Treatment of locally advanced rectal cancer includes chemotherapy, radiation, and surgery but patient responses to neoadjuvant treatment are variable. We have shown that rectal tumors are comprised of multiple genetically distinct sub-clones. Unique sub-clones within tumors may harbor mutations which contribute to inter-patient variation in response to neoadjuvant chemoradiotherapy (nCRT). Analysis of the influence of nCRT on the extent and nature of intra-tumoral genetic heterogeneity in rectal cancer may provide insights into mechanisms of resistance. Locally advanced rectal cancer patients underwent pre-treatment biopsies. At the time of surgery, tissue from the treated tumor was obtained and analyzed. Pre- and post-treatment specimens were subjected to whole exome and confirmatory deep sequencing for somatic mutations. Copy number variation was assessed using OncoScan SNP arrays. Genomic data were analyzed using PyClone to identify sub-clonal tumor population following nCRT. Alterations that persisted or were enriched in the post-treatment tumor specimen following nCRT were defined for each patient. Thirty-two samples were obtained from ten patients. PyClone identified 2 to 10 genetic sub-clones per tumor. Substantial changes in the proportions of individual sub-clones in pre- versus post-treatment tumor material were found in all patients. Resistant sub-clones recurrently contained mutations in TP53, APC, ABCA13, MUC16, and THSD4. Recurrent copy number variation was observed across multiple chromosome regions after nCRT. Pathway analysis including variant alleles and copy number changes associated with resistant sub-clones revealed significantly altered pathways, especially those linked to the APC and TP53 genes, which were the two most frequently mutated genes. Intra-tumoral heterogeneity is evident in pre-treatment rectal cancer. Following treatment, sub-clonal populations are selectively modified and enrichment of a subset of pre-treatment sub-clones is seen. Further studies are needed to define recurrent alterations at diagnosis that may contribute to resistance to nCRT.

中文翻译：

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直肠癌亚克隆对新辅助治疗的反应不同。

局部晚期直肠癌的治疗包括化疗，放疗和手术，但是患者对新辅助治疗的反应是多种多样的。我们已经表明，直肠肿瘤由多个遗传上不同的亚克隆组成。肿瘤内独特的亚克隆可能带有突变，这些突变会导致患者对新辅助放化疗的反应发生变异。分析nCRT对直肠癌中肿瘤内遗传异质性的程度和性质的影响可能会为耐药机制提供见解。局部晚期直肠癌患者接受了治疗前的活检。在手术时，从治疗的肿瘤中获得组织并进行分析。对治疗前后的标本进行完整的外显子组和体细胞突变的确认性深度测序。使用OncoScan SNP阵列评估拷贝数变异。使用PyClone分析基因组数据，以鉴定nCRT后的亚克隆肿瘤人群。为每位患者定义了在nCRT之后持续存在或在治疗后肿瘤样本中富集的变化。从十名患者中获得了三十二份样本。PyClone在每个肿瘤中鉴定出2至10个遗传亚克隆。在所有患者中，治疗前和治疗后肿瘤材料中各个亚克隆的比例均发生了实质性变化。抗性亚克隆通常包含TP53，APC，ABCA13，MUC16和THSD4中的突变。nCRT后在多个染色体区域观察到了重复的拷贝数变化。包括变异等位基因和与抗性亚克隆相关的拷贝数变化的途径分析显示，途径发生了显着改变，尤其是那些与APC和TP53基因相关的途径，这是两个最频繁突变的基因。肿瘤内异质性在治疗前直肠癌中很明显。在治疗之后，亚克隆群体被选择性地修饰，并且可以看到治疗前亚克隆子集的富集。需要进一步的研究来确定诊断时可能导致对nCRT耐药的复发性改变。亚克隆群体被选择性地修饰，并且可以看到治疗前亚克隆的一个子集的富集。需要进一步的研究来确定诊断时可能导致对nCRT耐药的复发性改变。亚克隆群体被选择性地修饰，并且可以看到治疗前亚克隆的一个子集的富集。需要进一步的研究来确定诊断时可能导致对nCRT耐药的复发性改变。