Single-Cell RNA-Seq Analysis of Patient Myeloid-Derived Suppressor Cells and the Response to Inhibition of Bruton's Tyrosine Kinase.
Himanshu SavardekarCarter AllenHyeongseon JeonJianying LiDionisia QuirogaEmily SchwarzRichard C WuSara ZelinskasGabriella LapurgaAlexander AbreoAndrew StiffJami ShafferBradley W BlaserMatthew OldRobert WesolowskiGang XinKari L KendraDongjun ChungWilliam E CarsonPublished in: Molecular cancer research : MCR (2023)
Myeloid-derived suppressor cell (MDSC) levels are elevated in cancer patients and contribute to reduced efficacy of immune checkpoint therapy. MDSC express Bruton's Tyrosine Kinase (BTK) and BTK inhibition with ibrutinib, an FDA-approved irreversible inhibitor of BTK, leads to reduced MDSC expansion/function in mice and significantly improves the anti-tumor activity of anti-PD-1 antibody treatments. Single-cell RNA sequencing (scRNA-seq) was used to characterize the effect of ibrutinib on gene expression of fluorescence activated cell sorting-enriched MDSC from patients with different cancer types (breast, melanoma, head and neck squamous cell cancer - HNSCC). Melanoma patient MDSC were treated in vitro for 4h with 5 µM ibrutinib or DMSO, processed for scRNA-seq using the Chromium 10x Genomics platform, and analyzed via the Seurat v4 standard integrative workflow. Baseline gene expression of MDSC from breast, melanoma, and HNSCC cancer patients revealed similarities among the top expressed genes. In vitro ibrutinib treatment of MDSC from melanoma patients resulted in significant changes in gene expression. GBP1, IL 1β and CXCL8 were among the top downregulated genes while RGS2 and ABHD5 were among the top upregulated genes (p<0.001). Double positive CD14+CD15+ MDSC and PMN-MDSC responded similarly to BTK inhibition and exhibited more pronounced gene changes compared to early MDSC and M-MDSC. Pathway analysis revealed significantly downregulated pathways including TREM1, nitric oxide signaling, and IL 6 signaling (p<0.004). Implications: ScRNA-seq revealed characteristic gene expression patterns for MDSC from different cancer patients and BTK inhibition led to the downregulation of multiple genes and pathways important to MDSC function and migration.
Keyphrases
- single cell
- tyrosine kinase
- rna seq
- gene expression
- high throughput
- epidermal growth factor receptor
- genome wide
- squamous cell
- dna methylation
- nitric oxide
- newly diagnosed
- stem cells
- cell proliferation
- squamous cell carcinoma
- hydrogen peroxide
- young adults
- induced apoptosis
- chronic lymphocytic leukemia
- skeletal muscle
- cell therapy
- oxidative stress
- signaling pathway
- basal cell carcinoma
- cell death
- data analysis