Identification Of Regulatory Molecular Targets Of Lung Adenocarcinoma/Breast Cancer And Their Related Mechanisms Based On Multi-omics Data Analysis

Big data analysis based on bioinformatics has become an important means of cancer research.In this thesis,high-throughput cancer data were analyzed through the integrated bioinformatics,and the molecular targets for tumor prognosis and treatment were explored and experimentally validated.The research contents are mainly divided into two parts:(1)To achieve accurate molecular classification of lung adenocarcinoma based on extracellular matrix characteristics and explore tumor therapeutic targets through high-throughput gene expression data analysis;(2)We systematically analyzed the expression and prognosis of WEE family kinases by integrating bioinformatics,highlighting the potential of PKMYT1 as a molecular target for breast cancer.The specific research contents are as follows:Part Ⅰ Molecular subtyping of lung adenocarcinoma based on extracellular matrix characteristics and the potential of the key gene LAD1 as a therapeutic targetLung cancer,whether in terms of incidence or death rate,is the rightful "king of cancers" worldwide.It is urgent to strengthen relevant mechanism research and find effective molecular targets to improve the survival rate of lung adenocarcinoma patients.Studies have shown that ECM is a key modulator of cell behavior and can affect tumor cell proliferation,differentiation,adhesion,metastasis,and sensitivity to chemotherapy and immunotherapy.However,the role of the ECM in determining the heterogeneity of LUAD and the potential role of immune cell infiltration in tumor characteristics remain unknown.In the first module of the first part of the study,34 ECM genes were screened based on the expression difference and prognostic correlation of ECM-related genes,and then the CNV,mutation frequency and gene expression correlation of these genes were analyzed,which showed that the extracellular matrix of LUAD patients had significant genetic changes.Lung cancer patients were categorized into three separate ECMCluster subgroups based on the expression features of the 34 ECM genes using consensus clustering algorithms.Survival analysis revealed substantial differences in survival across these three subtypes,with the ECMClusterA group having the greatest forecast and the ECMBlusterB/C group having the worst.According to the GSVA pathway enrichment analysis,sssGSEA,MCPcounter shows that ECMClusterA has an enriching pathway associated with full immune activation,ECMClusterB is closely related to the biological processes of the immune desert,and ECMClusterC is significantly enriched in the matrix and carcinogenic activation pathways,indicating immunosuppressive properties.Further,we analyzed the scRNA-seq data.According to the expression characteristics of the signaling pathway and the composition of various immune cells,the existence of the three ECMClusterA/B/C subtypes can be perfectly matched.In addition,based on 9 strongly expressed ECM genes,we constructed an ECMscore tag to predict the prognosis of patients.Analysis results at the pan-cancer level showed that the survival time of patients with high ECMscore in most cancer types was significantly reduced,indicating that tumor molecular subtypes based on ECM may be widespread.In this study,molecular typing of lung adenocarcinoma was obtained based on extracellular matrix characteristics,revealing the potential relationship between ECM and immune typing,which can provide a new way for clinical diagnosis and treatment.The second module analysis found that LAD1,an ECM gene,plays an independent role in the occurrence and development of lung adenocarcinoma.LAD1 is an anchored filament protein whose function is largely unknown due to less research.In this study,we conducted a series of analyses on the carcinogenic effect of LAD1 in lung adenocarcinoma.The results showed that mRNA and protein expression of LAD 1 were significantly increased in LUAD,and survival analysis showed that high expression of LAD 1 predicted poor prognosis of patients.Epigenetic analysis showed that LAD1 showed promoter hypomethylation in LUAD,which may contribute to the up-regulation of its mRNA.Posttranscriptional modification showed that LAD1 was hyperphosphorylated in LUAD,suggesting that it might be related to the development of lung adenocarcinoma.ssGSEA showed that acquired immunity was negatively correlated with LAD1 expression.GSVA showed that the high LAD1 expression group was associated with the downregulation of Immune-related pathway.It is very noteworthy that our analysis showed that Ras-dependent signaling was the only activated oncogenic signal in the group with high LAD1 expression.In addition,LAD1 knockdown can significantly inhibit the proliferation,migration and cell cycle progression of LUAD cells.The transplanted tumor model showed that LAD1 knockout significantly delayed tumor growth in nude mice.By testing the relationship between the expression of LAD1 and the sensitivity of some chemotherapy drugs,it was shown that LAD1 knockout can significantly promote the sensitivity of cells to gefitinib,KRas inhibitors and paclitaxel treatment.Therefore,our study demonstrates that LAD1 is a key prognostic biomarker for LUAD and has the potential as an intervention target for the treatment of lung adenocarcinoma.Part Ⅱ Systematic expression analysis of WEE family kinases reveals the importance of PKMYT1 in breast carcinogenesisMany cancer cells depend on G2 checkpoint mechanism regulated by WEE family kinases to maintain genomic integrity.The PKMYT1 gene,as a member of WEE family kinases,participates in G2 checkpoint surveillance and probably links with tumorigenesis,but its role in breast cancer remains largely unclear.In this study,we used a set of bioinformatic tools to jointly analyse the expression of WEE family kinases and investigate the prognostic value of PKMYT1 in breast cancer.The results indicated that PKMYT1 is the only frequently overexpressed member of WEE family kinases in breast cancer.KM plotter data suggests that abnormally high expression of PKMYT1 predicts poor prognosis,especially for some subtypes,such as luminal A/B and triple-negative(TNBC)types.Moreover,the upregulation of PKMYT1 was associated with HER2-positive(HER2+),basal-like(Basal-like),TNBC statuses and increased classifications of Scarff,Bloom and Richardson(SBR).Co-expression analysis showed PKMYT1 has a strong positive correlation with Polo-like kinase 1(PLK1),implying they may cooperate in regulating cancer cell proliferation by synchronizing rapid cell cycle with high quality of genome maintenance.Cell viability tests showed that the combination of PKMYT1 inhibitor and PLK1 inhibitor could synergistically inhibit the proliferation of breast cancer cells,suggesting that the combination of PKmyT1 inhibitor and PLK1 inhibitor could synergistically inhibit tumor.Collectively,this study demonstrates that overexpression of PKMYT1 is always found in breast cancer and predicts unfavourable prognosis,implicating it as an appealing therapeutic target for breast carcinoma.