Single Cell RNA Transcriptomics of Mantle Cell Lymphoma Reveals the Presence of Treatment-Resistant Subclones at the Time of Diagnosis - Supplementary Data

Supplemental Table 4. Results of optical genomic mapping for patient P009. The table lists genomic aberrations shared for diagnosis and relapse and those exclusive at both timepoints. Supplemental Table 5. Results of differential gene expression analysis between relapse and diagnosis MCL cells of four patients (P009, P022, P027 and P087) performed using Wilcoxon rank-sum test. Only genes with adjusted p-value < 0.05, absolute log2 fold change > 1, and expression in at least 25% of relapse cells are included. Supplemental Table 9. Copy number (CN) variations of the subclones detected using inferCNV. Supplemental Table 10. Copy number variations of the subclones detected using inferCNV clustering and intersected with copy number variations predicted using WES data. Supplemental Table 11. Gene Set Enrichment Analysis (GSEA) of GO Biological Processes for resistant vs. sensitive subclones at diagnosis. GSEA results showing enriched GO Biological Process terms in resistant versus sensitive MCL subclones at diagnosis for each patient (P009, P022, P027, P087). Positive NES values indicate enrichment in resistant subclones. Only terms with q-value < 0.05 are shown. Supplemental Table 12. Gene Set Enrichment Analysis of Hallmark pathways for resistant vs. sensitive subclones at diagnosis. GSEA results showing enriched MSigDB Hallmark pathways in resistant versus sensitive MCL subclones at diagnosis for each patient (P009, P022, P027, P087). Positive NES values indicate enrichment in resistant subclones. Only terms with q-value < 0.05 are shown. Supplemental Table 13. Results of differential gene expression comparison between relapse and diagnosis MCL cells of four patients (P009, P022, P027 and P087) performed using Wilcoxon rank-sum test. Only genes with adjusted p-value < 0.05, absolute log2 fold change > 1, and expression in at least 25% of cells in the upregulated group are included. Supplemental Table 14. Somatic nucleotide variants detected in P069 PBMC at diagnosis and in the infiltrated intestine (Int) at relapse. The variants were called using Mutect2 and annotated using Gencode43 database. Supplemental Data Object 1. SingleCellExperiment object with 58 702 cells passed QC and 36601 genes. Data columns include sample, patient, timepoint, compartment, cell type annotation (cell_type), cell cycle phase (Phase), tumor subclones (inferCNV_subclone).