Study Of Pathogenesis And Drug Repositioning For Tumors

Complex diseases can seriously endanger people's life and health,and they are formidable barriers in the modern medical research.They do not follow the simple Mendelian inheritance pattern,however,are caused by a variety of factors(including polygenes,mutations in one gene,a combination of genetic and environmental factors,etc.).Tumor is a typical complex disease affected by gene-environment interactions.The genomic characteristics of extremely complex inheritance patterns and heterogeneity make the genome-wide association studies(GWAS) that traditionally used in complex diseases have little effect on tumor research.The second-generation sequencing technology(NGS) with prominent advantages of high-throughput,single base resolution displays superiority in cancer research,not only greatly accelerates the comprehension of the tumor pathogenesis,but also provides the basement for the targeted drug therapy.In this thesis,three studies were focused on the genetic mechanism and drug repositioning of tumors.The first study was related to the exome sequencing of pituitary adenomas.We produced for the first time a comprehensive mutational landscape of all 7 subtypes of pituitary adenomas(PAs),412 mutational genes of which were found.We confirmed GNAS mutations in GH-PAs,USP8 mutations in ACTH-PAs(with mutational frequency> 50%).We identified kinesin heavy chain isoform 5A(KIF5A) and growth factor bound receptor 10(GRB10) as novel recurrent genes in PAs.We next display the Somatic copy number alterations in our panel of 125 PAs.We observed frequent loss and gain of large chromosomal region 9q34.11?16p13.3?3p21.31?7q21.11?16q12.2 in PAs.We found the associations between the subtypes of Pas were based on pathway enrichment analysis of the mutated gene.Interconnection based on pathway analysis between each subtype also suggested that GH-,PRL-,plurihormonal and ACTH-PAs are closely related with each other.On the other hand,TSH-and GTPAs were enriched for somatic mutations in a distinct set of molecular pathways.This finding suggested that some commonalities were existed in different subtypes of Pas.Next,this study also explored the targeted drugs that could be used for treatment of PAs and a total of 48 drugs were involved in 7 signaling pathways of the PAs,covering 28% of PA samples.Finally,we also analyzed the relationship between the invasion and drug-resistant clinical phenotype and mutant genes in pituitary tumors.It was also found that in all GH-secreting tumors,GNAS mutation was inversely correlated with tumor invasiveness and size as determined by clinical analysis,and they were more sensitive to somatostatin analogues.In addition,USP8 mutant tumors were also inversely correlated with the invasiveness and size of ACTH PAs.The second study was performed on pancreatic cancer exome sequencing.In this study,we analysed somatic mutations and copy numbers alternations of 50 matched PCs in Chinese Han population,and we confirmed the high mutational frequency of KRAS,TP53,SMAD4 and CDKN2 A genes in pancreatic cancer.In addition,we also found that ELF3,MKRN3,NF1 and other PCs novel recurrent gene,the mutational frequency of which were more than 5% in the Chinese Han population of PCs.Notably,the ELF3 gene has three frameshift mutations,implying this gene is loss-of-function,which has not been reported yet in PCs.Furthermore,we found that the ELF3 mutational samples in the pancreatic cancer were mutually exclusive to the KRAS/TP53 ones,indicating that the mechanism of the mutant tumor was completely different from the RAS pathway that was dependent on the common KRAS mutation in pancreatic cancer.ELF3 is a transcriptional activator,which transactivate TGFBR2,?-catenin and other genes.These genes involved in TGF-? signal pathway,WNT/?-catenin signaling pathways,which are active pathways in pancreatic cancer.Thus,we infer that ELF3 inactivation may play an important role in the growth and proliferation of pancreatic cancer.Moreover,we also performed somatic copy number alternations analysis in pancreatic cancer,which identified a total of 23 amplification and 66 loss chromosomal regions.The most significantly amplification regions were found to be the 14q32.31(Q = 5.30E-27).A large number of Micro RNAs(MIR329-1,MIR329-2,MIR494,MIR495,MIR758,MIR543 and MIR1193A)are involved in this region which can be related to the growth and proliferation of pancreatic cancer.It is suggested a possible role as an early diagnostic marker for pancreatic cancer.Another significant loss chromosome arm were 9p21.3(including CDKN2 A,CDKN2B genes)and 3p21.31(Q = 8.74E-06,SMARCC1).They were also reported to be associated with pancreatic cancer.Next,we integrated 764 samples from multi-centres to discover low-frequency significant genes in pancreatic cancer.A list of 46 novel significant genes were obtained,such as RREB1(2%),PEG3 2%),NFKBIZ(1%),EEF2(1%).They probably are pancreatic cancer-related genes though the mutational frequency is not high.Lastly,we also analyses the core signaling pathways associated with pancreatic cancer and classify them into ten.These ten pathways are closely linked to each other in the protein-protein interacting subnetworks.Among them,the pancreatic secretion pathway and phospholipase D signaling pathway are novel pathways in pancreatic cancer,which may be related to biological function such as secretion,proliferation and invasion of pancreatic cancer.This study provides the clue for pancreatic cancer research,and provides insights to the early diagnosis and personalized therapy for pancreatic cancer.The third study was related to a pan-cancer drug repositioning study.In this study,we collected the full cohort of 17,567 tumour samples covering 52 primary tumour types from 32 tissues or organs.Somatic copy number alternation(CNAs) and fusion events in various tumours were manually curated from the literatures.From the pancancer genomic analysis,969 mutational cancer drivers were identified across the cohort.Including some novel cancer drivers,such as CHD5,TENM1,BRINP3,were found to have higher(> 5%) mutational frequency some tumours.In addition,we also curated a number of 1675 FDA approved drugs from Drug Bank,KEGG and other Drug-Target Interactions databases.Repositioning analysis of direct drugs targeting cancer drivers was performed and 95 FDA-approved anticancer drugs were found to targeting 66 driver genes,which extend the possibility of known anticancer drugs to target other tumour types.In addition,we also found that 82 FDA-approved agents targeting 55 driver genes whose indications were not suitable for cancer therapy.The above-mentioned drugs direct targeting driver genes covered up to the fraction of 59% of cancer patients who could benefit from FDA-approved drugs.More over,to achieve the goal for repurposing more drugs for tumor targeting therapy,we proposed a novel method: a cancer drug repositioning approach based on the protein-protein interaction network.This approach employed combination scores of direct targets or indirect target from PPI network in each FDA approved agents to cancer driver genes,compared with the random background by permutation test.We employed this approach to 969 driver genes and obtain 90 candidates anticancer drugs.Our thorough search for literature reveals that,34 of drugs(37.8%) were reported to own potential anticancer properties,and 13 of drugs(14.4%) showed side effects with the risk of getting cancer.Finally,in order to confirm the accuracy of the cancer drug repositioning results,we selected 8 drugs that matched the activation IPA pathways in 206 cell lines for anti-cancer activity screening,and we found that 6 drugs including Nicardipine,Promethazine,Etonogestrel,Desogestrel,Levonorgestrel and Sulindac showed significant inhibitory effects on proliferation in several types of cancer cell line.Finally,we also employed this method to each tumour type for drug repositioning and identified 139 significant drugs targeting 51 tumour types.