Waldenström’s Macroglobulinemia (WM) Is Preceded By Clonal Lymphopoiesis Including MYD88 L265P in Progenitor B Cells

Background: The transformation from a normal to a cancer cell is driven by the multistep acquisition of genetic alterations. Recently, shared mutations between clonal B cells in MBL/CLL and CD34+ hematopoietic progenitor cells (HPC) have been identified. Similarly, a HPC origin of BRAF^V600E mutations in hairy cell leukemia (HCL) has been uncovered, strengthening the notion that at least a fraction of somatic mutations may occur in CD34+ HPC before the malignant transformation of some B cell neoplasms. Since almost all WM patients have mutated MYD88^L265P, it is worthy to investigate if this disease follows a similar pathogenic process than that of MBL/CLL or HCL.

Aim: Define the cellular origin of WM by comparing the genetic landscape of WM cells to that of CD34+ HPC, B cell precursors and residual normal B cells.

Methods: We used FACSorting to isolate 57 cell subsets from bone marrow (BM) aspirates of 10 WM patients: CD34+ HPC, B cell precursors, residual normal B cells (if detectable), WM B cells, plasma cells (PCs) and T cells (germline control). Whole-exome sequencing (WES, mean depth 79x) was performed with 10XGenomics Exome Solution for low DNA-input due to limited numbers of some cell types. Single-cell RNA and B-cell receptor sequencing (scRNA/BCRseq) was performed in total BM B cells and PCs (n=32,720) from 3 IgM MGUS and 2 WM patients. Accordingly, the clonotypic BCR detected in WM cells was unbiasedly investigated in all B cell maturation stages defined according to their molecular phenotype. In parallel, MYD88^p.L252P (orthologous position of the human L265P mutation) transgenic mice were crossed with conditional Sca1^Cre, Mb1^Cre, and Cγ1^Cre mice to selectively induce in vivo expression of MYD88 mutation in CD34+ HPC, B cell precursors and germinal center B cells, respectively. Upon immunization, mice from each cohort were necropsied at 5, 10 and 15 months.

Results: All 10 WM patients showed MYD88^L265P and 3 had mutated CXCR4. Notably, we found MYD88^L265P in B cell precursors from 1/10 cases and in residual normal B cells from 4/10 patients, which were confirmed by ASO-PCR and ddPCR. Indeed, these more sensitive methods detected MYD88^L265P in B cell precursors from 6/10 cases and in residual normal B cells from 6/10 patients. CXCR4 was simultaneously mutated in B cell precursors and WM B cells from one patient. Overall, CD34+ HPC, B-cell precursors and residual normal B cells shared a median of 2 (range, 0-45; mean VAF, 0.13), 3 (range, 1-44; mean VAF, 0.168), and 6 (range, 1-56; mean VAF, 0.29) somatic mutations with WM B cells; some being found all the way from CD34+ HPC to WM B cells and PCs. Interestingly, concordance between the mutational landscape of WM B cells and PCs was <100% (median of 79%, range: 55%-100%), suggesting that not all WM B cells differentiate into PCs.

A median of 18 mutations (range, 3-26; median CCF and range, 0.72 [0.07 - 1]) were unique to WM cells. Importantly, clonal mutations in WM B cells were undetectable in normal cells. Thus, the few WM subclonal mutations observed in patients’ lymphopoiesis could not result from contamination during FACSorting since in such cases, WM clonal mutations would become detectable in normal cells. Furthermore, copy number alterations (CNA) present in WM cells were undetectable in normal cells. scRNA/BCRseq unveiled that clonotypic cells were confined mostly within mature B cell and PC clusters in IgM MGUS, whereas a fraction of clonotypic cells from WM patients showed a transcriptional profile overlapping with that of B cell precursors. scRNA/BCRseq also uncovered transcriptional differences between clonal B cells from IgM MGUS vs WM patients (eg, proliferation, metabolism).

In mice, induced expression of mutated MYD88 led to a moderate increase in the number of B220+CD138+ plasmablasts and B220-CD138+ PCs in lymphoid tissues and BM, but no signs of clonality or hematological disease. Interestingly, such increment was more evident in mice with activation of mutated MYD88 in CD34+ HPC and B-cell precursors vs mice with MYD88 L252P induced in germinal center B cells.

Conclusions: We show for the first time that WM patients have somatic mutations, including MYD88^L265P and CXCR4 at the B cell progenitor level. Taken together, this study suggests that in some patients, WM could develop from B cell clones carrying MYD88^L265P rather than being the initiating event, and that other mutations or CNA are required for the expansion of B cells and PCs with the WM phenotype.