Study On The Open Areas Of Chromatin In The Development Of Lung Cancer And Glioma

The occurrence and development of malignant tumor is a complex process involving multiple genes and non-genetic factors,during which the chromatin accessibility of tumor cells changes greatly.Therefore,studying the characteristics of accessible chromatin in different kinds of tumors can not only understand the biological basis of tumor occurrence and development,but also be of great significance to molecular typing,early diagnosis and treatment evaluation of tumor.In the previous study,we first aimed at the problem that a large number of open chromatin information was lost in the ATAC-seq technology developed in 2013,which is widely used to study the open characteristics of chromatin,and established a new construction method of NGS library based on ss DNA,SALP.In this study,SALP technology was used to systematically investigate the accessible chromatin characteristics and genomic signature of open regions in two kinds of malignant tumor tissues,lung cancer and gliomas.The main research work includes:(1)The tumor tissues of patients with glioma were collected,the library was constructed by SALP technology,then Illumina Hiseq X Ten platform was used and bioinformatics analysis showed that most of the open regions of chromatin were located in the distal intergenic region,followed by the intron region,with the minimal distribution in the exon region.Compared with the cell samples from normal brain tissue,2925 chromatin regions of tumor tissue isolated cells were found to be more open and 8 chromatin regions were less open(FDR < = 0.05).Through gene annotation of Peak by Homer,we found that 1008 genes' chromatin opening state had changed;then we used PANTHER to analyze the GO enrichment of these genes,and found that the genes whose chromatin opening state had changed were enriched in biological functions such as neuron composition,synapse,plasma membrane protein complex,cell signal transduction,etc.Among the genes whose chromatin open state had significantly changed,we screened 16 genes such as TRPM4 and CHRFAM7 A,among which 6 genes have been reported to be related to malignant tumors and 11 have been reported to be related to nervous system diseases.Using the gene expression data and matched clinical data of related genes of glioma patients in the Chinese glioma Genome Atlas Database,we used the survival package to study them with Kaplan Meier method to further understand the relationship between these genes and the occurrence,development and prognosis of gliomas,we analyzed therelationship between the gene expression level and different WHO grades,IDH gene mutations and 1p/19 q codeletion status,and compared the expression level of related genes in primary gliomas and recurrent gliomas.Then we use MEME and DREME software to predict the pattern of tumor occurrence,Centri Mo to identify the motifs that are significantly enriched in the central region of the sequence.Tomtom software was used to predict the patterns of de novo motif.By comparing with the known motifs in HOCOMOCO human V10 database,we can determine the similarity between them,so as to analyze the transcription factors enriched in these regions.We reviewed the research of the predicted transcription factors in malignant tumors and nervous system diseases,and find that there are some common transcription factors related to tumorigenesis or nervous system diseases,such as FUBP1,MSX2,etc,and there are also some novel or less reported transcription factors,such as ZSCA4,ZN502 and ZIM3.(2)We collected tumor tissue of lung cancer patients,constructed library of tumor tissue by using SALP technology,and sequenced the library by using Illumina Hiseq X Ten platform.Through bioinformatics analysis,we found that most of the chromatin open regions were located in the distal intergenic region,followed by the intron region and promoter region,with the least distribution in the exon region;Compared with benign lesion tissues,1131 chromatin regions of tumor cells were found to be more open and 6812 chromatin regions were less open(FDR < = 0.05).Through gene annotation of Peak by Homer,4807 genes' chromatin open states were found to be changed.Then,PANTHER was used to enrich and analyze these genes Now,these genes with altered chromatin open state are enriched in the related functions of cell component movement,positive regulation of molecular function,negative regulation of stimulation response,cell movement,cell migration,etc.Among the genes with significant altered chromatin open state,we screened 33 genes such as Sema4 D,EGFR,TERT,all of which have been reported to be related to malignant tumors,31 of which have been reported to be related to lung cancer.In order to explore the pattern of malignant tumorigenesis regulated by different accessible chromatin regions in the process of lung cancer occurrence,we used MEME and DREME software to predict de novo motif,used Centri Mo to identify the motif significantly enriched in the central region of the sequence and used Tom Tom software to predict de novo motif.By comparing with the known motif in the HOCOMOCO human V10 database,we can determine the similarity between them,so as to analyze the transcription factors enriched in these regions.By reviewing the research status of the predicted transcription factors in malignant tumors and lung diseases,we find that there are some common transcription factors related to lung cancer or lung diseases,such as Bach2,FOSL1,KLF9 and E2F2,and there are also some novel or less reported transcription factors,such as SP2 and NEYC.(3)The matched blood plasma and cerebrospinal fluid of glioma patients and lung cancer patients were collected,and the QIASEQ cf DNA library kit was used to construct the library,after that high-throughput sequencing and bioinformatics analysis were carried out.At the same time,we analyzed the gene mutation in the chromatin open regions obtained in the previous study,and compared it with the gene mutation in the matched liquid biopsy samples to studied the gene mutation in the chromatin open region of glioma and lung cancer,and determined that there was a large heterogeneity between different gliomas and lung cancer patients.At the same time,we evaluated the detection of gene mutation in tissue samples and liquid biopsy samples,and determined that in gliomas,cerebrospinal fluid is a better liquid biopsy material compared with plasma;It is found that both liquid biopsy and tissue biopsy have advantages and disadvantages,so they should be combined in the actual detection and diagnosis;This study also found that in gliomas,the frequency of mutation of MUC6 gene is higher,and the distribution of mutation sites is more concentrated,although further study is needed.In conclusion,we studied the chromatin open state and gene mutation in the open region of glioma and lung cancer.This work not only found the characteristics of dynamic changes of chromatin during the development of lung cancer and glioma,genes with significant changes in chromatin open state,transcription factors that may play a role,and gene mutations in chromatin open region,but also revealed the potential value of using cf DNA to monitor the occurrence and development of malignant tumors,which provides a new important reference for the discovery of new tumor markers of two kinds of malignant tumors and their application in liquid biopsy.