Transcriptional profiling of human myeloid cells in healthy donors and oral cavity cancer (OCSCC) patients

This single-cell RNA sequencing (scRNA-seq) dataset profiles human myeloid cells from healthy donors and patients with advanced oral cavity squamous cell carcinoma (OCSCC). scRNA-seq was performed on isolated CD11b? cells from high- and low-density peripheral blood fractions and on isolated CD45? tumor-infiltrating cells from OCSCC patients (n=8), as well as on CD11b? high- and low-density peripheral blood cells from healthy donors (n=5). The dataset enables the characterization of compartment-specific transcriptional states of human myeloid cells and supports investigations into genes and pathways associated with pathologic activation and immune suppression. Overall design: This study (ClinicalTrials.gov identifier NCT03429036) was approved by the National Institutes of Health Institutional Review Board (IRB). Fresh peripheral blood and tumor samples were collected from 8 patients with newly diagnosed oral cavity squamous cell carcinoma (OCSCC) undergoing standard-of-care surgical procedures. All patients signed IRB-approved informed consent permitting the use of their blood and tumor tissue for research. Peripheral blood samples from 5 healthy donors were also obtained at the National Institutes of Health Clinical Center under informed consent. For single-cell profiling, whole blood was separated into high-density and low-density fractions by Ficoll-based density gradient centrifugation. CD11b? myeloid cells were enriched from both fractions in cancer patients and healthy donors to capture circulating myeloid populations. Tumor specimens were mechanically and enzymatically dissociated into single-cell suspensions, from which CD45? leukocytes were isolated. Enriched suspensions from each compartment (blood high-density CD11b?, blood low-density CD11b?, and tumor-infiltrating CD45?) were immediately processed for scRNA-seq using the 10x Genomics Chromium platform. This design allowed direct comparison of myeloid transcriptional states across circulation and tumor microenvironments in both healthy donors and OCSCC patients.