Screening Of LncRNA In Plasma Exosome Of Breast Cancer And Bioinformatics Analysis Of Candidate Molecular Markers

Background: Breast cancer is a global high incidence of malignant tumor that seriously endangers women’s health and life.Its early diagnosis and treatment can significantly improve the survival rate of patients.At present,imageological,ultrasonic and pathological examinations are still main techniques for diagnosis of breast cancer,but they have obvious limitations.For the past few years,the clinical application of targeted therapy has had significant progress in cancer treatment,however,its effects in the breast cancer are still not satisfactory,since the pathogenesis of breast cancer has not been fully elucidated.Exosomes exist in a variety of body fluids,containing some stable biomarkers reflected the source of cell and the characteristics of disease,which become helpful tools for clinical diagnosis and basic researches at present.It has also been found newly that,as carriers,carry special contents to intercellular substance and in body fluid,which may affect on tumor invasion,metastasis,recurrence,and other pathophysiological processes directly or indirectly.As a type of macromolecule RNA,the lncRNA does not have the ability to encode and translate from RNA to protein.Nonetheless,its expression in tissues is specific,and can be served as regulatory factors on tumor development.Therefore,the basic researches and clinical applications of lncRNAs and exosomes via liquid biopsy have becom e hotspots of tumor studies.Objective: Via detecting lncRNA expression in exosome of plasma samples obtained from breast cancer patients,screening out candidate lncRNA from transcriptomic data of breast cancertissue samples and related control tissues in TCGA database,and comparing analysis based on above two datasets,we intended to find more candidate lncRNAs related to breast cancer lesions,and then,to explore their potential diagnostic value and regulatory mechanism with bioinformatics analyses.Methods:(1)The 10 m L anticoagulant peripheral blood per patient and from total 20 patients per group(breast cancer and benign tumor groups)were collected,and the RNAs from plasma exosomes were extracted,and for lncRNA、mi RNA and mRNA sequencing data were analyzed.(2)The lncRNA data of breast cancer tissues were evaluated from TCGA with database information and R language.(3)The candidate differentially expressed lncRNAs and mRNAs were screened out by using weighted gene coexpression network analysis.(4)Functions of the module were assessed.(5)Diagnostic evaluation and survival analysis of lncRNAs were analyzed in selected modules.Results:(1)A total of 155 diferrentially expressed lncRNAs(72 upregulated and 83 downregulated)and 2450 differentially expressed mRNAs(1619 upregulated and 831 downregulated)were screened out in plasma exosomes of breast cancer patients with high-throughput gene sequencing,compared with that in same type of samples of patients suffered from breast benign tumors.(2)An expressive dataset containing 866 breast cancer tissue samples and paired paratourose tumor samples in TCGA database was analyzed,and the differentially expressed 4879 lncRNAs(2883 upregulated and 1996 downregulated)and 5304 mRNAs(3226 upregulated and 2078 downregulated)were identified,especially 41 lncRNAs were also differentially expressed in exosome samples of breast cancer patients,compared with that in comtrol.(3)A total of 19 modules were identified by weighted gene coexpression network analysis,among which the blue-green module,yellow module,purple module,blue module and brown module were significantly correlated with the clinical stage of breast cancer.These five modules contained 28 candidate lncRNAs.(4)Functional analyses of the modules wererevealed that the blue-green module was mainly related to the imbalance of cancer transcription,peroxisome proliferator-activated receptor(PPARs),and PI3K-AKT signal pathway;the yellow module was related to cellular signal transduction and intercellular interaction;the purple module was related to the regulation of protein digestion and absorption,as well as the interaction of extracellular matrix receptors;the blue module might be related to cell cycle regulation,DNA replication and damage repair;the brown module could be involved in the metabolism of pyrimidine nucleotides.(5)The ROC diagnostic curves of breast cancer for 28 candidate lncRNAs in above modules were drawn,and the survival analysis of patients was carried out.The AUC areas under ROC curves of 8 lncRNAs were more than 80%,indicating that they could well distinguish breast cancer patients from normal controls.In addition,2 lncRNAs showed poor prognosis at low expression,suggesting that they might also be served as biomarkers of prognosis in patients suffer from breast cancer.Conclusion: In this study,28 candidate lncRNAs related to breast cancer lesions were identified via data comparing analysis of plasma exosome expression profiles between breast cancer and benign tumor tissues in TCGA.From the points of functional view,it is revealed that candidate lncRNAs were related to the pathogenesis of breast cancer,as well as the proliferation and migration of cancer cells.It was found that LINC01340,AL355974.2,AC009414.2,AC135584.1,HOXA-AS3,MBNL1-AS1,MIR222 HG and KCNJ2-AS1 have good diagnostic potential,while AC124798.1 and AL355974.2 may be used as molecular markers for the prognosis of breast cancer.In addition,there are a number of unknown lncRNAs,which are closely related to the occurrence and development of breast cancer.and it is needed to explore their biological significance and pathophysiological role(s)in the course of breast cancer.