Molecular Change Patterns And Molecular Networks In The BCL2 Family Of Gynecologic And Breast Cancers Based On Multi-omics Big Data

The BCL2 family proteins have been extensively studied over the past three decades for their important roles in apoptosis,tumorigenesis,and anticancer therapy.However,the similarities and differences in the molecular patterns of the BCL2 gene family in gynecologic cancer are not well understood and explored,so this study investigated the correlations between the frequency of BCL2 family gene alteration,gene expression,chromatin accessibility and prognosis,and immunohistochemistry in gynecologic and breast cancer using data from multiple databases at the multi-omics level,including TCGA and GEO.We investigated the common and differential molecular characteristics of BCL2 family genes in gynecologic cancer,aiming to systematically and comprehensively reveal the possible roles and networks of BCL2 family in gynecologic cancer and provide theoretical basis and possible therapeutic targets for gynecologic cancer treatment.The main contents and results of this thesis are as follows.First,the genetic changes,m RNA expression levels,prognosis and immunostaining levels of BCL2 family members were first investigated using a large number of samples.Anti-apoptotic members are not widely expressed in gynecologic tumors,and low expression levels and deletion of anti-apoptotic members were observed in some patient samples,such as BCL2,BCL2L2 and MCL1,which showed amplification and up-regulation of m RNA expression,but their expression was down-regulated relative to normal samples.At the same time,key members such as BCL2L1 were found,which is the only up-regulated member among the anti-apoptotic members in gynecological cancers.However,the expression patterns of these members are consistent with the BCL2 apoptosis regulatory model,with BCL2L1 and MCL1 showing higher levels of expression compared to other BCL2 family members,which is consistent with the results of gene amplification frequency.The effector BAK1 and BAX among the pro-apoptotic members showed significantly differential up-regulated expression,which is required for tumor cells to maintain their steady state in a rapid and sustained manner;and the initiators(PMAIP1,BIK,and BID)were also overexpressed relative to normal samples.Prognostic results showed that BAD,BIK and BAK1 have significant prognostic effects in gynecologic tumors.Immunohistochemical analysis revealed that,with the exception of BOK,BMF,and HRK,these BCL2 family genes were immunohistochemically stained and were mostly distributed in the cytoplasmic and cytosolic regions of patient samples.In contrast,a wide range of adipocytes,glandular cells,and myoepithelial cells in normal tissues typically had low levels or undetectable staining.Similar low-level staining was observed in specific normal tissues,including squamous epithelial cells,cells in the endometrial stroma,ovarian stromal cells,and follicular cells.Normal tissues and tumor samples exhibited different staining between them,mapping the different patterns of protein regulation of the BCL2 family.Second,open regions of chromatin were used to study the epigenetic regulation of BCL2 family members,involving DNA methylation,histone modifications,and distal regulation.Our study provides the first systematic study of the distal regulation(active peak-promoter region)of the BCL2 family.The chromatin active regions with distal non-coding regions are sex-and tissue-specific.We also found a class of active peaks near the transcriptional start site that were consistently devoid of gender and tissue specificity,and these regions were largely active in different gynecologic tumors,following the same pattern for both anti-apoptotic and pro-apoptotic members: active peaks in the promoter region and its adjacent regions were universal.We also found that more than half of the BCL2 family members have distal regulatory signals,and the transcriptional activity of these members is generally higher than that of normal samples.The chromatin activity of the genome was positively correlated with the m RNA expression level.Active chromatin at the level of a single sample of TCGA was compared with the m RNA level of a single sample,and it was found that the higher the number of active peaks,the higher the m RNA expression level;conversely,the lower the number of active peaks,the lower the m RNA expression level.Third,we analyzed the regulatory network of the BCL2 family in gynecologic tumors using the integration of the previous multi-omics data(including BCL2 family mutations and expression)as well as the PPI network and transcriptional regulation to investigate what common or different features exist in the regulatory network of the BCL2 family in gynecologic tumors,and found that the co-mutation signatures of TP53 and PIK3 CA with BCL2L1 were specific in the previous gynecologic cancer studies which have not been identified.co-mutations in TP53 and PIK3 CA are major mediators of anti-apoptotic protein inhibition by MOMP and may be able to lead to a worse prognostic phenotype in breast cancer.These proteins are linked by co-mutation signatures.m RNA expression levels of MCL1 and BCL2L1 are high,consistent with chromatin accessibility in the regions surrounding the genes,and their transcriptional expression may be particularly enhanced by strong distal chromatin accessibility signals.Therefore,we speculate that the co-mutation signals of TP53 and PIK3 CA act to stimulate the formation of chromatin loops at the BCL2L1 gene locus to enhance its transcriptional activity.In gynecologic cancer,BCL2L1,as the only upregulated anti-apoptotic member and protector,prevents activation and oligomerization of pro-apoptotic members and maintains mitochondrial membrane potential homeostasis,thereby preventing cytochrome c release and inhibiting caspase.Therefore,the use of BCL2L1,TP53/TP63 and PIK3 CA as potential prognostic markers may be a key factor for gynecologic cancer diagnosis and effective methods for treatment.In addition,the specificity of the regulatory network: specific differences in YWHAZ amplification in BRCA,PIK3 CB amplification in CESC,PIK3R1 mutation in UCEC and down-regulation of XRCC6,NMT1 and CASP3 in OV,suggest that the BCL2 family protein network can be used to identify different types of gynecological tumors and provide new ideas for the design of targeted drugs.In conclusion,this study integrates and analyzes BCL2 family DNA mutations,expression,active chromatin and regulatory networks in gynecologic tumors using multi-omics techniques,reveals the molecular patterns,possible roles and mechanisms of BCL2 family in gynecologic tumors in a comprehensive and systematic manner,and provides a theoretical basis and possible therapeutic targets for gynecologic tumor treatment,as well as a reference for other pan-tumor and multi-omics studies involved in the integrative analysis of ideas and experiences.