Prevalence and Clinical Impact of Clonal Hematopoiesis of Indeterminate Potential (CHIP) in Chronic Lymphocytic Leukemia and Richter Transformation

BACKGROUND: Clonal hematopoiesis of indeterminate potential (CHIP) is associated with a variety of different diseases but its role in the prognosis and transformation of chronic lymphocytic leukemia (CLL) is unclear.

METHODS: Genomic DNA was extracted from granulocytes of CLL patients referring at our institution at the time of diagnosis. Multicenter cohorts of CLL patients with available granulocytes before and after fixed-duration venetoclax-based therapy and BTK inhibitors were analyzed. Samples were analyzed by targeted next-generation sequencing (NGS), employing a custom panel of genes (N=28) recurrently mutated in CHIP. Libraries were sequenced using the NextSeq550 (Illumina).

RESULTS: A total of 367 patients with CLL have been sequenced. Patient characteristics were consistent with an unselected real-word cohort of newly diagnosed CLL. The median age was 70.3 years, 9.9% harbored TP53 disruption and 33.8% unmutated IGHV. The most frequently mutated genes, as reported in patients without CLL, were DNMT3A in 89 (24.3%) patients, followed by TET2 in 52 (14.1%) and ASXL1 in 10 (2.7%). As expected, the presence of at least one CHIP mutation significantly correlated with older age (p=0.004). By analyzing CHIP mutations in sorted CLL cells, CD3+ T cells and CD14+ monocytes from 11 patients, CHIP mutations were also identified in the CLL cells of 2 patients suggesting that, at least in few cases, CLL may possibly arise from an ancestor clone that already harbored CHIP. After a median follow-up of 13.9 years, the presence of any CHIP mutations associated with shorter overall survival (OS) (HR 1.34, 95% CI 1.02-1.78, p=0.037) but not with shorter time to first treatment (TTFT) in Binet A CLL (N=299) (HR 0.98, 95% CI 0.65-1.47, p=0.979). By analyzing the clinical impact of different gene mutations, TET2 mutated patients showed the strongest association with OS with a median OS of 7.9 years compared to 13.1 years for TET2 wild type patients (p=0.006). TET2 mutations (HR 1.65, 95% CI 1.13-2.40, p=0.009) maintained an independent association with shorter OS in multivariate analysis when adjusted for age, IGHV mutational status and TP53 disruption. The presence of CHIP overall did not correlate with a higher risk of Richter transformation (HR 0.57, 95% CI 0.33-1.75, p=0.515). Conversely, by analyzing the impact of each CHIP gene, ASXL1 mutated patients showed a significantly higher risk of Richter transformation with a 10-year probability of Richter transformation of 43.7% compared to 6.4% for ASXL1 wild type patients (p<0.0001). In multivariate analysis, ASXL1 mutations maintained an independent association with a higher risk of Richter transformation (HR 6.80, 95% CI 1.54-30.14, p=0.01) when adjusted for TP53 disruption and NOTCH1mutations. Longitudinal analysis in 25 patients treated with chemoimmunotherapy (CIT) showed that CIT led to an increase in the number of CHIP mutations and in the variant allele frequency (VAF) of pre-existing mutations (p=0.004). At variance with CIT, CHIP dynamics before and after fixed-duration venetoclax therapy in 15 patients showed no significant differences in VAF pre- and post-therapy (p=0.344). Subsequently, the impact of CHIP in terms of therapy tolerability was assessed. By analyzing 30 patients treated with fixed duration venetoclax-based therapy, the presence of non-DNMT3A CHIP mutations (i.e. at least one CHIP mutation other than DNMT3A) associated with higher risk of grade >3 neutropenia during venetoclax treatment. More precisely, 82.4% of patients with non-DNMT3A CHIP mutations presented grade >3 neutropenia compared to 30.8% of patients without non-DNMT3A CHIP mutations (p=0.004). In patients receiving continuous treatment with BTK inhibitors (N=73), the relationship between CHIP and cardiovascular side effects was assessed. SF3B1 CHIP mutations associated with an increased risk of atrial fibrillation compared to SF3B1 wild type patients (p<0.0001).

CONCLUSIONS: The analysis of the myeloid compartment suggests that CHIP may harbor potential clinical relevance for CLL and Richter transformation. Also, the presence of different CHIP mutations predisposes to high grade neutropenia in venetoclax treated patients and to high rate of atrial fibrillation in BTK inhibitors treated patients. These results suggest that CHIP might be considered as a biomarker to prevent and manage therapy-related toxicities.