Table1_Comparative Analysis of Differentially Mutated Genes in Non-Muscle and Muscle-Invasive Bladder Cancer in the Chinese Population by Whole Exome Sequencing.XLSX

Objective: To characterize the spectra of mutations in non-muscle invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC) in the Chinese population to identify any mutational features and find potential therapeutic targets.
Materials and methods: We collected fresh bladder tumor samples from NMIBC (n = 9) and MIBC patients (n = 11) along with adjacent normal bladder tissue specimen and peripheral blood sample. Using whole exome sequencing (WES), we analyzed the mutation spectra of those NMIBC and MIBC bladder cancer (BCa) specimen.
Results: Our results demonstrated that 95% of BCa patients (19/20) had varying degrees of driver gene mutations, FGFR3 (45%), KMT2D (40%), PIK3CA (35%), ARID1A (20%), EP300 (20%), KDM6A (20%), KMT2C (20%), and STAG2 (20%) were the most frequently mutated genes in BCa patients. NMIBC and MIBC exhibited different genomic alterations. FGFR3 (67%), PIK3CA (56%), and RHOB (44%) were the most frequently mutated genes in NMIBC patients. Of note, RHOB mutation only occurred in NMIBC, whereas mutations of KMT2D (55%), TP53 (36%) and KMT2B (27%) were frequently detected in MIBC, and TP53 and KMT2B mutation only occurred in MIBC. The frequency of mutations in DNA-damage repair (DDR) gene was higher in MIBC than that in NMIBC (91 vs 78%, 6.2 vs 2.4 gene mutations per patient). Copy number alterations (CNAs) occurred at more diverse chromosomal locations in NMIBC, but the CNA burden was higher in MIBC [9.01 (2.07–31.51) vs 4.98 (0.99–9.73) mutations/Mb]., the trend of which was consistent with the tumor mutation burden (TMB) [8.26 (4.63–21.84) vs 5.58 (3.87–9.58) mutations/Mb]. Among the current set of single-base substitution (SBS) signatures including SBS 1, 2, 5, 13, and 40, we identified one differently expressed signature between NMIBC and MIBC patients: SBS13.
Conclusions: There were different gene mutational characteristics and signatures between NMIBC and MIBC in the Chinese population. Frequency of DDR, CNA burden and TMB were higher in MIBC. Our analysis revealed that several genes in NMIBC did not overlap with those reported in MIBC, suggesting that a fraction of NMIBC and MIBC likely developed secondary to different precursor lesions.

研究目的：表征中国人群中非肌层浸润性膀胱癌（non-muscle invasive bladder cancer, NMIBC）与肌层浸润性膀胱癌（muscle-invasive bladder cancer, MIBC）的突变谱，以明确其突变特征并挖掘潜在治疗靶点。
材料与方法：本研究采集了9例非肌层浸润性膀胱癌患者与11例肌层浸润性膀胱癌患者的新鲜膀胱肿瘤样本，同时收集对应癌旁正常膀胱组织标本及外周血样本。采用全外显子组测序（whole exome sequencing, WES）对上述膀胱癌（bladder cancer, BCa）标本的突变谱进行分析。
研究结果：本研究结果显示，95%的膀胱癌患者（19/20）存在不同程度的驱动基因（driver gene）突变。FGFR3（45%）、KMT2D（40%）、PIK3CA（35%）、ARID1A（20%）、EP300（20%）、KDM6A（20%）、KMT2C（20%）及STAG2（20%）为膀胱癌患者中最常见的突变基因。非肌层浸润性膀胱癌与肌层浸润性膀胱癌展现出截然不同的基因组改变特征：非肌层浸润性膀胱癌患者中高频突变基因为FGFR3（67%）、PIK3CA（56%）与RHOB（44%），其中RHOB突变仅出现于非肌层浸润性膀胱癌；而肌层浸润性膀胱癌患者的高频突变基因为KMT2D（55%）、TP53（36%）与KMT2B（27%），TP53及KMT2B突变仅见于肌层浸润性膀胱癌。DNA损伤修复（DNA-damage repair, DDR）基因的突变频率在肌层浸润性膀胱癌中高于非肌层浸润性膀胱癌（91% vs 78%，每位患者的突变基因数分别为6.2 vs 2.4）。拷贝数变异（copy number alterations, CNAs）在非肌层浸润性膀胱癌中涉及更多样的染色体区域，但肌层浸润性膀胱癌的拷贝数变异负荷更高[9.01（2.07~31.51）vs 4.98（0.99~9.73）突变/Mb]，该趋势与肿瘤突变负荷（tumor mutation burden, TMB）的变化趋势一致[8.26（4.63~21.84）vs 5.58（3.87~9.58）突变/Mb]。在包含SBS1、SBS2、SBS5、SBS13及SBS40的单碱基替换（single-base substitution, SBS）特征谱中，我们识别出非肌层浸润性膀胱癌与肌层浸润性膀胱癌患者间存在差异的突变特征：SBS13。
研究结论：中国人群中非肌层浸润性膀胱癌与肌层浸润性膀胱癌存在不同的基因突变特征与突变特征谱。肌层浸润性膀胱癌的DNA损伤修复基因突变频次、拷贝数变异负荷及肿瘤突变负荷均高于非肌层浸润性膀胱癌。本研究分析显示，非肌层浸润性膀胱癌中的部分基因与肌层浸润性膀胱癌中已报道的基因存在差异，提示部分非肌层浸润性膀胱癌与肌层浸润性膀胱癌可能起源于不同的前驱病变。