在 DNA 样本中估算胰腺癌细胞分数。

Pancreatic Cancer Cell Fraction Estimation in a DNA Sample.

机构信息

Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.

Department of Urology, Tokyo Women's Medical University, Tokyo, Japan.

出版信息

Oncology. 2018;95(6):370-379. doi: 10.1159/000491637. Epub 2018 Aug 27.

DOI:10.1159/000491637

PMID:30149376

Abstract

OBJECTIVE

Pancreatic cancers are characterized by dense stroma. To estimate the degree of interference by coexisting noncancer cells in molecular analyses, we aimed to develop a DNA methylation marker that assesses a cancer cell fraction in DNA samples.

METHODS

The microarray data of 22 pancreatic cancer tissues from the The Cancer Genome Atlas database and 9 noncancer tissues were used for genome-wide screening. Thirty-one surgical tumor samples (10 intraductal papillary mucinous neoplasms [IPMNs] and 21 pancreatic cancers), 4 normal, and 26 nontumor samples were used for validation. Gene-specific methylation analysis was conducted by bisulfite pyrosequencing.

RESULTS

Genome-wide screening isolated SIM1, MIR129-2, NR1I2, and HOXB-AS4, as specifically methylated in pancreatic cancer cells. Bisulfite pyrosequencing validated that one or more of three genes (SIM1, MIR129-2, and NR1I2) were methylated in 22 (71.0%) tumor samples (8 IPMNs and 14 cancers), and all showed low levels of methylation in 26 (86.7%) normal and nontumor samples. Therefore, the three genes collectively constituted one marker for a pancreatic cancer cell fraction. The cancer cell fraction estimated by the marker was highly correlated with that estimated using the KRAS mutant allele frequency (R = 0.79).

CONCLUSION

The DNA methylation marker is useful to estimate the pancreatic cancer cell fraction in DNA samples.

摘要

目的

胰腺癌的特征是基质密集。为了评估共存非癌细胞对分子分析的干扰程度，我们旨在开发一种可评估 DNA 样本中癌细胞分数的 DNA 甲基化标志物。

方法

使用来自癌症基因组图谱数据库的 22 个胰腺癌细胞组织和 9 个非癌组织的微阵列数据进行全基因组筛选。31 个手术肿瘤样本（10 个导管内乳头状黏液性肿瘤 [IPMNs] 和 21 个胰腺癌）、4 个正常组织和 26 个非肿瘤样本用于验证。通过亚硫酸氢盐焦磷酸测序进行基因特异性甲基化分析。

结果

全基因组筛选分离出 SIM1、MIR129-2、NR1I2 和 HOXB-AS4，它们在胰腺癌细胞中特异性甲基化。焦磷酸测序验证了一个或多个三个基因（SIM1、MIR129-2 和 NR1I2）在 22 个（71.0%）肿瘤样本（8 个 IPMNs 和 14 个癌症）中发生甲基化，并且在 26 个（86.7%）正常和非肿瘤样本中均显示出低甲基化水平。因此，这三个基因共同构成了一个胰腺癌细胞分数的标志物。该标志物估计的癌细胞分数与 KRAS 突变等位基因频率（R = 0.79）高度相关。