Insights into the genomic landscape of MYD88 wild-type Waldenström macroglobulinemia

Abstract

Activating MYD88 mutations are present in 95% of Waldenström macroglobulinemia (WM) patients, and trigger NF-κB through BTK and IRAK. The BTK inhibitor ibrutinib is active in MYD88-mutated (MYD88 ^MUT ) WM patients, but shows lower activity in MYD88 wild-type (MYD88 ^WT ) disease. MYD88 ^WT patients also show shorter overall survival, and increased risk of disease transformation in some series. The genomic basis for these findings remains to be clarified. We performed whole exome and transcriptome sequencing of sorted tumor samples from 18 MYD88 ^WT patients and compared findings with WM patients with MYD88 ^MUT disease. We identified somatic mutations predicted to activate NF-κB (TBL1XR1, PTPN13, MALT1, BCL10, NFKB2, NFKBIB, NFKBIZ, and UDRL1F), impart epigenomic dysregulation (KMT2D, KMT2C, and KDM6A), or impair DNA damage repair (TP53, ATM, and TRRAP). Predicted NF-κB activating mutations were downstream of BTK and IRAK, and many overlapped with somatic mutations found in diffuse large B-cell lymphoma. A distinctive transcriptional profile in MYD88 ^WT WM was identified, although most differentially expressed genes overlapped with MYD88 ^MUT WM consistent with the many clinical and morphological characteristics that are shared by these WM subgroups. Overall survival was adversely affected by mutations in DNA damage response in MYD88 ^WT WM patients. The findings depict genomic and transcriptional events associated with MYD88 ^WT WM and provide mechanistic insights for disease transformation, decreased ibrutinib activity, and novel drug approaches for this population.

Graphical abstract

Figure 1.

Mutations identified in MYD88^WTWM by whole exome sequencing. (A) The median number of somatic mutations for patients with paired tumor/germline samples was 33 and the number of mutations per patient for these individuals are shown. (B) Somatic mutations were associated with NF-κB signaling, epigenetic regulation, and DNA damage response. Each row represents a unique patient. Patient identifiers in bold type indicate that the patient is deceased. *Patients with disease that later transformed. (C) Location of conserved motifs in the protein coding domains of top affected genes are shown. ★Location of a somatic mutation.

Figure 2.

Comparison of findings for MYD88^WTand MYD88^MUTWM. Comparison of somatic mutation frequencies between MYD88^WT and MYD88^MUT WM patients. (A) Data for mutation frequencies for 53 MYD88^MUT WM patients were acquired from our previous whole genome sequencing results, using high-quality somatic variants supported by at least 3 reads.^, (B) Kaplan-Meier curves for overall survival from time of diagnosis for WM patients with MYD88^MUT, and MYD88^WT with and without DDR mutations (log-rank P < .0001).

Figure 3.

Findings from next-generation gene expression studies in MYD88^WTWM. (A) The top 100 most statistically significant genes between samples from 18 MYD88^WT and 75 MYD88^MUT patients are shown, demonstrating a uniform gene signature associated with the MYD88^WT population. (B) Principal component analysis of the top 500 high variance genes revealed a clustering of MYD88^WT and MYD88^MUT WM samples, regardless of CXCR4 mutation status that was distinct from healthy donor peripheral blood B, memory B, and plasma cells. (C) These findings were also recapitulated in the supervised clustering of the top 100 most statistically significant differentially expressed genes between healthy donor memory B cells and MYD88^WT WM samples, in which gene expression levels were very similar between all WM samples regardless of MYD88 and CXCR4 mutation status.

Figure 4.

Genomic variants identified in MYD88 wild-type WM that affect NF-κB signaling. Red triangle denotes variants identified by whole exome sequencing in MYD88 wild-type WM patients.