Single-Cell Transcriptomes Combining with Consecutive Genomics Reveal Clonal Evolution and Gene Regulatory Networks in Relapsed and Refractory Multiple Myeloma.

Jiadai Xu,Zheng Wei,Liang Ren,Yian Zhang,Yawen Wang,Shiyang Gu,Yifeng Sun,Yu Zhang,Panpan Li,Chen Chen,Jifeng Jiang,Yue Wang,Peng Liu,Jing Li,Jingli Zhuang

doi:10.3389/fcell.2021.794144

Abstract

This study attempted to investigate how clonal structure evolves, along with potential regulatory networks, as a result of multiline therapies in relapsed/refractory multiple myeloma (RRMM). Eight whole exome sequencing (WES) and one single cell RNA sequencing (scRNA-seq) were performed in order to assess dynamic genomic changes in temporal consecutive samples of one RRMM patient from the time of diagnosis to death (about 37 months). The 63-year-old female patient who suffered from MM (P1) had disease progression (PD) nine times from July 2017 [newly diagnosed (ND)] to Aug 2020 (death), and the force to drive branching-pattern evolution of malignant PCs was found to be sustained. The mutant-allele tumor heterogeneity (MATH) and tumor mutation burden (TMB) initially exhibited a downward trend, which was then upward throughout the course of the disease. Various somatic single nucleotide variants (SNVs) that had disappeared after the previous treatment were observed to reappear in later stages. Chromosomal instability (CIN) and homologous recombination deficiency (HRD) scores were observed to be increased during periods of all progression, especially in the period of extramedullary plasmacytoma. Finally, in combination with WES and scRNA-seq of P1-PD9 (the nineth PD), the intro-heterogeneity and gene regulatory networks of MM cells were deciphered. As verified by the overall survival of MM patients in the MMRF CoMMpass and GSE24080 datasets, RUNX3 was identified as a potential driver for RRMM.

Highlights

Multiple myeloma (MM) is a plasma cell malignancy that is characterized by highly intra-clonal heterogeneity
whole exome sequencing (WES) was conducted with a mean coverage depth of 167× for CD138 + plasma cells and 173× for PB mononuclear cells (PBMC), consistent with the recommendations for WES
Temporal consecutive genetic analysis provided evidence of heterogeneity in MM and unmasked the evolutionary trajectories of plasma cells (PCs) derived by multi-line therapies

Summary

Introduction

Multiple myeloma (MM) is a plasma cell malignancy that is characterized by highly intra-clonal heterogeneity. Large-scale genomic sequencing studies have provided deep insights into the genetic landscape of MM (Robiou du Pont et al, 2017; Walker et al, 2018), which may provide potential targeted candidates for personalized therapy. Most of these studies obtained only a single, or at most two, samples from each individual patient. In 2012, three landmark studies provided insight into the intra-clonal heterogeneity early at the diagnosis and different stages of MM after relapse (Egan et al, 2012; Keats et al, 2012; Walker et al, 2012), suggesting a Darwinian model of tumor evolution in MM

Methods

Results

Conclusion