DataSheet_1_Evaluating the role of IDO1 macrophages in immunotherapy using scRNA-seq and bulk-seq in colorectal cancer.docx

BackgroundMacrophage infiltration is crucial for colorectal cancer (CRC) immunotherapy. Detailed classification of macrophage subsets will facilitate the selection of patients suitable for immunotherapy. However, the classification of macrophages in CRC is not currently detailed.
MethodsIn this study, we combined single-cell RNA sequencing (scRNA-seq) and bulk-seq to analyze patients with colorectal cancer. scRNA-seq data were used to study cell-cell communication and to differentiate immune-infiltrating cells and macrophage subsets. Bulk-seq data were used to further analyze immune infiltration, clinical features, tumor mutational burden, and expression of immune checkpoint molecules in patients with CRC having different macrophage subsets.
ResultsSeven macrophage subpopulations were identified, among which indoleamine 2,3 dioxygenase 1 (IDO1) macrophages had the most significant difference in the degree of infiltration among normal, microsatellite-unstable, and microsatellite-stable populations. We then performed gene set variation analysis using 12 marker genes of IDO1 macrophages and divided the patients into two clusters: high-IDO1 macrophages (H-IDO1M) and low-IDO1 macrophages (L-IDO1M). H-IDO1M showed higher infiltration of immune cells, higher expression of immune checkpoints, and less advanced pathological stages than L-IDO1M (p < 0.05).
ConclusionsThis study elucidated that IDO1-macrophage-based molecular subtypes can predict the response to immunotherapy in patients with CRC. The results provide new insights into tumor immunity and help in clinical decisions regarding designing effective immunotherapy for these patients.

背景：巨噬细胞浸润对于结直肠癌（colorectal cancer, CRC）免疫治疗至关重要。对巨噬细胞亚群进行精准分型，将有助于筛选适合免疫治疗的患者，但目前结直肠癌中巨噬细胞的分型尚不够细致。
方法：本研究联合单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）与bulk-seq技术，对结直肠癌患者展开分析：利用scRNA-seq数据探究细胞间通讯机制，并区分免疫浸润细胞与巨噬细胞亚群；利用bulk-seq数据进一步分析不同巨噬细胞亚群结直肠癌患者的免疫浸润特征、临床表型、肿瘤突变负荷以及免疫检查点分子的表达水平。
结果：本研究共鉴定出7种巨噬细胞亚群，其中吲哚胺2,3-双加氧酶1（indoleamine 2,3 dioxygenase 1, IDO1）巨噬细胞在正常、微卫星不稳定（microsatellite-unstable）与微卫星稳定（microsatellite-stable）人群中的浸润程度差异最为显著。随后，本研究依托IDO1巨噬细胞的12个标记基因开展基因集变异分析，将患者划分为两个聚类簇：高IDO1巨噬细胞群（H-IDO1M）与低IDO1巨噬细胞群（L-IDO1M）。相较于L-IDO1M组，H-IDO1M组患者的免疫细胞浸润程度更高、免疫检查点分子表达水平更强，且病理分期更偏早期（p < 0.05）。
结论：本研究证实，基于IDO1巨噬细胞的分子亚型可预测结直肠癌患者的免疫治疗响应情况。本研究结果为肿瘤免疫领域提供了全新的研究视角，同时可为临床制定结直肠癌患者的个体化有效免疫治疗方案提供决策依据。