肿瘤浸润淋巴细胞（TIL）对于实体瘤的有效免疫检查点阻断（ICB）治疗至关重要。然而，约 70% 的肿瘤表现出较差的淋巴细胞浸润，导致 ICB 疗法效果较差。我们开发了一个生物信息学流程，整合了多个先前未考虑的因素或数据集，包括肿瘤细胞免疫相关途径、拷贝数变异 (CNV) 和单一肿瘤细胞测序数据以及肿瘤 mRNA-seq 数据和患者生存数据，以确定可以潜在改善 T 细胞浸润并增强 ICB 疗效的靶标。此外，我们进行了湿实验室实验并成功验证了其中一个最重要的基因。我们将这一流程应用于癌症基因组图谱 (TCGA) 的实体瘤，并在 18 种癌症类型中鉴定了一组可能改善淋巴细胞浸润的基因和ICB疗效，为进一步探索提供了宝贵的药物靶点资源。重要的是，我们在小鼠结肠癌同基因模型中通过实验验证了 SUN1，该基因此前并未与 T 细胞浸润和 ICB 治疗相关，但它是基于管道的 3 种癌症类型中最确定的基因靶标之一。我们发现 Sun1 KO 可以显着增强抗原呈递，增加 T 细胞浸润，并提高抗 PD1 治疗效果。此外，通过单细胞多组分析，我们确定了亚基因调控网络（sub-GRN），显示 Stat 蛋白在增强 Sun1-KO 癌细胞的免疫相关通路中发挥着重要作用。这项研究不仅建立了一个计算管道，用于发现癌细胞中阻止 T 细胞浸润的新基因靶标和信号通路，同时也提供了一个基因靶标库，用于进一步探索改善实体瘤中的淋巴细胞浸润和 ICB 功效。为这项研究做出贡献的资助机构的完整列表可以在可在致谢部分找到。版权所有 © 2024 作者。由 Elsevier B.V. 出版。保留所有权利。

Tumour-infiltrating lymphocytes (TILs) are crucial for effective immune checkpoint blockade (ICB) therapy in solid tumours. However, ∼70% of these tumours exhibit poor lymphocyte infiltration, rendering ICB therapies less effective.We developed a bioinformatics pipeline integrating multiple previously unconsidered factors or datasets, including tumour cell immune-related pathways, copy number variation (CNV), and single tumour cell sequencing data, as well as tumour mRNA-seq data and patient survival data, to identify targets that can potentially improve T cell infiltration and enhance ICB efficacy. Furthermore, we conducted wet-lab experiments and successfully validated one of the top-identified genes.We applied this pipeline in solid tumours of the Cancer Genome Atlas (TCGA) and identified a set of genes in 18 cancer types that might potentially improve lymphocyte infiltration and ICB efficacy, providing a valuable drug target resource to be further explored. Importantly, we experimentally validated SUN1, which had not been linked to T cell infiltration and ICB therapy previously, but was one of the top-identified gene targets among 3 cancer types based on the pipeline, in a mouse colon cancer syngeneic model. We showed that Sun1 KO could significantly enhance antigen presentation, increase T-cell infiltration, and improve anti-PD1 treatment efficacy. Moreover, with a single-cell multiome analysis, we identified subgene regulatory networks (sub-GRNs) showing Stat proteins play important roles in enhancing the immune-related pathways in Sun1-KO cancer cells.This study not only established a computational pipeline for discovering new gene targets and signalling pathways in cancer cells that block T-cell infiltration, but also provided a gene target pool for further exploration in improving lymphocyte infiltration and ICB efficacy in solid tumours.A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.