Spatiotemporal Assessment of Immunogenomic Heterogeneity in Multiple Myeloma

Introduction:

Therapy and immune mediated processes are associated with clonal evolution in multiple myeloma (MM). In this study, we performed whole-exome sequencing (WES) and single cell RNA sequencing (scRNA-seq) on plasma cells (PC) from bone marrow aspirates of the iliac crest (BM) and corresponding osteolytic lesions (OL) to investigate spatial heterogeneity in patients with newly diagnosed (NDMM) and relapsed/refractory MM (RRMM). Next generation flow (NGF) and T-cell receptor sequencing (TCRseq) were performed to investigate the immunogenomic landscape surrounding malignant PC.

Methods:

In a prospective trial, 18 patients (NDMM: n=10; RRMM: n=8) consented to an imaging-guided biopsy of an OL in addition to the regular BM sampling. At inclusion, 37 different locations were biopsied. Follow-up samples were obtained from 5 patients in remission after therapy. After CD138+ selection, PC were subjected to WES and scRNA-seq (Chromium, 10x genomics). TCRseq was performed using multiplex PCR (ImmunoSEQ, Adaptive biotechnologies) on the CD138- fraction. For scRNA-seq data analyses, Cell Ranger (v3.1.0) and the Seurat R toolkit (v3.1) were used. TCRseq data were analyzed with immunoSEQ ANALYZER (v3.0) and the immunarch R toolkit (v0.6.6.). NGF was performed to study subsets of T-, B-, NK- and dendritic cells (DC).

Results:

Median PC infiltration was higher in OL compared to random BM (50.0% vs 12.5%, p=0.041). WES revealed more mutations in RRMM compared to NDMM (median; range: 189;120-523 vs 71;23-136, p<0.001). Based on mutational profiles from WES, 4 of 18 patients showed a branching evolution in PC isolated from OL. Three of the 4 patients had RRMM and one patient with NDMM had a prior history of solitary plasmacytoma. PC were obtained from OL with adjacent extramedullary disease (EMD) in 3 of 4 patients with branching evolution. Among site-specific mutations, we found in one patient two distinct BRAF mutations: V600E in the BM and G469R in the OL. An additional NRAS mutation (G12D) was found in the OL. BRAF G469R and NRAS G12D cause resistance to BRAF inhibitors, although this patient was naïve to BRAF-inhibitors. Clonal evolution was also reflected by chromosomal aberrations, including site-specific chromothripsis of chromosome 1 in a patient with RRMM. Even in patients without spatially divergent clones as detected by WES, scRNA-seq of more than 150,000 PC from 10 patients and 21 different locations revealed multiple clones. Distinct PC clones were identified by differential expression of genes associated with homing to the BM (CXCR4), malignant transformation (Jun/Fos, CD27, CD79a), apoptosis (BCL-2) bone disease (DKK1) and LAMP-5. In a patient with NDMM in remission after induction therapy, scRNA-seq demonstrated the emergence of a PC clone characterized by the overexpression of Interferon-induced genes (ISG15, IFI27, IFI44L) compared to the initially predominant PC clones. Next, we investigated spatiotemporal differences of immune cells. Estimation of median TCR richness using an abundance-based estimator (Chao1) revealed significantly lower values in patients with RRMM (120444; 57706-212744) compared to NDMM (389341; 50318-525082, p<0.001) and nine healthy individuals (460278; 138326-696419, p<0.001). No significant differences were found for TCR clonality as indicated by Simpson’s D. While longitudinal tracking of TCR clones at primary diagnosis showed no clonal expansion after treatment, induction therapy restored sample richness in patients with NDMM to levels of healthy individuals (p=0.61). Overlap analysis showed a high concordance of TCR repertoires from OL and random BM with Morisita indices ranging in 90% of patients from 0.80 to 0.95. Nevertheless, significant site-specific expansion of TCR clones was detected. In accordance with TCRseq, NGF showed in the BM of patients with RRMM more regulatory T-cells (p=0.048) and less myeloid DC (p=0.024), Th9 cells and CD8 effector memory T-cells compared to NDMM.

Conclusion:

We report the first prospective clinical trial to investigate spatiotemporal immunogenomic heterogeneity in multiple myeloma as assessed by WES and scRNA-seq of PC and NGF and TCRseq of the non-PC compartment. We demonstrate spatial evolution and reduced TCR diversity especially in patients with RRMM and/or EMD. ScRNA-seq adds another layer of complexity compared to WES and helps identifying how PC create an immune suppressive BM niche.