A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery

We developed a single-cell transcriptomics pipeline for high-throughput pharmacotranscriptomic screening. We explored the transcriptional landscape of three HGSOC models (JHOS2, a representative cell line; PDC2 and PDC3, two patient-derived samples) after treating their cells for 24 hours with 45 drugs representing 13 distinct classes of mechanism of action. Our work establishes a new precision oncology framework for the study of molecular mechanisms activated by a broad array of drug responses in cancer.
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├── 3D UMAPs/ → Interactive 3D UMAPs of cells treated with the 45 drugs used for multiplexed scRNA-seq. Related to Figure 4.
Coordinates: x = UMAP 1; y = UMAP 2; z = UMAP 3.
Legend: green = PDC1; blue = PDC2; red = JHOS2.
│ ├── DMSO_3D_UMAP_Dini.et.al.html → 3D UMAP of untreated cells.
│ └── drug_3D_UMAP_Dini.et.al.html → 3D UMAP of cells treated with (drug).
├── QC_plots/ → Diagnostic plots. Related to Figures 2–4.
│ ├── model_QC_violin_plot_2023.pdf → Violin plots of the QC metrics used to filter the data.
│ ├── model_col_HTO or model_row_HTO before and after filt → Heatmaps of the row or column HTO expression in each cell.
│ └── model_counts_histogram_2023.pdf → Histogram of the distribution of the total counts per cell after filtering for high-quality cells.
├── scRNAseq/ → scRNA-seq data. Related to Figures 2–4.
│ ├── AllData_subsampled_DGE_edgeR.csv.gz → Differential gene expression analyses results between treated and untreated cells via pseudobulk of aggregate subsamples, for each of the three models. Related to Figure 3.
│ └── All_vs_all_RNAclusters_DEG_signif.txt → Differential gene expression analysis results (p.adj < 0.05) of FindAllMarkers for the Leiden/RNA clusters.
├── PDCs.transcript.counts.tsv → Bulk RNA-seq count data for PDCs 1–3 processed by Kallisto. Related to Figure S6.
└── PDCs.transcript.TPM.tsv → Bulk RNA-seq TPM data for PDCs 1–3 processed by Kallisto. Related to Figure S6.

本研究团队开发了一套针对高通量药理转录组学筛选的单细胞转录组学分析流程。我们针对三种高级别浆液性卵巢癌（HGSOC）模型（JHOS2，一种代表性细胞系；PDC2和PDC3，两种患者来源的样本）进行了处理，其细胞在经过24小时与代表13种不同作用机制类别的45种药物处理后，探讨了其转录组景观。本研究为研究由广泛药物反应激活的分子机制建立了一种新的精准肿瘤学框架。