Identification And Validation Of The Biological Function Of SNRPD1 In Breast Cancer

Breast cancer is highly heterogeneous,resulting in different clinical phenotypes that requires different treatment according to the patient's condition.Inappropriate classification and treatment will likely lead to poor prognosis and even recurrence and metastasis.Currently,few therapies are available,especially for the triple-negative breast cancer or patients with recurrence.Hence,it is important to find new diagnostic and therapeutic bio-markers for breast cancer,especially for triple-negative subtype.Using high-throughput multi-omics techniques and bioinformatics,we are equipped to find potential bio-markers through data mining of the genomics,epigenomics,transcriptomics,proteomics and metabolomics data.Abnormal methylation level occurs in the early stage of cancer.In this study,bioinformatics analysis on methylation data were used to search for differently methylated CpG sites between cancer tissues and normal tissues,where CpG sites with prognostic value were screened out.At the same time,we verified the classification and prognostic ability of these sites and genes involved using multiple data sets.For promising markers,bioinformatics prediction of the function of the genes in the development of cancer was performed and validated in combination with molecular experiments.Our study uses multi-group data to search for potential prognostic and subtyping bio-markers,followed by experimental validation,offering SNRPD1 as a novel breast cancer biomarker,which could be a promising target in personalized treatment and drug development.The main results are as follows:(1)The overall methylation level was significantly different between breast cancer and normal tissues,significant difference among different breast cancer subtypes was also observed.Differential analysis and survival analysis identified 313 CpG sites that are differentially methylated in triple-negative subtype,including 183 hypermethylated sites and 130 hypomethylated sites;(2)Using multiple dataset,we verified the subtyping and prognostic ability of the differentially methylated prognostic genes;(3)Multi-omics analysis revealed 8 genes that are differentially methylated and expressed in triple-negative breast cancer,and showed significant prognostic ability;(4)SNRPD1 is one of the 8 prognostic candidate genes.Compared with normal tissues,SNRPD1 is highly expressed in almost all cancers.In breast cancer,the expression of SNRPD1 was higher in triple-negative subtype than the other two;(5)Functional enrichment analysis of co-expressed genes showed that SNRPD1 is not only a key player in mRNA splicing,but also a crucial member in cell cycle,its implication in cell cycle may further involve the development and migration of cancer;(6)Luminal cell line MCF7 and the triple-negative cell line MDA-MB-231 are used in molecular assays.knockdown of SNRPD1 will reduce the proliferation of both cell lines and lead to G1/S cycle arrest.The transcription and protein expression of CCNA2 and CCND1,key players in cell cycle regulation is also down-regulated significantly with increased drug resistance to Doxorubicin.