- EXOMA2 研究对 2409 例肿瘤行全外显子测序，以 FACETS、TITAN 将 MTAP 拷贝数分为野生型、纯合缺失或可能杂合缺失。
- 三种 MTAP 抗体（MTAP-RBT、2G4、1813）IHC 与基因组分类在野生型及纯合缺失中高度一致；IHC 可将大量 NGS「杂合」判读重分类，蛋白缺失常对应 FISH 证实的纯合缺失。
- NGS 杂合判读并非仅由肿瘤纯度低所致；结合蛋白水平评估与 FISH 有助于更准确、快速、经济地筛选 MTAP 缺失肿瘤，对接 PRMT5–MAT2A 等靶向策略。
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摘要
甲硫腺苷磷酸化酶（MTAP）基因缺失是多种恶性肿瘤中常见的基因组事件，常与相邻 CDKN2A 位点缺失相关。MTAP 缺失近来成为有前景的生物标志物，可用于包括 PRMT5–MAT2A 轴抑制剂在内的新型靶向治疗。尽管二代测序（NGS）可检测 MTAP 拷贝数改变，但在肿瘤纯度低或拷贝数评分处于临界时判读可能困难。本研究在 EXOMA2 研究（NCT06550687）中，对 2409 例经全外显子测序的肿瘤，用 FACETS 与 TITAN 算法分析 MTAP 拷贝数状态，分为野生型、纯合缺失或可能杂合缺失。对其中有组织可用的亚组，采用三种 MTAP 抗体克隆（MTAP-RBT、2G4 与 1813）进行免疫组化（IHC）正交验证，部分病例进一步行荧光原位杂交（FISH）与 RNA 测序。结果显示，在野生型或纯合缺失的肿瘤中，IHC 与基因组分类高度一致。重要的是，IHC 使相当比例最初被 NGS 判为杂合的肿瘤得以重分类；这些病例的蛋白表达缺失与 FISH 证实的基因组纯合缺失相关。此外，NGS 杂合判读与低肿瘤细胞比例并无关联。上述发现表明，MTAP 免疫组化是评估 MTAP 状态、澄清模糊 NGS 结果的稳健且易开展的方法，而模糊结果并非仅由低肿瘤纯度驱动。将蛋白水平评估与 FISH 确认相结合，有助于更好识别 MTAP 缺失肿瘤，从而更准确、快速、经济地为新兴靶向治疗筛选患者。
PubMed abstract only. Modern Pathology is labeled hybrid OA, but ScienceDirect / publisher pages returned Cloudflare challenges from this site’s egress (including browser), so full text and figures were not collected.
Abstract
The deletion of the methylthioadenosine phosphorylase (MTAP) gene is a frequent genomic event across various malignancies, often associated with the loss of the adjacent CDKN2A locus. MTAP deficiency has recently emerged as a promising biomarker for novel targeted therapeutic strategies including inhibitors of the PRMT5-MAT2A axis. Although next-generation sequencing (NGS) allows detection of MTAP copy number alterations, interpretation may be challenging in samples with low tumor purity or borderline copy number scores. In this study, we analyzed MTAP copy number status in a cohort of 2,409 tumors profiled by whole-exome sequencing within the EXOMA2 study (NCT06550687) using the FACETS and TITAN algorithms. Tumors were categorized as wild-type, homozygous deletion, or probable heterozygous deleted. A subset of these cases with available tissue underwent orthogonal validation by immunohistochemistry (IHC) using three MTAP antibody clones (MTAP-RBT, 2G4, and 1813), with selected cases further analyzed by fluorescence in situ hybridization (FISH) and RNA sequencing. Our results show high concordance between IHC and genomic classification in tumors with either wild-type, or homozygous deletion MTAP status. Importantly, IHC enabled reclassification of a substantial proportion of tumors initially classified as heterozygous by NGS; loss of protein expression in these cases correlated with homozygous genomic deletion confirmed by FISH. Moreover, heterozygous NGS calls were not associated with low tumor cellularity. These findings demonstrate that MTAP immunohistochemistry represents a robust and accessible approach for assessing MTAP status and for resolving ambiguous NGS results, an issue not solely driven by low tumor cellularity. Incorporating protein-level assessment analyses with FISH confirmation improve the identification of MTAP-deficient tumors and facilitate more accurate, rapid, and cost-effective patient selection for emerging targeted therapies.