Identification of a drug-response gene in multiple myeloma through longitudinal single-cell transcriptome sequencing.

Multiple myeloma (MM) is a life-threatening, chronic, and incurable hematological malignancy, which is characterized by clonal proliferation of malignant plasma cells. Despite recent therapeutic advances, relapse is very common during a long-term exposure to drugs with no therapeutic effects. Here, we conducted longitudinal single-cell transcriptome sequencing (scRNA-seq) of bone marrow cells from a single patient with relapsed and refractory MM, who had been treated with multiple anti-myeloma drugs, and found five UMAP subclusters (clusters 0-4) of MM cells, which appeared and/or disappeared in response to the therapeutic pressure. A small cell cluster 3, which emerged during lenalidomide treatment and disappeared after the addition of a proteasome inhibitor (PI), ixazomib. Among the differentially expressed genes in cluster 3, we found a candidate drug-response gene; pellino E3 ubiquitin protein ligase family member 2 (PELI2), which is responsible for PI-induced cell death in in vitro cell cultured assay. Kaplan-Meier survival analysis of datasets from pan-cancer prognostic database revealed that higher expression of PELI2 is associated with better prognosis. The data of this study suggest that PELI2 is a predictive biomarker of the PI response in patients with MM. Our integrated strategy combining longitudinal scRNA-seq analysis, in vitro functional assay, and database analysis would facilitate the understanding of clonal dynamics of MM in response to anti-myeloma drugs and identification of drug response genes. Longitudinal scRNA-seq of myeloma cells from a patient with relapse and refractory disease.

多发性骨髓瘤（Multiple myeloma, MM）是一类致命、慢性且无法治愈的血液系统恶性肿瘤，以恶性浆细胞的克隆性增殖为核心特征。尽管近年来治疗手段取得进展，但在长期使用无治疗获益的药物过程中，疾病复发仍极为常见。本研究对一名经多种抗骨髓瘤药物治疗的复发难治性MM患者的骨髓细胞开展了纵向单细胞转录组测序（single-cell RNA sequencing, scRNA-seq），共鉴定出5个MM细胞的UMAP亚簇（簇0至4），这些亚簇会随治疗压力的施加出现或消失。其中小细胞簇3在来那度胺（lenalidomide）治疗期间出现，在联用蛋白酶体抑制剂（proteasome inhibitor, PI）伊沙佐米（ixazomib）后消失。对簇3的差异表达基因进行分析后，我们发现了一个候选药物响应基因：pellino E3泛素蛋白连接酶家族成员2（PELI2），体外细胞培养实验证实其介导了PI诱导的细胞死亡。基于泛癌预后数据库的Kaplan-Meier生存分析结果显示，PELI2高表达与更优的临床预后显著相关。本研究数据表明，PELI2可作为MM患者对PI治疗产生响应的预测生物标志物。本研究采用的整合策略——结合纵向scRNA-seq分析、体外功能实验与数据库分析——将有助于阐明MM细胞在抗骨髓瘤药物作用下的克隆动力学特征，并推动药物响应基因的鉴定工作。本研究的测序数据来源于一名复发难治性疾病患者的骨髓瘤细胞纵向单细胞转录组测序。