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

Supplementary 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. Supplementary Table 5. Sheet A: 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 < 0.01, absolute log2 fold change > 1, and expression in at least 25% of cells in the upregulated group are included. Sheet B: Results of GO biological process enrichment analysis performed using clusterProfiler on upregulated and downregulated genes from each patient comparison. Multiple testing correction was performed using the Benjamini-Hochberg method. Only terms with q-value < 0.01 are shown. Supplementary Table 6. Proportions of cells at four cell cycle phases (G0, G1, S, and G2M) at diagnosis (DG) and their changes after relapse (REL) in four aggressive MCL patients. Statistical analysis was performed using chi-square test. Supplementary Table 7. Characterization of lymphoma sub-clones detected using CNV inference. Sheet A: Cell counts and proportions (prop) relative to total MCL cells in each subclone at diagnosis (DG) and relapse (REL). prop_FC – proportion fold change at relapse compared to diagnosis (calculated as prop_REL/prop_DG for expanding clones, or prop_DG/prop_REL for contracting clones). Subclone labels indicate putative treatment sensitivity: "Sens" denotes subclones that contracted or disappeared at relapse (suggesting chemotherapy sensitivity), while "Res" denotes subclones that expanded at relapse (suggesting chemotherapy resistance). Sheet B: CNV profiles of MCL subclones identified through inferCNV analysis. Each row specifies chromosomal coordinates (chr, start, end), copy number state (cn), cytogenetic location (cytobands), and genes within altered regions. Copy number states: cn=1 (deletion), cn=2 (normal), cn=3+ (amplification). Supplementary Table 8. Differential gene expression analysis between resistant and sensitive MCL subclones. Sheet A: Summary of pairwise subclone comparisons. For each comparison between resistant (Res) and sensitive (Sens) subclones, the table reports counts of total, upregulated and downregulated differentially expressed genes and their ratio, enriched Gene Ontology (GO) terms and Hallmark gene sets in each direction. Sheet B: Complete list of differentially expressed genes from all pairwise subclone comparisons. Each row represents a single gene with statistical metrics including p-value, adjusted p-value, average log2 fold change (avg_log2FC), expression percentages in each subclone (pct.1, pct.2), regulatory direction (up/down), and gene description. Sheet C: Gene Ontology (GO) enrichment analysis results for differentially expressed genes. Only significantly enriched (q-value < 0.05) biological processes are shown with enrichment statistics including gene ratio, background ratio, fold enrichment, z-score, adjusted p-values, and lists of genes contributing to each enriched term. Sheet D: Hallmark gene set enrichment analysis (GSEA) results identifying coordinated expression programs differentially active between resistant and sensitive subclones. Results