the GO molecular function (2018) terms in proteomic analysis. (E) Illustration of GO cellular component (2018) shows proteomic analysis. (F) The graph of GO biological process (2018) terms in proteomic analysis.

Fig. 8

Different plots have been analyzed by using prognoscan server: (a) Expression plot: Patients are ordered in terms of CSN1S1 expression values. The cumulative number of patients are plotted against the expression value. The optimal cut points are shown by the straight lines (cyan) in which patients are separated into high (red) and low (blue) expression groups. (b) Expression histogram: The distribution of the expression value is presented where the X-axis represents the number of patients and the Y-axis represents the expression value on the same scale as the expression plot. The optimal cutpoint line (cyan) is also present. (c) p-value plot: Calculations are done on patients regarding survival difference between high and low expression groups. The X-axis indicates the cumulative number of patients on the same scale as the expression plot where the raw P-values (log scale) is presented in Y - axis. The cutpoint to minimize the P-value which is determined and indicated by the cyan line. The gray line indicates the 5% significance level. (d) Survival Plot: The events (relapse, progression, death) may not be observed for some individuals within the study time period, producing censored observations. The X-axis represents the cumulative number of patients while Y-axis represents the study time. The cut point is indicated by the cyan line. (e) Attribute plot: Patients are separated based on grade and Receptor Expression. The X-axis represents the cumulative number of patients on the same scale as the expression plot whereas the Y-axis represents parameters based on which we mentioned. The cut point is indicated by the cyan line. (f) Kaplan-Meier plot: Survival curves for high (red) and low (blue) expression groups are separated at the optimal cut point. Times are plotted against the survival rate. 95% confidence intervals for each group are also indicated by dotted lines. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)