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整合单细胞和空间分析可识别头颈癌免疫检查点阻断反应中依赖于背景的髓系细胞与T细胞相互作用。

Integrated single-cell and spatial analysis identifies context-dependent myeloid-T cell interactions in head and neck cancer immune checkpoint blockade response.

作者信息

Golfinos-Owens Athena E, Lozar Taja, Khatri Parth, Hu Rong, Harari Paul M, Lambert Paul F, Fitzpatrick Megan B, Dinh Huy Q

机构信息

McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792.

University of Ljubljana, Ljubljana, Slovenia.

出版信息

bioRxiv. 2025 Mar 28:2025.03.24.644582. doi: 10.1101/2025.03.24.644582.


DOI:10.1101/2025.03.24.644582
PMID:40196610
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11974738/
Abstract

BACKGROUND: Approximately 15-20% of head and neck cancer squamous cell carcinoma (HNSCC) patients respond favorably to immune checkpoint blockade (ICB). Previous single-cell RNA-Seq (scRNA-Seq) studies identified immune features, including macrophage subset ratios and T-cell subtypes, in HNSCC ICB response. However, the spatial features of HNSCC-infiltrated immune cells in response to ICB treatment need to be better characterized. METHODS: Here, we perform a systematic evaluation of cell interactions between immune cell types within the tumor microenvironment using spatial omics data using complementary techniques from both 10X Visium spot-based spatial transcriptomics and Nanostring CosMx single-cell spatial omics with RNA gene panel including 435 ligands and receptors. In this study, we used integrated bioinformatics analyses to identify cellular neighborhoods of co-localizing cell types in single-cell spatial transcriptomics and proteomics data. In addition, we used both publicly available scRNA-Seq and in-house spatial RNA-Seq data to identify spatially constrained Ligand-Receptor interactions in Responder patients. RESULTS: With 522,399 single cells profiled with both RNA and protein from 26 patients, in addition to spot-resolved spatial RNA-Seq from 8 patients treated with ICB together with bioinformatics analysis of publicly available single-cell and bulk RNA-Seq, we have identified a spatial and cell-type specific context-dependency of myeloid and T cell interaction difference between Responders and Non-Responders. We defined further cellular neighborhood and the sources of chemokine CXCL9/10-CXCR3 interactions in Responders, emerging targets in ICB, as well as CXCL16-CXCR6, CCL4/5-CCR5, and other underappreciated and potential markers and targets for ICB response in HNSCC. In addition, we have contributed a rich data resource of cell-cell Ligand Receptor interactions for the immunotherapy and HNSCC research community. DISCUSSION: Our work provides a comprehensive single-cell and spatial atlas of immune cell interactions that correlate with response to ICB in HNSCC. We showcase how integrating multiple technologies and bioinformatics approaches can provide new insights into potential immune-based biomarkers of ICB response. Our results suggested refining future studies using preclinical animal models in a more context-specific manner to elucidate potential underlying mechanisms that lead to improved ICB responses.

摘要

背景:大约15%-20%的头颈癌鳞状细胞癌(HNSCC)患者对免疫检查点阻断(ICB)反应良好。先前的单细胞RNA测序(scRNA-Seq)研究确定了HNSCC ICB反应中的免疫特征,包括巨噬细胞亚群比例和T细胞亚型。然而,HNSCC浸润免疫细胞对ICB治疗反应的空间特征需要更好地表征。 方法:在这里,我们使用基于10X Visium斑点的空间转录组学和包含435种配体和受体的RNA基因面板的Nanostring CosMx单细胞空间组学的互补技术,对肿瘤微环境中免疫细胞类型之间的细胞相互作用进行系统评估。在本研究中,我们使用综合生物信息学分析来识别单细胞空间转录组学和蛋白质组学数据中共定位细胞类型的细胞邻域。此外,我们使用公开可用的scRNA-Seq和内部空间RNA-Seq数据来识别反应者患者中空间受限的配体-受体相互作用。 结果:对26名患者的522399个单细胞进行了RNA和蛋白质分析,此外,对8名接受ICB治疗的患者进行了斑点解析空间RNA-Seq,并对公开可用的单细胞和批量RNA-Seq进行了生物信息学分析,我们确定了反应者和非反应者之间髓系和T细胞相互作用差异的空间和细胞类型特异性上下文依赖性。我们进一步定义了反应者中的细胞邻域以及趋化因子CXCL9/10-CXCR3相互作用的来源,这是ICB中的新兴靶点,以及CXCL16-CXCR6、CCL4/5-CCR5,以及其他未被充分认识的HNSCC中ICB反应的潜在标志物和靶点。此外,我们为免疫治疗和HNSCC研究界贡献了丰富的细胞-细胞配体受体相互作用数据资源。 讨论:我们的工作提供了一个与HNSCC中ICB反应相关的免疫细胞相互作用的全面单细胞和空间图谱。我们展示了整合多种技术和生物信息学方法如何能够为ICB反应的潜在免疫生物标志物提供新的见解。我们的结果建议以更具上下文特异性的方式使用临床前动物模型来完善未来的研究,以阐明导致ICB反应改善的潜在机制。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/67077a082c9c/nihpp-2025.03.24.644582v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/639aa152760e/nihpp-2025.03.24.644582v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/6785b8991538/nihpp-2025.03.24.644582v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/15821a9e5905/nihpp-2025.03.24.644582v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/7b9b1a76a531/nihpp-2025.03.24.644582v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/2d82bb8c5592/nihpp-2025.03.24.644582v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/67077a082c9c/nihpp-2025.03.24.644582v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/639aa152760e/nihpp-2025.03.24.644582v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/6785b8991538/nihpp-2025.03.24.644582v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/15821a9e5905/nihpp-2025.03.24.644582v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/7b9b1a76a531/nihpp-2025.03.24.644582v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/2d82bb8c5592/nihpp-2025.03.24.644582v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4618/11974738/67077a082c9c/nihpp-2025.03.24.644582v1-f0006.jpg

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本文引用的文献

[1]
Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.

Cell. 2024-12-12

[2]
CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics.

Nat Protoc. 2025-1

[3]
CXCL9/10-engineered dendritic cells promote T cell activation and enhance immune checkpoint blockade for lung cancer.

Cell Rep Med. 2024-4-16

[4]
Unraveling the role of M1 macrophage and CXCL9 in predicting immune checkpoint inhibitor efficacy through multicohort analysis and single-cell RNA sequencing.

MedComm (2020). 2024-3-1

[5]
Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8 T-myeloid cell networks in melanoma.

Sci Immunol. 2024-2-2

[6]
Deciphering head and neck cancer microenvironment: Single-cell and spatial transcriptomics reveals human papillomavirus-associated differences.

J Med Virol. 2024-1

[7]
B-cell infiltration is associated with survival outcomes following programmed cell death protein 1 inhibition in head and neck squamous cell carcinoma.

Ann Oncol. 2024-4

[8]
Spatial and Single-Cell Transcriptomics Reveal a Cancer-Associated Fibroblast Subset in HNSCC That Restricts Infiltration and Antitumor Activity of CD8+ T Cells.

Cancer Res. 2024-1-16

[9]
Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response.

Nat Commun. 2023-8-18

[10]
macrophage polarity identifies a network of cellular programs that control human cancers.

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