Kay, Neil E.

Abstract Multiple studies including ours have shown that the interaction of chronic lymphocytic leukemia (CLL) B cells with the bone marrow (BM) microenvironment promotes cell survival and protects these cells from the cytotoxic effects of therapy. A detailed understanding of this interaction will help better understand CLL leukemic cell survival and drug resistance mechanisms. We performed RNA-seq in paired CLL B cells isolated from untreated blood and BM (n=6) and in untreated CLL B cells (n=4) cultured alone or co-cultured with bone marrow stromal cells (BMSCs) derived from either normal individuals (n=2) or CLL patients (n=2). We found upregulation of 232 and 917 genes in CLL B cells from BM and in co-cultured CLL B cells compared to the CLL B cells from the same patient’s blood and CLL B cells cultured alone respectively (p<0.05, fold change >1.5). However we found only 13 genes overlapped between BM CLL B cells and co-cultured CLL B cells. To explore the functional importance of these 13 genes, we analyzed the expression of these genes in CLL blood B cells from an additional 169 untreated patients by RNA-seq and found a positive relationship between 5 of these 13 genes (MKI67, PNP, C16orf54, MOB3A, CDK2AP2) with CLL patient’s clinical outcome including overall survival (OS), progression free survival (PFS), and time to first treatment (TTFT) [univariate Cox regressions analysis (UCRA) p<0.05]. Out of 5 genes, purine nucleotide phosphorylase (PNP) which is an enzyme in the purine salvage pathway, showed the significant association for patient’s OS, PFS, and TTFT using UCRA [hazard ratio (HR) {95% CI}: 2.8 {1.8-4.3}, 2.7 {1.9-3.8}, 2.9 {2.0-4.2}, respectively, p<.0001], suggesting purine metabolism plays an important role in BM induced CLL B cell survival. We also observed an increase in PNP protein levels in CLL B cells co-cultured with BMSCs or from BM using Western blot analysis. Untargeted metabolomic profiling (LC-MS+GC-MS) showed an increased level of purine salvage pathway metabolites adenosine, inosine, and hypoxanthine in co-cultured CLL B cells. Consistent with this altered nucleotide metabolism data, we also found increased pyrimidine pathway enzyme thymidylate synthase (TYMS) at RNA and protein levels in co-cultured CLL B cells and in BM CLL B cells. We further analyzed the RNA-seq data generated from the 169 CLL patients and it also showed a positive association of TYMS gene with their OS, PFS and TTFT using UCRA [HR (95% CI): 1.35 (1.0-1.8), 1.3 (1.0-1.6), 1.63 (1.3-2.1) respectively, p<0.05]. In conclusion, these results indicate that active purine/pyrimidine metabolism in CLL B cells may be augmented by the BM environment to support CLL B cell survival. Future studies to understand the exact mechanism of PNP and TYMS mediated CLL B cell survival for both untreated and treated CLL B cells will uncover unique approaches for therapy. Citation Format: Sutapa Sinha, Zhiquan Wang, Weiguo Han, Kari G. Rabe, Susan L. Slager, Chantal E. McCabe, Daniel R. O'Brien, Sameer A. Parikh, Esteban Braggio, Neil E. Kay. Role of purine and pyrimidine metabolism in CLL B cell survival and drug resistance mediated via interaction with bone marrow microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1252.

Abstract TP53 aberrations, including mutations and deletion of 17p13, are important adverse prognostic markers in chronic lymphocytic leukemia (CLL) but are less studied in high count monoclonal B-cell lymphocytosis (HCMBL), an asymptomatic pre-malignant stage of CLL. Here we estimated the prevalence and impact of TP53 aberrations in 1,230 newly diagnosed treatment-naïve individuals (849 CLL, 381 HCMBL). We defined TP53 state as: wild-type (no TP53 mutations and normal 17p), single-hit (del(17p) or one TP53 mutation), or multi-hit (TP53 mutation and del(17p), TP53 mutation and loss of heterozygosity, or multiple TP53 mutations). Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for time to first treatment and overall survival by TP53 state. We found 64 (7.5%) CLL patients and 17 (4.5%) HCMBL individuals had TP53 mutations with variant allele fraction >10%. Del(17p) was present in 58 (6.8%) of CLL and 11 (2.9%) of HCMBL cases. Most individuals had wild-type (N=1,128, 91.7%) TP53 state, followed by multi-hit (N=55, 4.5%) and then single-hit (N=47, 3.8%) TP53 state. The risk of shorter time to therapy and death increased with the number of TP53 abnormalities. Compared to wild-type patients, multi-hit patients had 3-fold and single-hit patients had 1.5-fold increased risk of requiring therapy. Multi-hit patients also had 2.9-fold increased risk of death compared to wild-type. These results remained stable after accounting for other known poor prognostic factors. Both TP53 mutations and del(17p) may provide important prognostic information for HCMBL and CLL that would be missed if only one were measured.

Abstract The consequences of immune dysfunction in B-Chronic Lymphocytic Leukemia (CLL) likely relate to the incidence of serious recurrent infections and second malignancies that plague CLL patients. The known immune abnormalities are not able to consistently explain these complications and it is not easy to correct their immune status. Here, we report bone marrow (BM) hematopoietic dysfunction in early and late stage untreated CLL patients. We found reduced functional capacity of hematopoietic progenitors in BM using colony forming unit assays and flow cytometry revealed significant reductions in frequencies of hematopoietic stem and progenitor cell (HSPC) populations. Consistent with the reduction in HSPCs, monocytes and natural killer cells in BM were reduced and the reduction in BM was recapitulated in blood. Finally, we report imbalances in protein levels of the transcriptional regulators HIF-1α, PU.1, and GATA-2 in CLL patient BM, providing molecular insight into the basis of HSPC dysfunction. Importantly, PU.1 and GATA-2 were rapidly increased when healthy HSPCs were exposed in vitro to TNFα, a cytokine constitutively produced by CLL B cells. Together, these findings reveal BM hematopoietic dysfunction in untreated CLL patients, adding to the complex immunodeficiency state of these patients and the reduced capacity of the innate immune system.