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Single-cell RNA sequencing reveals cellular and molecular immune profile in a Pembrolizumab-responsive PD-L1-negative lung cancer patient

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Abstract

High expression of PD-L1 predicts PD-1/PD-L1 inhibitor benefit, meanwhile a few PD-L1-negative patients still benefit from these drugs. In this study, we aimed to explore the underlying cellular and molecular characteristics via single-cell sequencing. Before and after treatment with Pembrolizumab, peripheral blood mononuclear cells (PBMCs) were isolated via Ficoll gradient. Thereafter, single-cell RNA sequencing was performed, and clinical significance was validated with The Cancer Genome Atlas (TCGA) cohort. All 3423 cells of 16 clusters were classified into eight cell types, including NKG7+ T, NKG7+ NK, Naïve T, CDC1C+ dendritic cells, CD8+ T cells, B cells, macrophages and erythrocytes. Cell proportion, the clinical significance of differentially expressed genes and significant pathways of NKG7+ T, NKG7+ NK, Naïve T and CD8+ T cells were analyzed. Ubiquitin-mediated proteolysis/cell cycle/natural killer cell-mediated cytotoxicity were identified as PD-1 blockage-responsive pathways in NKG7+ NK cells. Apoptosis/Th1 and Th2 cell differentiation were proposed as Pembrolizumab-affected pathways in NKT cells. In gene level, ID2, PIK3CD, UQCR10, MATK, MZB1, IL7R and TRGC2 showed a significant correlation with PD-1 expression after TCGA dataset validation, which could possess potential as predictive markers for patients with PD-L1-negative lung squamous cell carcinoma who can benefit from Pembrolizumab.

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All relevant data can be acquired by contacting the correspondent author.

Abbreviations

FDA:

Food and Drug Administration

KEGG:

Kyoto Encyclopedia of Genes and Genomes

NK:

Natural killer

NSCLC:

Non-small cell lung cancer

PBMCs:

Peripheral blood mononuclear cells

PD-1:

Programmed cell death 1

PD-L1:

Programmed cell death 1 ligand 1

TCGA:

The Cancer Genome Atlas

t-SNE:

t-distributed Stochastic Neighbor Embedding

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Funding

This work was supported by the Natural Science Foundation of Shanghai (19ZR1449700) and Shanghai Chest Hospital-Collaborative Innovation Project (YJXT20190204).

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Author notes

  1. Runbo Zhong and Yunbin Zhang are equal contribution.

Authors and Affiliations

  1. Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Huaihai West Road No.241, Shanghai, 200030, China

    Runbo Zhong, Dongfang Chen, Shuhui Cao, Baohui Han & Hua Zhong

  2. Department of Critical Care, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China

    Yunbin Zhang

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  1. Runbo Zhong
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  6. Hua Zhong
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Contributions

Runbo Zhong (RZ) and Yunbin Zhang (YZ) conducted the single-cell sequencing and bioinformatics analysis. Dongfang Chen (DC) collected the samples and Shuhui Cao (SC) collected the clinical data. Baohui Han (BH) and Hua Zhong (HZ) designed the study and revised the manuscript.

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Correspondence to Baohui Han or Hua Zhong.

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The ethics committee of Shanghai Chest Hospital approved our study, and the patient provided written inform consent.

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Zhong, R., Zhang, Y., Chen, D. et al. Single-cell RNA sequencing reveals cellular and molecular immune profile in a Pembrolizumab-responsive PD-L1-negative lung cancer patient. Cancer Immunol Immunother 70, 2261–2274 (2021). https://doi.org/10.1007/s00262-021-02848-0

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