Cell | A Pan-Cancer Single Cell Panorama of Human Natural Killer Cells
On Aug. 21st, 2023, the Zhang Lab from Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG) in Peking University, collaborating with Hui Peng’s team from University of Science and Technology of China, published a paper entitled “A Pan-Cancer Single-Cell Panorama of Human Natural Killer Cells” in Cell, which collected a broad spectrum of published and newly generated scRNA-seq data to construct a comprehensive tumor-infiltrating human NK cell atlas and explored the heterogeneity of NK cells across cancer types and tissues.
Enabling new technologies and interpreting complex phenomena through bioinformatics has become a powerful tool for exploring and solving important scientific questions. Recently, single-cell RNA sequencing (scRNA-seq) technologies have facilitated the characterization of the heterogeneity of tumor-infiltrating immune cells1. This study focused on Natural killer (NK) cells, which serve as alternative sources of cytotoxic activities and combat tumor cells with low mutation load and aberrant expression of MHC class I compared with T cells2. However, previous reports of NK cell subpopulations and their function lacked systematical analyses, given that within the tumor tissue NK cells are relatively rare among CD45+ cells. Thus, it is essential to build such a large-scale single-cell human NK cell atlas to overcome the difficulty. These data covered 24 cancer types, including 1,223 samples from 716 patients across different tissues, and 60 healthy controls. To unbiasedly define the pan-cancer population structure of NK cells, this work integrated scRNA-seq data with minimal batch effects among datasets and performed unsupervised clustering. Based on the high expression of canonical cell markers, NCAM1 and FCGR3A, two well-characterized major cell types, CD56brightCD16lo and CD56dimCD16hi, were distinguished. Specifically, the CD56brightCD16lo compartment can be further subdivided into 5 subsets, whereas 9 CD56dimCD16hi subsets were identified (Figure 1). The phenotype and heterogeneity of these NK cell populations as well as their subsets were systematically characterized in this study.
Figure 1: Scheme of the overall study design
Based on the integrative data, remarkable compositional changes in NK cell subsets were exhibited across tissues, including blood, tumor and adjacent non-tumor tissues. Differentially expressed genes between blood and tissue were selected to further assess their sensitivity and specificity to distinguish the tissue origin of NK cells. Consequently, RGS1 (Regulator of G protein signaling 1) was pronouncedly recognized, which was exclusively expressed in NK cells within tumor and adjacent non-tumor tissues, but barely detectable in blood. Compared with aforementioned conventional tissue-resident markers, RGS1 showed much higher sensitivity and specificity. Thus, this work recognized RGS1 as a key marker of tissue-infiltrating NK cells at the transcriptome level.
In the tumor microenvironment (TME), a tumor-enriched NK cell subset in potentially dysfunctional states was identified and named as TaNK cells. TaNK cells had lower expression of cytotoxic granules, and higher expression of inhibitory receptors and stress-associated genes. The high abundance of these cells was related to unfavorable prognosis and immunotherapy resistance in multiple cancer types. Further exploration of larger cohorts is expected to corroborate the functional roles of TaNK cells in both tumor progression and immune checkpoint blockade (ICB) treatment. These findings implicate the role of TaNK cells in clinical settings, and provide new insights into NK-cell-based immunotherapy. In addition, the bioinformatic analyses and experimental evidence support myeloid cells as core mediators of NK cells. Specifically, LAMP3+ DCs can serve as a crucial regulator and potentially inhibit CD56dimCD16hi NK cells (Figure 2).
Figure 2: Major findings of this study
In summary, the comprehensive analyses enhance the current understanding of NK cells from a pan-cancer view, revealing composition changes of NK cell populations as well as their expression pattern. The large-scale data can provide a platform for the exploration of biomarker, and further promote the application of NK cell-based immunotherapy to a broader range of cancer patients.
Ph.D. candidate Fei Tang, Ph.D. candidate Jinhu Li are the co-first authors of the paper. Prof. Zemin Zhang, Dr. Dongfang Wang, Prof. Hui Peng and Dr. Linnan Zhu are the co-corresponding authors of the paper. The project was funded by the National Natural Science Foundation of China and Beijing Municipal Science and Technology Commission.
1、Stuart, T., and Satija, R. (2019). Integrative single-cell analysis. Nature Reviews Genetics 20, 257-272. 10.1038/s41576-019-0093-7.
2、Myers, J.A., and Miller, J.S. (2021). Exploring the NK cell platform for cancer immunotherapy. Nature Reviews Clinical Oncology 18, 85-100. 10.1038/s41571-020-0426-7.