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Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping.

ABSTRACT: The functional diversity of natural killer (NK) cell repertoires stems from differentiation, homeostatic, receptor-ligand interactions and adaptive-like responses to viral infections. In the present study, we generated a single-cell transcriptional reference map of healthy human blood- and tissue-derived NK cells, with temporal resolution and fate-specific expression of gene-regulatory networks defining NK cell differentiation. Transfer learning facilitated incorporation of tumor-infiltrating NK cell transcriptomes (39 datasets, 7 solid tumors, 427 patients) into the reference map to analyze tumor microenvironment (TME)-induced perturbations. Of the six functionally distinct NK cell states identified, a dysfunctional stressed CD56^bright state susceptible to TME-induced immunosuppression and a cytotoxic TME-resistant effector CD56^dim state were commonly enriched across tumor types, the ratio of which was predictive of patient outcome in malignant melanoma and osteosarcoma. This resource may inform the design of new NK cell therapies and can be extended through transfer learning to interrogate new datasets from experimental perturbations or disease conditions.

SUBMITTER: Netskar H

PROVIDER: S-EPMC11291284 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping.

Netskar Herman H Pfefferle Aline A Goodridge Jodie P JP Sohlberg Ebba E Dufva Olli O Teichmann Sarah A SA Brownlie Demi D Michaëlsson Jakob J Marquardt Nicole N Clancy Trevor T Horowitz Amir A Malmberg Karl-Johan KJ

Nature immunology 20240702 8

The functional diversity of natural killer (NK) cell repertoires stems from differentiation, homeostatic, receptor-ligand interactions and adaptive-like responses to viral infections. In the present study, we generated a single-cell transcriptional reference map of healthy human blood- and tissue-derived NK cells, with temporal resolution and fate-specific expression of gene-regulatory networks defining NK cell differentiation. Transfer learning facilitated incorporation of tumor-infiltrating NK ...[more]

PMID: 38956379

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Project description:An emerging cellular immunotherapy for cancer is based on the cytolytic activity of natural killer (NK) cells against a wide range of tumors. Although in vitro activation, or "priming," of NK cells by exposure to pro-inflammatory cytokines, such as interleukin (IL)-2, has been extensively studied, the biological consequences of NK cell activation in response to target cell interactions have not been thoroughly characterized. We investigated the consequences of co-incubation with K562, CTV-1, Daudi RPMI-8226, and MCF-7 tumor cell lines on the phenotype, cytokine expression profile, and transcriptome of human NK cells. We observe the downregulation of several activation receptors including CD16, CD62L, C-X-C chemokine receptor (CXCR)-4, natural killer group 2 member D (NKG2D), DNAX accessory molecule (DNAM)-1, and NKp46 following tumor-priming. Although this NK cell phenotype is typically associated with NK cell dysfunction in cancer, we reveal the upregulation of NK cell activation markers, such as CD69 and CD25; secretion of pro-inflammatory cytokines, including macrophage inflammatory proteins (MIP-1) α /β and IL-1β/6/8; and overexpression of numerous genes associated with enhanced NK cell cytotoxicity and immunomodulatory functions, such as FAS, TNFSF10, MAPK11, TNF, and IFNG. Thus, it appears that tumor-mediated ligation of receptors on NK cells may induce a primed state which may or may not lead to full triggering of the lytic or cytokine secreting machinery. Key signaling molecules exclusively affected by tumor-priming include MAP2K3, MARCKSL1, STAT5A, and TNFAIP3, which are specifically associated with NK cell cytotoxicity against tumor targets. Collectively, these findings help define the phenotypic and transcriptional signature of NK cells following their encounters with tumor cells, independent of cytokine stimulation, and provide insight into tumor-specific NK cell responses to inform the transition toward harnessing the therapeutic potential of NK cells in cancer.

Project description:ObjectiveInfiltrating immune cells play a central role in degenerative joint disease associated with osteoarthritis (OA) and particle-mediated periprosthetic osteolysis. The goal of this study was to characterize a newly identified population of synovial tissue-infiltrating natural killer (NK) cells obtained from patients with OA or patients with periprosthetic joint inflammation.MethodsSynovial and interfacial tissue samples were collected from patients with OA who were undergoing primary or revision total joint replacement (TJR) surgery. The histologic features of OA synovium obtained from patients undergoing primary surgery and interfacial tissue obtained from patients undergoing revision surgery were determined by immunohistochemistry and immunofluorescence. Synovial tissue-infiltrating NK cells were evaluated for the expression of surface receptors, using flow cytometry. Chemoattractant and cytokine protein and RNA levels in synovial and interfacial tissue and fluid were assessed by Luminex assay and real-time quantitative polymerase chain reaction. Cytokine production and degranulation by stimulated synovial tissue versus normal blood NK cells were evaluated by intracellular cytokine staining.ResultsNK cells comprised nearly 30% of the CD45+ mononuclear cell infiltrate in synovial tissue obtained from patients undergoing primary TJR and from patients undergoing revision TJR. NK cells from both groups expressed CXCR3, CCR5, L-selectin, α4 integrins, and cutaneous lymphocyte antigen. Synovial fluid from patients undergoing revision surgery contained elevated concentrations of the NK cell attractants CCL4, CCL5, CXCL9, and CXCL10; all levels in synovial fluid obtained from patients undergoing revision surgery were higher than those in synovial fluid from patients undergoing primary surgery. Cytokine-stimulated interferon-γ production was significantly impaired in NK cells derived from primary and revision TJRs compared with blood NK cells.ConclusionNK cells are a principal tissue-infiltrating lymphocyte subset in patients with OA and patients with periprosthetic inflammation and display a quiescent phenotype that is consistent with postactivation exhaustion.

Project description:Objective: Neoadjuvant chemoimmunotherapy has improved outcomes in resectable non-small cell lung cancer (NSCLC), yet its real-world implementation is often challenged by surgical delays, cancellations, immune-related fibrosis, and increased postoperative complications. Smokers with NSCLC, despite being at higher risk for postoperative complications, have enhanced responses to neoadjuvant chemoimmunotherapy. This study aimed to identify smoking-associated immune cell determinants that could inform treatment strategies. Methods: Single-cell RNA sequencing was performed on 61 lung samples from non-smokers, smokers, and patients with chronic obstructive pulmonary disease (COPD), as well as 8 invasive lung adenocarcinomas, to define smoking-related immune signatures. Using RNA sequencing data from 102 resected NSCLC and 24 NSCLC patients treated with neoadjuvant chemoimmunotherapy, we conducted in silico deconvolution to evaluate associations between cellular composition and clinical outcomes. Results: Among 140 lung cellular phenotypes, two natural killer (NK) cell subsets were strongly associated with smoking and COPD severity. “Stress-responsive NK (NKSR)” cells exhibited immature features and cytokine-responsive signatures. “Exhausted NK (NKExh)” cells showed mature features and elevated multiple immune checkpoint expression (PDCD1, TIGIT, and LAG3). Abundant intratumoral NKSR cells were associated with significantly improved survival after surgery, particularly in current smokers. Conversely, tumors with low NKSR and high NKExh cell profiles were associated with better responses to neoadjuvant chemoimmunotherapy. Conclusions: Tumor-infiltrating NK cell phenotyping may aid in therapeutic stratification in smokers with NSCLC. NKSR cell preservation predicts favorable outcomes with upfront surgery, while NKExh cell enrichment indicates greater benefit from neoadjuvant chemoimmunotherapy. These profiles may help optimize treatment by balancing therapeutic benefit and risk.

Dataset Information

Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping.

Publications

Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping.

Similar Datasets

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