Single-cell and spatial transcriptomic analysis reveals that an immune cell-related signature could predict clinical outcomes for microsatellite-stable colorectal cancer patients receiving immunotherapy

Shijin YUAN; Yan XIA; Guangwei DAI; Shun RAO; Rongrong HU; Yuzhen GAO; Qing QIU; Chenghao WU; Sai QIAO; Yinghua XU; Xinyou XIE; Haizhou LOU; Xian WANG; Jun ZHANG

doi:10.1631/jzus.B2300679

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Research Article | Updated：2025-04-23

Single-cell and spatial transcriptomic analysis reveals that an immune cell-related signature could predict clinical outcomes for microsatellite-stable colorectal cancer patients receiving immunotherapy
Single-cell and spatial transcriptomic analysis reveals that an immune cell-related signature could predict clinical outcomes for microsatellite-stable colorectal cancer patients receiving immunotherapy
单细胞联合空间转录组分析揭示免疫细胞相关特征可以预测微卫星稳定结直肠癌患者接受免疫治疗的临床结局
Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology) Vol. 26, Issue 4, Pages: 371-392(2025)
Affiliations：

1.Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
2.Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
3.Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310016, China
4.Yongkang Hospital of Traditional Chinese Medicine Medical Community Xicheng Branch, Jinhua 321300, China
Funds：
DOI：10.1631/jzus.B2300679
CLC：
CSTR：
Received：21 September 2023，

Revised：25 January 2024，

Published：23 April 2025
Accepted：

袁世进,夏艳,代广卫等.单细胞联合空间转录组分析揭示免疫细胞相关特征可以预测微卫星稳定结直肠癌患者接受免疫治疗的临床结局[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2025,26(04):371-392.

Shijin YUAN, Yan XIA, Guangwei DAI, et al. Single-cell and spatial transcriptomic analysis reveals that an immune cell-related signature could predict clinical outcomes for microsatellite-stable colorectal cancer patients receiving immunotherapy[J]. Journal of zhejiang university-science b (biomedicine & biotechnology), 2025, 26(4): 371-392.
袁世进,夏艳,代广卫等.单细胞联合空间转录组分析揭示免疫细胞相关特征可以预测微卫星稳定结直肠癌患者接受免疫治疗的临床结局[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2025,26(04):371-392. DOI： 10.1631/jzus.B2300679.

Shijin YUAN, Yan XIA, Guangwei DAI, et al. Single-cell and spatial transcriptomic analysis reveals that an immune cell-related signature could predict clinical outcomes for microsatellite-stable colorectal cancer patients receiving immunotherapy[J]. Journal of zhejiang university-science b (biomedicine & biotechnology), 2025, 26(4): 371-392. DOI： 10.1631/jzus.B2300679.

摘要

近期研究表明，血管内皮生长因子受体抑制剂（VEGFRi）可以增强程序性死亡受体1（PD-1）抗体对微卫星稳定（MSS）结直肠癌（CRC）的抗肿瘤活性。然而，与标准三线VEGFRi治疗相比，这种联合治疗的疗效尚未明确，且目前缺乏可靠的生物标志物。本研究中，我们回顾性纳入了接受PD-1抗体联合VEGFRi（联合组，

=54）或单独VEGFRi（VEGFRi组，

=32）治疗的MSS CRC患者，并评估了其疗效和安全性。我们通过单细胞和空间转录组数据进一步研究了MSS CRC肿瘤微环境（TME）的免疫特征，构建了一个预测接受免疫治疗的MSS CRC患者临床结局的MSS CRC免疫细胞相关特征（MCICRS），并在内部队列中对其进行验证。研究发现，与单独VEGFRi治疗相比，PD-1抗体联合VEGFRi治疗能显著延长患

者的生存期（中位无进展生存期：4.4个月 vs. 2.0个月，

=0.0024；中位总生存期：10.2个月 vs. 5.2个月，

=0.0038），且两组间不良事件的发生率相当。进一步通过单细胞和空间转录组分析，我们确定了10种MSS CRC富集的免疫细胞类型及其空间分布，包括幼稚CD4

T细胞、调节性CD4

T细胞、CD4

Th17细胞、耗竭CD8

T细胞、细胞毒性CD8

T细胞、增殖CD8

T细胞、自然杀伤（NK）细胞、浆细胞和经典/中间型单核细胞。基于meta分析和10种机器学习算法，我们构建了MCICRS，其是一个独立的MSS CRC患者的预后风险因素。通过进一步分析，MCICRS低风险组患者表现出更高的免疫细胞浸润和免疫相关通路激活，同时与泛癌免疫治疗的客观反应率和无进展生存有显著关联。最后，MCICRS在MSS CRC接受免疫治疗的预测价值也在内部队列中得到了验证。综上所述，PD-1抗体联合VEGFRi可以改善MSS CRC的临床结局且可控制毒性，同时MCICRS可以作为一个强大且有前景的工具，用于预测接受免疫治疗的MSS CRC患者的临床结局。

Abstract

Recent data suggest that vascular endothelial growth factor receptor inhibitor (VEGFRi) can enhance the anti-tumor activity of the anti-programmed cell death-1 (anti-PD-1) antibody in colorectal cancer (CRC) with microsatellite stability (MSS). However

the comparison between this combination and standard third-line VEGFRi treatment is not performed

and reliable biomarkers are still lacking. We retrospectively enrolled MSS CRC patients receiving anti-PD-1 antibody plus VEGFRi (combination group

=54) or VEGFRi alone (VEGFRi group

=32)

and their efficacy and safety were evaluated. We additionally examined the immune characteristics of the MSS CRC tumor microenvironment (TME) through single-cell and spatial transcriptomic data

and an MSS CRC immune cell-related signature (MCICRS) that can be used to predict the clinical outco

mes of MSS CRC patients receiving immunotherapy was developed and validated in our in-house cohort. Compared with VEGFRi alone

the combination of anti-PD-1 antibody and VEGFRi exhibited a prolonged survival benefit (median progression-free survival: 4.4 vs. 2.0 months

=0.0024; median overall survival: 10.2 vs. 5.2 months

=0.0038) and a similar adverse event incidence. Through single-cell and spatial transcriptomic analysis

we determined ten MSS CRC-enriched immune cell types and their spatial distribution

including naive CD4

regulatory CD4

CD4

Th17

exhausted CD8

cytotoxic CD8

proliferated CD8

natural killer (NK) cells

plasma

and classical and intermediate monocytes. Based on a systemic meta-analysis and ten machine learning algorithms

we obtained MCICRS

an independent risk factor for the prognosis of MSS CRC patients. Further analyses demonstrated that the low-MCICRS group presented a higher immune cell infiltration and immune-related pathway activation

and hence a significant relation with the superior efficacy of pan-cancer immunotherapy. More importantly

the predictive value of MCICRS in MSS CRC patients receiving immunotherapy was also validated with an in-house cohort. Anti-PD-1 antibody combined with VEGFRi presented an improved clinical benefit in MSS CRC with manageable toxicity. MCICRS could serve as a robust and promising tool to predict clinical outcomes for individual MSS CRC patients receiving immunotherapy.

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