疫苗和传染病司Evan W. Newell团队在研究中取得进展。他们提出了细胞模拟作为细胞分割。相关论文发表在2025年5月22日出版的《自然—方法学》杂志上。

该研究组采用从头开始细胞模拟的方法，在一种称为Proseg（概率分割）的方法中，快速推断形态上可移植的细胞边界。对三个商业平台生成的数据集进行基准测试，结果表明Proseg的性能和计算效率优于现有方法。研究小组表明，提高细胞分割的准确性大大有助于检测难以分割的肿瘤浸润性免疫细胞，如中性粒细胞和T细胞。最后，通过改进其描述肿瘤浸润T细胞亚群的能力，研究小组发现表达CXCL13的CD8⁺ T细胞与肿瘤细胞的关系往往比表达CXCL13的阴性T细胞更密切。

据介绍，单细胞空间转录组学有望非常详细地了解细胞的转录状态和微环境，然而不准确的细胞分割可能会错误地将大量转录本归因于附近的细胞或变出不存在的细胞，从而使这些数据变得模糊。

附：英文原文

Title: Cell simulation as cell segmentation

Author: Jones, Daniel C., Elz, Anna E., Hadadianpour, Azadeh, Ryu, Heeju, Glass, David R., Newell, Evan W.

Issue&Volume: 2025-05-22

Abstract: Single-cell spatial transcriptomics promises a highly detailed view of a cell’s transcriptional state and microenvironment, yet inaccurate cell segmentation can render these data murky by misattributing large numbers of transcripts to nearby cells or conjuring nonexistent cells. We adopt methods from ab initio cell simulation, in a method called Proseg (probabilistic segmentation), to rapidly infer morphologically plausible cell boundaries. Benchmarking applied to datasets generated by three commercial platforms shows superior performance and computational efficiency of Proseg when compared to existing methods. We show that improved accuracy in cell segmentation aids greatly in detection of difficult-to-segment tumor-infiltrating immune cells such as neutrophils and T cells. Last, through improvements in our ability to delineate subsets of tumor-infiltrating T cells, we show that CXCL13-expressing CD8+ T cells tend to be more closely associated with tumor cells than their CXCL13-negative counterparts in data generated from samples from patients with renal cell carcinoma.

DOI: 10.1038/s41592-025-02697-0

Source: https://www.nature.com/articles/s41592-025-02697-0