Table2_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：解析中国人群中非肌肉浸润性膀胱癌（non-muscle invasive bladder cancer, NMIBC）与肌肉浸润性膀胱癌（muscle-invasive bladder cancer, MIBC）的突变谱特征，以明确其突变相关特点并筛选潜在治疗靶点。
材料与方法：本研究收集了9例NMIBC患者、11例MIBC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与外周血样本。采用全外显子测序（whole exome sequencing, WES）对上述膀胱癌（bladder cancer, BCa）标本的突变谱进行分析。
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突变，其中FGFR3（45%）、KMT2D（40%）、PIK3CA（35%）、ARID1A（20%）、EP300（20%）、KDM6A（20%）、KMT2C（20%）与STAG2（20%）为膀胱癌患者中突变频率最高的基因。NMIBC与MIBC展现出不同的基因组变异特征：NMIBC患者中突变频率最高的基因为FGFR3（67%）、PIK3CA（56%）与RHOB（44%），其中RHOB突变仅见于NMIBC；而MIBC患者中高频突变基因为KMT2D（55%）、TP53（36%）与KMT2B（27%），TP53与KMT2B突变仅出现于MIBC。DNA损伤修复（DNA-damage repair, DDR）基因的突变频率在MIBC中高于NMIBC（91% vs 78%，每位患者平均突变基因数为6.2 vs 2.4）。拷贝数变异（copy number alterations, CNAs）在NMIBC中涉及的染色体区域更为多样，但MIBC的CNA负荷更高[9.01（2.07~31.51）vs 4.98（0.99~9.73）突变/Mb]，这一趋势与肿瘤突变负荷（tumor mutation burden, TMB）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与SBS40的现有单碱基替换（single-base substitution, SBS）特征谱中，我们鉴定出NMIBC与MIBC患者间存在差异表达的特征：SBS13。
结论：中国人群中NMIBC与MIBC存在不同的基因突变特征与突变谱。MIBC的DDR基因突变频率、CNA负荷与TMB均高于NMIBC。本研究分析显示，NMIBC中的部分突变基因与MIBC中已报道的突变基因不存在重叠，提示部分NMIBC与MIBC可能起源于不同的前驱病变。