Study On Genomic Evolution Of Rectal Cancer Under Chemoradiotherapy And Genetic Variations Associated With Sensitivity And Survival In Rectal Cancer Patients Of Locally Advanced Rectal Cancer Receiving Preoperative Chemoradiotherapy

In China,colorectal cancer(CRC)ranks the fifth leading cause of cancer death.Individuals with locally advanced rectal cancer are commonly treated with concurrent capecitabine,oxaliplatin and radiotherapy combined with total mesorectal excision surgery.Patients vary in their response to the preoperative chemoradiotherapy because of tumor heterogeneity and genetic variations and so on.Chemoradiotherapy plays an important role as selective pressure to proceeding clones with mutations related to resistance to get growth advantage.We sought to identify the genomic effect of chemoradiotherapy and the mechanism of tumor evolution and genetic variations associated with chemoradiotherapy sensitivity and survival,which could contribute to personalized medicine.All the patients enrolled in our study were treated with capecitabine-based neoadjuvant concurrent chemoradiotherapy combined with surgery for locally advanced rectal cancer.After preoperative chemoradiotherapy treatment,the Tumor Regression Grading(TRG)of biopsies obtained from surgery was from TRG3 to TRG5,as chemoradiotherapy-resistant.Whole-exome triplets i.e.,the pre-treatment tumor sample,the post-treatment tumor sample,and the peripheral blood DNA,were sequenced for 31 patients.Our analysis provides several insights:(i)Chemoradiotherapy influenced tumor heterogeneity at both mutation and somatic copy number alterations(SCNA)levels,(ii)KRAS,APC,CTDSP2,TP53,TTN and CCDC168 mutations were potentially associated with chemoradiotherapy resistance in locally advanced rectal cancer.(iii)The branched evolution pattern and linear evolution pattern existed between pre-treatment tumor samples and paired post-treatment resistant rectal cancer.(iv)There was a significant increase of the number of C>T in post-treatment samples than the matched pre-treatment samples and we observed a significant enrichment in MMR deficiency-induced mutations in post-treatment tumors.Therefore,the MMR deficiency mutational process was associated with chemoradiotherapy resistance and could drive the evolution of advanced rectal cancer.(v)We defined and assessed heterogeneity as the proportion of mutations in pre-or post-treatment cohort,and we found that high tumor heterogeneity predicted worse overall survival.Genetic variations play important roles in patients's response to preoperative chemoradiotherapy and clinical outcome.It is not commonly reported about the associations between genetic variations in DNA mismatch repair genes and preoperative chemoradiotherapy sensitivity and survival of patients with locally advanced rectal cancer.Fourteen tagging single nucleotide polymorphisms(tagSNPs)of MLH1,MLH3 and MSH2 genes were genotyped by Sequenom MassARRAY method in 146 patients with locally advanced rectal cancer receiving preoperative chemoradiotherapy.The associations were measured by odds ratios(ORs)or the hazard ratios(HRs)and 95%confidence intervals(Cls),using unconditional logistic regression model and Cox proportional regression model.We found that MLH3 rsl75057 C>T and MSH2 rs13019654 G>T were associated with preoperative chemoradiotherapy sensitivity,with ORs of 0.42(95%Cl = 0.19-0.91,P = 0.029)and 0.49(95%Cl = 0.24-0.98,P = 0.047),respectively.In addition,we found that MLH3 rs175057 C>T,MSH2 rs3771273 T>A,rs10188090 A>G and rs10191478 T>G were also associated with overall survival time of locally advanced rectal cancer,with HRs of 0.44(95%CI= 0.20-0.96,P = 0.038),1.74(95%Cl = 1.06-2.84,P = 0.028),1.64(95%Cl= 1.01-2.66,P= 0.046),1.71(95%Cl=1.01-2.91,P= 0.047),respectively.In conclusion,we found that KRAS,APC,CTDSP2,TP53,TIN and CCDC168 mutations were associated with chemoradiotherapy resistance and high tumor heterogeneity could predict worse overall survival.Meanwhile,we identified two evolution patterns during treatment.In addition,we found that MMR deficiency was associated with chemoradiotherapy resistance and continued to shape the evolution of rectal cancer.Association studies of genetic variations and chemoradiotherapy sensitivity and survival showed that genetic variations located in MMR-associated genes decreased risk of resistance or associated with survival.These results provide insight into the clinical and genomic dynamics of rectal cancer evolution with capecitabine-based neoadjuvant chemoradiotherapy,suggest mechanisms of clinical resistance,and inform development of clinically relevant biomarkers.