PO.BCS01.03 · 生物信息与计算

A transcriptomic framework to predict response and prioritize indications for p53 restoration therapy

海报缩略图:A transcriptomic framework to predict response and prioritize indications for p53 restoration therapy
编号 2701 展板 26 🕑 4/20 02:00–05:00 📍 Section 1 主讲 Hosun Lee, BS;PhD
分会场 Application of Bioinformatics to Cancer Biology 3
📄 查看 PDF ⬇ 下载 PDF 🔒 需登录后查看 / 下载(免费注册) 🔗 AACR 官方页面

作者与单位 Authors & Affiliations

Hosun Lee, Seunghwan Jung, Boram Kim, Seung-Hyun Shin, Yong Ho Heo, Yu-Yon Kim, Daejin Kim, Haemin Chon, In Young Choi

Hanmi R&D Center, Hanmi Pharm. Co. Ltd., Gyeonggi-do, Korea, Republic of

摘要 Abstract

Introduction: TP53 has been recognized as a promising therapeutic target because of its pivotal role in tumor suppression and the high prevalence of its functional alterations in cancer. However, sensitivity to p53 restoration varies markedly across cancer cell lines and is not determined solely by the presence or absence of intact p53. These findings suggest that additional, pathway-level factors may modulate responsiveness to p53 reactivation. In this study, focusing on p53 restoration therapy, we aimed to (1) elucidate molecular mechanism underlying variable responses, (2) build a transcriptomic prediction model capable of estimating restoration sensitivity, and (3) apply this framework to prioritize clinical indications across tumor types. Methods: In vitro results of p53 restoration were curated from 28 cell lines (20 sensitive [S], 8 resistant [R]). Transcriptomic differences between S and R were evaluated by Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) using p53-related gene sets from MSigDB. RNA expression data were normalized by Non-paranormal (NPN) transformation, and singscore values were computed to quantify pathway activity. A logistic regression model was trained to estimate the probability of S or R classification, with the cutoff (specificity ≥0.9) stabilized through bootstrap resampling and fixed at the median. External datasets - CCLE, TCGA, cBioPortal, and GEO (GSE271757, GSE223463, GSE169321) - were analyzed to explore appropriate clinical indications. Results: GSEA revealed a distinct downregulation of DNA elongation and Mismatch repair pathways in the S group, indicating reduced baseline DNA repair activity in S cells. Among gene sets tested, Signature A, achieved the strongest discriminatory power between S and R (PR AUC = 0.754). For indication prioritization, integrative analysis combining Signature A-based predictions from CCLE and TCGA, together with TP53 alteration prevalence from cBioPortal, identified lung, head and neck, ovarian cancers as Tier 1 indications. By investigating the biological nature of Signature A, we observed that DNA-damaging therapies may enhance p53 restoration sensitivity. Consistently, analysis of GEO cohorts with pre- and post-treatment RNA-seq data revealed an increased fraction of S from 52% to 96% in ovarian cancer, and 85% to 92% in pancreatic cancer following DNA-damaging therapy. Conclusion: Signature A, a transcriptomic signature, stratifies p53 restoration responsiveness across cancer types and provides a robust, reproducible framework for indication prioritization and for understanding the mechanistic context of p53 restoration during the patient treatment journey.
利益披露 Disclosure
H. Lee, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. S. Jung, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. B. Kim, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. S. Shin, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. Y. Heo, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. Y. Kim, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. D. Kim, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. H. Chon, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment. I. Choi, Hanmi R&D Center, Hanmi Pharm. Co. Ltd. Employment.

🔍 在海报库中搜索更多海报 →