State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China.
Shanghai SPH Jiaolian Pharmaceutical Technology Company, Limited, Buliding 4, 998 Ha Lei Road, Pudong District, Shanghai 201203, China.
Brief Bioinform. 2024 Jul 25;25(5). doi: 10.1093/bib/bbae422.
In this study, we introduce Robust estimation of Cell type proportions by Integrating single-reference-based DEconvolutions (ReCIDE), an innovative framework for robust estimation of cell type proportions by integrating single-reference-based deconvolutions. ReCIDE outperforms existing approaches in benchmark and real datasets, particularly excelling in estimating rare cell type proportions. Through exploratory analysis on public bulk data of triple-negative breast cancer (TNBC) patients using ReCIDE, we demonstrate a significant correlation between the prognosis of TNBC patients and the proportions of both T cell and perivascular-like cell subtypes. Built upon this discovery, we develop a prognostic assessment model for TNBC patients. Our contribution presents a novel framework for enhancing deconvolution accuracy, showcasing its effectiveness in medical research.
在这项研究中，我们引入了 Robust estimation of Cell type proportions by Integrating single-reference-based DEconvolutions (ReCIDE)，这是一种通过整合基于单参考的去卷积来进行稳健的细胞类型比例估计的创新框架。ReCIDE 在基准和真实数据集上优于现有方法，特别是在估计罕见细胞类型比例方面表现出色。通过使用 ReCIDE 对三阴性乳腺癌 (TNBC) 患者的公共批量数据进行探索性分析，我们证明了 TNBC 患者的预后与 T 细胞和类似血管周围细胞亚型的比例之间存在显著相关性。基于这一发现，我们为 TNBC 患者开发了一种预后评估模型。我们的贡献提出了一种增强去卷积准确性的新框架，展示了它在医学研究中的有效性。