include normalized enrichment scores (NES), statistical significance, leading edge metrics, and core enrichment genes for each pathway. Supplementary Table 9. Somatic variants in P069 samples. The variants were identified using a consensus approach integrating three variant callers (Mutect2, VarScan2, and Strelka2) and filtered using SomaticSeq with a PASS threshold score of 0.5. The table includes sample identifiers, genomic coordinates (hg38), variant allele frequencies (VAF) and genotypes (GT) for matched normal and tumor samples, sequencing depth (DP), and comprehensive functional annotations generated by Funcotator using GENCODE and HGNC databases. Key annotation fields include gene symbols, variant classifications, transcript information, protein changes, and gene ontology details. Only variants passing consensus filtering criteria with VAF ≥1% for heterozygous and ≥85% for homozygous calls are included. Supplementary Data Object 1. SingleCellExperiment object with 57751 cells post-QC and 36601 genes. Data columns include sample, patient, timepoint, compartment, cell type annotation (cell_type_manual), cell cycle phase (tricyclePhase), tumor subclones (subclone_label).补充表4 患者P009的光学基因组图谱（optical genomic mapping）分析结果。本表收录了诊断与复发阶段共有的基因组畸变，以及仅在诊断阶段或复发阶段单独出现的基因组畸变。 补充表5 表A：采用威尔科克森秩和检验（Wilcoxon rank-sum test），对4例患者（P009、P022、P027、P087）的复发与诊断阶段套细胞淋巴瘤（Mantle Cell Lymphoma, MCL）细胞进行差异基因表达分析的结果。仅纳入校正后p值<0.01、绝对log2倍数变化>1，且上调组中至少25%的细胞检测到表达的基因。表B：采用clusterProfiler软件，对每例患者配对比较得到的上调与下调基因进行基因本体（Gene Ontology, GO）生物学过程富集分析的结果。采用本雅明尼-霍赫贝格法（Benjamini-Hochberg method）进行多重检验校正，仅展示q值<0.01的条目。 补充表6 4例侵袭性套细胞淋巴瘤患者诊断阶段（DG）的细胞在G0、G1、S、G2M四个细胞周期时相的占比，以及复发阶段（REL）的占比变化情况。采用卡方检验进行统计学分析。 补充表7 基于拷贝数变异（Copy Number Variation, CNV）推断检测到的淋巴瘤亚克隆特征。表A：诊断阶段（DG）与复发阶段（REL）各亚克隆的细胞数及其占总套细胞淋巴瘤细胞的比例（prop）。prop_FC为复发阶段相较于诊断阶段的比例倍数变化（扩增克隆的计算方式为prop_REL/prop_DG，缩减克隆的计算方式为prop_DG/prop_REL）。亚克隆标签代表推测的治疗敏感性：“Sens”表示在复发阶段缩减或消失的亚克隆（提示对化疗敏感），“Res”表示在复发阶段扩增的亚克隆（提示对化疗耐药）。表B：通过inferCNV分析鉴定的套细胞淋巴瘤亚克隆的拷贝数变异图谱。每一行标注了染色体坐标（chr、起始位点、终止位点）、拷贝数状态（cn）、细胞遗传学定位（染色体带型，cytobands）以及变异区域内的基因。拷贝数状态定义为：cn=1为缺失，cn=2为正常，cn=3+为扩增。 补充表8 耐药与敏感套细胞淋巴瘤亚克隆间的差异基因表达分析结果。表A：亚克隆两两比较汇总信息。针对耐药（Res）与敏感（Sens）亚克隆的每一组配对比较，本表列出了总差异表达基因、上调差异表达基因、下调差异表达基因的数量及其比值，以及两个方向上富集的基因本体（GO）条目与标志性基因集（Hallmark gene sets）。表B：所有亚克隆两两比较得到的差异表达基因完整列表。每一行对应单个基因，包含统计学指标：p值、校正后p值、平均log2倍数变化（avg_log2FC）、各亚克隆中的表达占比（pct.1、pct.2）、调控方向（上调/下调）以及基因描述信息。表C：差异表达基因的基因本体富集分析结果。仅展示q值<0.05的显著富集生物学过程，附带富集统计指标：基因比值、背景比值、富集倍数、z得分、校正后p值，以及每个富集条目对应的贡献基因列表。表D：标志性基因集富集分析（Hallmark gene set enrichment analysis, GSEA）结果，用于鉴定耐药与敏感亚克隆间差异活跃的协同表达程序。结果包含每条通路的标准化富集得分（NES）、统计学显著性、前沿指标（leading edge metrics）以及核心富集基因。 补充表9 样本P069中的体细胞变异。本数据集通过整合3款变异检测工具（Mutect2、VarScan2、Strelka2）的共识方法鉴定变异，并采用SomaticSeq软件以0.5的PASS阈值评分进行过滤。本表收录了匹配的正常与肿瘤样本的样本标识符、基因组坐标（hg38）、变异等位基因频率（VAF）、基因型（GT）、测序深度（DP），以及由Funcotator工具基于GENCODE和HGNC数据库生成的全面功能注释信息。核心注释字段包括基因符号、变异分类、转录本信息、蛋白质改变以及基因本体细节。仅纳入符合共识过滤标准的变异：杂合变异的VAF≥1%，纯合变异的VAF≥85%。 补充数据对象1：质控后包含57751个细胞与36601个基因的SingleCellExperiment对象。数据列包含样本、患者、时间点、细胞分区、细胞类型注释（cell_type_manual）、细胞周期时相（tricyclePhase）以及肿瘤亚克隆（subclone_label）。