Background: Mutations in the DNA polymerase delta 1 (POLD1) exonuclease domain cause DNA proofreading defects, hypermutation, hereditary colorectal and endometrial cancer, and are predictive of immunotherapy response. Exonuclease activity is carried out by two magnesium cations, bound to four highly conserved, negatively charged amino acids (AA) consisting of aspartic acid at amino acid position 316 (p.D316), glutamic acid at position 318 (p.E318), p.D402, and p.D515 (termed DEDD motif). Germline polymorphisms resulting in charge-discordant AA substitutions in the DEDD motif are classified as variants of uncertain significance (VUSs) by laboratories and thus would be considered clinically inactionable. We hypothesize this mutation class is clinically pathogenic. Methods: A review of clinical presentation was performed in our index patient with a POLD1(p.D402N) heterozygous proband with endometrial cancer. Implications of this mutation class were evaluated by a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)-guided systematic review, in silico analysis with orthogonal biochemical confirmation, and whole-exome and RNA sequencing analysis of the patient’s tumor and engineered cell lines. Results: Our systematic review favored a Mendelian disease mutation class associated with endometrial and colorectal cancers. In silico analysis predicted defective protein function, confirmed by biochemical assay demonstrating loss of nuclease activity. APOLD1-specific mutational signature was found in both the patient’s tumor andPOLD1(p.D402N) overexpressing cell. Furthermore, paired whole-exome/transcriptome analysis of endometrial tumor demonstrated hypermutation and T cell-inflamed gene expression profile (GEP), which are joint predictive biomarkers for pembrolizumab. Our patient showed a deep, durable response to immune checkpoint inhibitor (ICI). Conclusion: Charge-discordant AA substitution in the DEDD motif ofPOLD1is detrimental to DNA proofreading and should be reclassified as likely pathogenic and possibly predictive of ICI sensitivity.
背景：DNA聚合酶δ1（POLD1）外切酶结构域的突变会导致DNA校对缺陷、高突变、遗传性结直肠癌和子宫内膜癌，并能预测免疫治疗反应。外切酶活性由两个镁阳离子执行，它们与四个高度保守的带负电荷的氨基酸结合，这些氨基酸包括位于氨基酸位置316的天冬氨酸（p.D316）、位置318的谷氨酸（p.E318）、p.D402和p.D515（称为DEDD基序）。导致DEDD基序中电荷不一致氨基酸替换的种系多态性被实验室归类为意义未明的变异（VUSs），因此在临床上被视为不可操作。我们假设此类突变具有临床致病性。方法：我们对一名携带POLD1(p.D402N)杂合突变的子宫内膜癌先证者（索引患者）的临床表现进行了回顾。通过遵循系统评价和荟萃分析优先报告条目（PRISMA）指南的系统评价、结合正交生化验证的计算机分析，以及对患者肿瘤和工程化细胞系的全外显子组和RNA测序分析，评估了此类突变的影响。结果：我们的系统评价支持此类突变属于与子宫内膜癌和结直肠癌相关的孟德尔疾病突变类别。计算机分析预测蛋白质功能缺陷，生化实验证实了核酸酶活性的丧失。在患者肿瘤和过表达POLD1(p.D402N)的细胞中均发现了POLD1特异性突变特征。此外，对子宫内膜肿瘤进行的配对全外显子组/转录组分析显示存在高突变和T细胞炎症基因表达谱（GEP），这两者是派姆单抗的联合预测生物标志物。我们的患者对免疫检查点抑制剂（ICI）表现出深度且持久的反应。结论：POLD1 DEDD基序中的电荷不一致氨基酸替换损害DNA校对功能，应被重新归类为可能致病性突变，并可能预测对ICI的敏感性。
肿瘤(癌症)患者之家