Multi-Omic Analysis Identifies Deletions in Chr17p and High ROR1 Expression, but Not TP53 Mutations As Predictors of Overall Survival in Patients with Untreated Waldenstrom's Macroglobulinemia (WM)
Authors: Hunter Zachary R , Gamero Andres Felipe Ramirez , Guerrera Maria Luisa , Tsakmaklis Nickolas , Kofides Amanda , Liu Xia , Liu Shirong , Peachey Abigail , Sun Hao , Flynn Catherine A. , Meid Kirsten , Gutine Joshua , Patterson Christopher J , Sarosiek Shayna R , Castillo Jorge J. , Treon Steven P. 
Published: December 2024

Overall survival (OS) analysis is difficult in Waldenstrom's Macroglobulinemia (WM) due to improved therapeutics and the indolent nature of the disease necessitating many years of follow up. Using a multi-omic dataset of 199 untreated MYD88 mutated WM patients for whom RNASeq and whole exome sequencing data was available we sought to identify key predictors of overall survival in WM.

The median age of diagnosis for the cohort was 62.7 (range 31-91.1) years and 83/199 (42%) were female. At the time of biopsy, the median values were 3,221 mg/dl (range 241-9,274 mg/dl), 11.4 g/dl (range 7.4-16.8 g/dl), and 50% (range 4-95%) for serum IgM, hemoglobin, and WM bone marrow (BM) involvement, respectively. Mutations in CXCR4 were identified 88/199 (44%) of patients with 47/88 (53%) of them being frame shift mutations. Deletions in Chr6q were noted in 70/199 (35%) of patients with 24/70 (34%) accompanied by amplifications of Chr6p. Median follow up from diagnosis was 9.9 years (range 0.7 - 33.8 years) during which time 33/199 (17%) of the patients had died. The time from biopsy to first therapy was 1.4 months (range 0-141.7 months). To find relevant predictors for overall survival, the random forest based Boruta feature selection package in R was employed. Analyzed features included, gender, age at diagnosis, BM, WBC, IgM, IgG, IgA, Hgb, Plt, familial history of B-cell malignancies, adenopathy, splenomegaly, and WM Subtype. Genomic events included mutations in CXCR4, ARID1A, ARID1B, CD79B, TP53, BIRC3, and 20 other recurrently mutated genes associated with WM. Recurrent copy number alterations analyzed included amplifications of chr3q, chr4q, chr6p, and trisomy 18 as well as deletions in chr6q, and chr17p. This analysis identified only age and chr17p deletions status as significant predictors. The top 500 high variance genes within WM that were also differentially expressed between WM and healthy donor memory B-cells (HDMB) were added to the model which retained the first two findings but added high ROR1 expression as a poor prognostic factor. Both the presence of Chr17p deletions found in 6/199 (3%) of the samples and splitting the population on median ROR1 expression resulted in significant OS stratification by univariate log-rank analysis with p&lt;0.0001 and p=0.024, respectively. A multivariate cox proportional hazard analysis of age, gender, deletion Chr17p, ROR1 expression and mutations in CXCR4 and TP53 confirmed only age, Chr17p and ROR1 to be significant predictors with hazard ratios of 1.09 (95% CI 0.41 - 1.71), 7.32 (95% CI 2.52 - 21.31) and 1.06 (95% CI 1.01 - 1.12), respectively.

Deletion of Chr17p is a known poor prognostic marker in multiple malignancies. Notably, it only co-occurred with TP53 mutation status in 1 patient. Mutations in TP53, located in Chr17p, were found in only 5 (2.5%) of patients. While this is in line with the other studies, several studies have suggested the rate of TP53 mutations may rise significantly following therapeutic relapse in WM which may explain the lack significance the untreated population. ROR1 expression is significantly elevated in WM with a median of 1.9 transcripts per million (TpM; range 0-36.2 TpM) compared with HDMB at 0.3 TpM (range 0-0.7 TpM; p&lt;0.0001). The ROR1 ligand, WNT5A, is aberrantly expressed in some WM subtypes but no correlation between WNT5A and ROR1 expression was noted in this series. ROR1 expression is a documented marker of poor prognosis in many solid tumors as well was in chronic lymphocytic leukemia and is now reported for the first time in WM. ROR1is known to activate downstream signaling through ERK and AKT. Our studies provide a framework for investigating Chr17p deletions and the WNT5A/ROR1 signaling axis as predictors of high risk disease in WM.