Bowland Kirsten, Lai Jiaying, Skaist Alyza, Zhang Yan, Teh Selina Shiqing K, Roberts Nicholas J, Thompson Elizabeth, Wheelan Sarah J, Hruban Ralph H, Karchin Rachel, Bailey Matthew H, Iacobuzio-Donahue Christine A, Eshleman James R
Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.
PLoS One. 2024 Dec 19;19(12):e0298490. doi: 10.1371/journal.pone.0298490. eCollection 2024.
Metastatic cancer affects millions of people worldwide annually and is the leading cause of cancer-related deaths. Most patients with metastatic disease are not eligible for surgical resection, and current therapeutic regimens have varying success rates, some with 5-year survival rates below 5%. Here, we test the hypothesis that metastatic cancer can be genetically targeted by exploiting single base substitution mutations unique to individual cells that occur as part of normal aging prior to transformation. These mutations are targetable because ~10% of them form novel tumor-specific "NGG" protospacer adjacent motif (PAM) sites targetable by CRISPR-Cas9.
Whole genome sequencing was performed on five rapid autopsy cases of patient-matched primary tumor, normal and metastatic tissue from pancreatic ductal adenocarcinoma decedents. CRISPR-Cas9 PAM targets were determined by bioinformatic tumor-normal subtraction for each patient and verified in metastatic samples by high-depth capture-based sequencing.
We found that 90% of PAM targets were maintained between primary carcinomas and metastases overall. We identified rules that predict PAM loss or retention, where PAMs located in heterozygous regions in the primary tumor can be lost in metastases (private LOH), but PAMs occurring in regions of loss of heterozygosity (LOH) in the primary tumor were universally conserved in metastases.
Regions of truncal LOH are strongly retained in the presence of genetic instability and, therefore, represent genetic vulnerabilities in pancreatic adenocarcinomas. A CRISPR-based gene therapy approach targeting these regions may be a novel way to genetically target metastatic cancer.
转移性癌症每年影响全球数百万人，是癌症相关死亡的主要原因。大多数转移性疾病患者不符合手术切除条件，目前的治疗方案成功率各不相同，有些方案的5年生存率低于5%。在此，我们检验这样一个假设，即转移性癌症可以通过利用个体细胞特有的单碱基替换突变进行基因靶向治疗，这些突变是在转化前正常衰老过程中出现的。这些突变是可靶向的，因为其中约10%会形成可被CRISPR-Cas9靶向的新型肿瘤特异性“NGG”原间隔相邻基序（PAM）位点。
对5例胰腺导管腺癌死者的患者匹配的原发性肿瘤、正常组织和转移组织进行快速尸检的全基因组测序。通过生物信息学肿瘤-正常组织减法确定每个患者的CRISPR-Cas9 PAM靶点，并通过基于深度捕获的测序在转移样本中进行验证。
我们发现总体上90%的PAM靶点在原发性癌和转移灶之间得以保留。我们确定了预测PAM丢失或保留的规则，即原发性肿瘤杂合区域中的PAM在转移灶中可能丢失（私有杂合性缺失），但原发性肿瘤中杂合性缺失（LOH）区域出现的PAM在转移灶中普遍保守。
在存在基因不稳定的情况下，主干型杂合性缺失区域强烈保留，因此代表胰腺腺癌中的基因脆弱性。针对这些区域的基于CRISPR的基因治疗方法可能是对转移性癌症进行基因靶向治疗的一种新途径。
