Genomic Characterization And Molecular Classification Of Chinese Upper Tract Urothelial Carcinoma

Background:Due to the extensive use of Chinese herbal medicine containing aristolochic acid(AA)in China,the epidemiological and clinicopathological characteristics of upper tract urothelial carcinoma(UTUC)in China are significantly different from those in western countries.Therefore,this study aims to explore the genomic characteristics and molecular subtypes of Chinese UTUC patients.Methods:We performed whole genome sequencing(WGS)for 90 UTUC primary tumor samples and extracted single nucleotide variation mutational signature and copy number signature by non-negative matrix factorization.We validated the feasibility and consistency of mutational signature and copy number signature in urines of 26 UTUC patients and 68 bladder cancer patients.Kaplan-Meier method and multivariate Cox regression analysis were used to evaluate the association between genomic molecular subtype and prognostic data.Results:1.WGS revealed that MUC16,KMT2(A-D),TP53,FRG2C and MUC4 were the most common mutated genes in primary UTUC tumors.2.Based on the contribution of AA mutation signature,the 90 patients were divided into AA Sig and No-AA Sig subgroup,and 27 patients(30%)with UTUC were in AA Sig subgroup.AA Sig subgroup was significantly associated with AA exposure,poor renal function,multifocal and non-muscle invasive tumors.Survival analysis showed that AA Sig subgroup was associated with favorable cancer-specific survival and metastasis-free survival.In addition,patients with AA Sig subtype had higher tumor mutation load,predictive neoantigens and infiltrating lymphocytes.3.The AA mutational signature was identified in urothelium specimens and tumor tissues in multifocal AA Sig patients,and field cancerization and intraluminal seeding could co-contribute to multifocality and bladder recurrence in AA Sig subtype patients.Besides,AA could induce typical AA mutational signature in human renal tubular epithelial cell after AA treatment in vitro.In addition,based on low-depth WGS,we can also detect AA mutational signature in cfDNA of urines.4.We identified six copy number signatures:Sig1?6.On the basis of the contribution of Sig6 and genomic integrity,we divided 90 patients into three subgroups:Sig6high,Sig61ow and wGIIlow subtype.The Sig6high subgroup was associated with higher microsatellite instability,papillary tumor and had a better outcome.Patients with a low weighted genome integrity index,were associated with positive lymph node and showed a worst outcome.Multivariate analysis showed that Sig6high was an independently prognostic factor for UTUC patients.TCGA bladder cancer cohort also identified that Sig6high subgroup was associated with better survival.5.Compared with copy number variation patterns,copy number signatures retained great concordance between primary tumor and urinary cfDNA.Conclusion:1.The recurrent mutated genes in our cohort were similar to previous studies,but the AA exposure in domestic patients also resulted in a difference in the frequency of recurrent mutated genes compared with that in foreign studies.2.This study confirmed that the AA mutational signature as a screening tool defines low-risk UTUC with therapeutic relevance.The AA mutational signature,as a molecular prognostic marker using either ureteroscopy and/or urinary cell-free DNA,was especially useful for diagnostic uncertainty when kidney-sparing treatment and/or immune checkpoint inhibitor therapy were considered.3.This study identified that copy number signature assessment for risk stratification was feasible and provided a basis for clinical studies that evaluate prognosis and therapeutic interventions.Although the copy number signature profile of urines is consistent to that of primary tumors,but further research is still needed to explore the risk stratification ability and therapeutic value of copy number signature in line with urines.