Zhao Feilong, Wang Shu, Bai Yuezong, Cai Jinping, Wang Yuhao, Ma Yuxuan, Wang Haoyuan, Zhao Yan, Wang Juan, Zhang Cheng, Gao Jing, Yang Jianjun
Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University Xi'an 710032, Shaanxi, China.
State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Fourth Military Medical University Xi'an 710032, Shaanxi, China.
Am J Cancer Res. 2024 Nov 25;14(11):5551-5567. doi: 10.62347/AIWP6518. eCollection 2024.
Microsatellite instability-high (MSI-H) is a critical biomarker for immunotherapy, yet primary resistance remains a significant challenge. Current MSI-H detection methods evaluate the proportion of MSI-H loci, termed molecular MSI-H score, which can be affected by intratumoral heterogeneity (ITH). To address this limitation, we propose evaluating MSI-H at the cellular level to improve the prediction of immunotherapy outcomes. Using bulk tissue (TCGA-CRC) and cell line (CCLE-CRC) datasets, we identified genes highly expressed in MSI-H and MSS samples. These signatures were applied to a single-cell RNA sequencing (scCRC) dataset for enrichment analysis, enabling classification of tumor cells into MSI-H, MSS, and microsatellite dual (MSD) clusters using a Gaussian finite mixture model. Validation showed that MSI-H and MSS enrichment scores were higher in mismatch repair-deficient (MMRd) and mismatch repair-proficient (MMRp) patients, respectively. Functional enrichment analysis revealed that MSI-H cells were associated with pathways such as carboxylic acid catabolism, inflammatory responses, and IL-6/JAK2/STAT3 signaling. We developed a cellular MSI-H signature using genes specifically expressed in the MSI-H cell cluster and transformed the scCRC dataset into a cell-type-specific pseudobulk expression matrix. Using this matrix as a reference, we performed reference-based deconvolution on TCGA-CRC data. We defined the deconvolution score of MSI-H cell as cellular MSI-H score. This score strongly correlated with the molecular MSI-H score (R = 0.55, P < 0.001) and showed modest correlations with macrophage (MoMac, R = 0.14) and CD8+ T-cell (R = 0.11). To investigate its potential for clinical application, we applied the cellular MSI-H signature to the BJ-cohort, comprising 97 immunotherapy-treated gastrointestinal patients sequenced with a 395-gene panel. The cellular MSI-H score was significantly higher in responders (P = 0.002), positively correlated with tumor reduction percentage (R = 0.29, P = 0.006), and associated with improved progression-free survival (PFS) (HR: 0.00, 95% CI: 0.00-0.31, P = 0.021). In summary, the cellular MSI-H score reflects the MSI-H cell level within a tumor and demonstrates superior accuracy compared to molecular MSI-H status in predicting immunotherapy response and PFS. This underscores its potential as a more robust biomarker for guiding immunotherapy decisions.
微卫星高度不稳定（MSI-H）是免疫治疗的关键生物标志物，但原发性耐药仍然是一个重大挑战。目前的MSI-H检测方法评估MSI-H位点的比例，即分子MSI-H评分，这可能受肿瘤内异质性（ITH）影响。为解决这一局限性，我们建议在细胞水平评估MSI-H，以改善对免疫治疗结果的预测。使用批量组织（TCGA-CRC）和细胞系（CCLE-CRC）数据集，我们鉴定了在MSI-H和错配修复缺陷（MSS）样本中高表达的基因。这些特征被应用于单细胞RNA测序（scCRC）数据集进行富集分析，使用高斯有限混合模型将肿瘤细胞分类为MSI-H、MSS和微卫星双态（MSD）簇。验证表明，MSI-H和MSS富集评分在错配修复缺陷（MMRd）和错配修复 proficient（MMRp）患者中分别更高。功能富集分析显示，MSI-H细胞与羧酸分解代谢、炎症反应和IL-6/JAK2/STAT3信号传导等途径相关。我们使用在MSI-H细胞簇中特异性表达的基因开发了一种细胞MSI-H特征，并将scCRC数据集转化为细胞类型特异性的伪批量表达矩阵。以该矩阵为参考，我们对TCGA-CRC数据进行了基于参考的反卷积。我们将MSI-H细胞的反卷积评分定义为细胞MSI-H评分。该评分与分子MSI-H评分密切相关（R = 0.55，P < 0.001），与巨噬细胞（MoMac，R = 0.14）和CD8 + T细胞（R = 0.11）呈适度相关。为研究其临床应用潜力，我们将细胞MSI-H特征应用于BJ队列，该队列由97例接受免疫治疗的胃肠道患者组成，使用395基因panel进行测序。细胞MSI-H评分在反应者中显著更高（P = 0.002），与肿瘤缩小百分比呈正相关（R = 0.29，P = 0.006），并与无进展生存期（PFS）改善相关（HR：0.00，95%CI：0.00 - 0.31，P = 0.021）。总之，细胞MSI-H评分反映了肿瘤内的MSI-H细胞水平，在预测免疫治疗反应和PFS方面比分子MSI-H状态具有更高的准确性。这突出了其作为指导免疫治疗决策的更可靠生物标志物的潜力。
