# Mutational Landscape and Clinical Impact of SPEN Mutations in Patients with Chronic Lymphocytic Leukemia

## TL;DR

This study finds that SPEN mutations in chronic lymphocytic leukemia are linked to worse patient outcomes and should be considered in diagnostic testing.

## Contribution

The study identifies SPEN mutations as a prognostic marker in CLL and reports their frequency and associated clinical features in a large patient cohort.

## Key findings

- SPEN mutations are found in 2.9% of CLL patients and are associated with shorter time-to-first treatment.
- SPEN-mutated patients show higher frequencies of IGHV unmutated status, CD38 positivity, ZAP70 positivity, and trisomy 12.
- NOTCH1 mutations are the most common co-occurring alterations with SPEN mutations in CLL.

## Abstract

SPEN mutations have been described in a limited number of CLL cases and previous studies have suggested that mutations in the NOTCH1 regulatory pathway including SPEN are associated with adverse patient outcomes. However, the clinicopathologic features including the molecular landscape of SPEN mutations in CLL patients have not been extensively studied. We conducted this study to assess the frequency of SPEN mutations and their potential clinical impact on outcomes in a large cohort of CLL patients. We also describe co-occurring gene alterations in this cohort. We show in this study that SPEN mutations are associated with shorter time-to-first treatment in CLL patients.

Background/Objectives: NOTCH1 is frequently mutated in chronic lymphocytic leukemia (CLL) and is a marker of poor prognosis. In addition to NOTCH1, mutations in the NOTCH1 regulatory pathway including SPEN have been described in a limited number of CLL cases and others have suggested that these mutations are also associated with adverse patient outcomes Methods: In this study, 1617 CLL cases were assessed using targeted sequencing and a 29-gene panel and the results were correlated with prognosis. Results: SPEN mutations were detected in 48 (2.9%) CLL patients: 92.4% were deleterious (frameshift or truncating nonsense mutations) and the remaining (7.6%) were missense. Compared with SPEN wild type CLL patients, SPEN mutated patients had a statistically higher frequency of IGHV unmutated status (79.5% vs. 57.8%, p = 0.004), CD38 positivity (73.3% vs. 52.4%, p = 0.01), ZAP70 positivity (77.3% vs. 58.3%, p = 0.01) and trisomy 12 (43.5% vs. 13.7%, p < 0.001). The most common gene mutations co-occurring with SPEN mutations were as follows: NOTCH1 (43.7%), TP53 (22.9%), BIRC3 (12.5%), SF3B1 (10.4%), XPO1 (8.3%), MUC2 (6.2%), ATM (4.2%), FBXW7 (4.2%), and BTK (4.2%). Patients with SPEN mutated CLL had a significantly shorter time-to-first treatment compared to CLL patients with wild type SPEN (2.5 vs. 4.07 years, p = 0.01). The finding of shorter time-to-first treatment in SPEN mutated CLL patients was not maintained in a multivariable analysis. IGHV unmutated status, TP53 disruption, and trisomy 12 remained independently predictive of a shorter time-to-first treatment in a multivariable analysis. Conclusions: These data show that SPEN mutations in CLL are associated with adverse prognostic impact and should be included in sequencing assays performed for the prognostic workup of CLL patients.