| Background:Unfortunately, both the incidence and mortality of gastric cancer in China are ranked first in the world. Gastric cancer has become a major public health issue influencing people’s livelihood severely and should be solved urgently in China. With the advent of the era of precision medical, patient-derived xenograft (PDX) mouse models of gastric cancer has been playing increasingly important role on exploring the mechanism of gastric cancer development, drug discovery and establishing the personalized treatment program. However, how well do PDX mouse models actually resemble patient tumors especially on omics (such as genomics, transcriptomics and epigenomics) level? Also, it is still unclear that dynamic changes occurred cross different passages on omics level.Objectives:The main goal of this study is to investigate the dynamic changes of genome, transcriptome and DNA methylome in patient gastric tumors, corresponding PDXs mouse model and subcutaneously passages, which will reveal how well do PDXs mouse models actually resemble patient tumors on omics and provide an important basis for the reliability of clinical translation process.Methods:To address these two closely related issues, first, we intend to construct subcutaneous patient-derived xenograft mouse models of gastric cancer (SPDXMM) after collecting tumor tissues from patients with gastric cancer. Accordingly, the variation in genomes, gene expression data and DNA methylation sites can be detected in the tumor tissues and corresponding models through genome resequencing, RNA-seq and whole-genome bisulfite sequencing respectively. Then, comparing analyses on genome, transcriptome and DNA methylome will be performed among the original tumor tissues, PDX mouse models and corresponding passages. Thus, the fidelity and utility of SPDXMM in gastric cancer can be evaluated systematically on omics level. Finally, based on collecting the information of FDA approved cancer drugs and corresponding target genes, the expression and DNA methylation of the target genes are analyzed among the original tumor tissues, PDX mouse models and corresponding passages.Results:Through the multi-omics analyses, the results demonstrated that the genetic consistence among the PDX mouse models, corresponding passages and original tumors reaches up to 95%. Subsequently, we mainly focus on the genetic divergence. First, through variation analysis on genomic level, we found that 35 gene mutations occurred only in passages but primary carcinoma. And it is indicated that these genes are primarily associated with GO:0060759 regulation of response to cytokine stimulus, GO:0008202 steroid metabolic process as well as GO:0005244 voltage-gated ion channel activity related by functional enrichment analysis. Secondly, through analyzing the expression level of mRNA on transcriptomic level, we found that compared with the expression in original tumor tissue,337 genes (12 up-regulated genes and 325 down-regulated genes) were significantly differentially expressed (qvalue<0.05) in passages. Further analyses disclosed that those genes were enriched in signaling pathways mainly including Focal adhesion, Extracellular matrix organization and Inflammation mediated by chemokine and cytokine signaling pathway. Moreover, through analyzing the expression level of lncRNA on transcriptomic level, we found that 10 lncRNA in passages were significantly differentially expressed, in which only RP11-72L22.1 gene was significantly down-regulated and all others were up-regulated. Third, based on measuring DNA methylation level, the genes embedded in differentially DNA methylation region are identified. And through enrichment analysis, it is demonstrated that the passage xenografts have three common significantly enriched pathway associated with cardiomyopathy, respectively, Arrhythmogenic right ventricular cardiomyopathy (ARVC), Hypertrophic cardiomyopathy (HCM) and Dilated cardiomyopathy (DCM) pathway, implying that some underlying mechanisms may links the subcutaneous tumors in mouse gastric PDXs and cardiomyopathy. Finally, based on collecting FDA-approved cancer drugs and corresponding target genes, five target genes were found to be mutated or undergoing gene fusion events in transplanted tumors. Moreover, the expression and DNA methylation of the target genes are analyzed among the original tumor tissues, PDX mouse models and corresponding passages. The results shown that five gastric cancer drug target genes (PGFRA_HUMAN, PGFRB_HUMAN, VGFR1_HUMAN, VGFR2_HUMAN and DDR2_HUMAN) were differentially expressed in passages. And FDA-approved cancer drugs targeting on these genes includes Imatinib Mesylate, Sunitinib Malate, Ramucirumab and Regorafenib. Also, through analyzing the common DMR regions in the transplanted tumors and passages, it showed that 22 common drug target genes were in embedded in DMRs, in which only one gene(ABL1_HUMAN) was the FDA-approved target of gastric cancer drugs. Those genes were mainly involved in Cytokine-cytokine receptor interaction and Focal adhesion signaling pathways.Conclusions:(1) The genetic faithfulness of the progenitor tumor tissue can be maintained in the studied mouse gastric PDXs models and passages. The relatively stable inheritance detected in omics level can provide the ground to design the target drug for gastric cancer. (2) The analyses on genome and transcriptome level showed that there are only 35 genes which harbor no mutations in the original cancer tissues but have mutations in the transplanted tumors. There were 337 genes (12 up-regulated genes and 325 down-regulated genes) which were found significantly differentially expressed in the transplanted tumors. Function analyses showed that these mutated genes were mainly involved in the adaptation of tumor tissues to new microenvironment. (3) The methylation level of the transplanted tumor was found to be higher than that of the original cancer tissue. There were 43 DMR regions commonly found in the transplanted tumor, including 26 hypermethylation regions and 17 low methylation regions. And function analyses revealed that they were mainly associated with specific cancer signaling pathways. (4) Through collecting the FDA-approved cancer drugs and corresponding target genes, five target genes were found to be mutated or undergoing gene fusion events in transplanted tumors.Moreover, there were 5 gastric cancer drug target genes significantly differentially expressed in the transplanted tumors and passages. Also, through analyzing the common DMR regions in the transplanted tumors and passages, it showed that 22 common drug target genes were in embedded in DMRs, in which only one gene(ABL1_HUMAN) was the FDA-approved target of gastric cancer drugs. It implies that attentions should be paid to these changed genes and the potential influence on clinical drug response. |
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