Whole-Exome Sequencing Revealed No Recurrent Mutations within the PI3K Pathway in Relapsed Chronic Lymphocytic Leukemia Patients Progressing Under Idelalisib Treatment
Authors: Ghia Paolo , Ljungström Viktor , Tausch Eugen , Agathangelidis Andreas , Scheffold Annika , Scarfo Lydia , Jebaraj Billy Michael Chelliah , Owen Carolyn J. , Barrientos Jacqueline C. , Zapatka Marc , Munugalavadla Veerendra , Degenhardt Jeremiah D. , Kim Yeonhee , Dubowy Ronald L. , Dreiling Lyndah K. , Rosenquist Richard , Stilgenbauer Stephan 
Published: October 2019

Abstract
Introduction: Idelalisib (IDELA) is an ATP-competitive, reversible, and selective small molecule inhibitor of the delta isoform of phosphatidylinositol 3-kinase (PI3Kδ) approved for the treatment, in combination with rituximab, of patients with relapsed chronic lymphocytic leukemia (CLL). In the relapsed CLL randomized, controlled trials, IDELA + rituximab showed high response rates with improved progression-free and overall survival as compared with placebo + rituximab. While IDELA therapy has significant efficacy, disease progression after response occurs, indicating that escape mechanisms may develop. However, the molecular basis for relapse or progressive disease (PD) in CLL patients treated with IDELA has not yet been characterized.
Methods: Peripheral blood mononuclear cells (PBMCs) were collected from 13 CLL patients enrolled in the phase 3 studies; NCT01539512 (study 116; IDELA + rituximab vs placebo + rituximab), 116 extension study NCT01539291 (study 117) and NCT01659021 (study 119; IDELA + ofatumumab). Sample selection criteria included treatment period of at least 180 days (range: 243-703 days), achieving at least partial nodal response followed by PD, PD did not occur within a drug interruption window, PD was not associated with Richter's transformation, and PBMC samples were available from both baseline and time of PD. Whole-exome sequencing (WES) was conducted on the matched samples from 13 subjects fitting the above criteria. In 6/13 cases, DNA was available from CD19+/CD5+ enriched tumor cells, and neutrophils or T-lymphocytes served as a source of germline DNA. These 6 patients were considered as a discovery set for mutational analysis. Established bioinformatics tools were used for detection of somatic mutations and for the comparison of baseline and PD samples.
Results: Baseline clinical patient profiles indicated that 12 of 13 patients with PD had unmutated IGHV genes and 8 patients carried TP53 aberrations (ie, 17p deletion and/or TP53 mutation). WES resulted in a mean read depth of 106X within the targeted coding region across samples. In the discovery set, on average 25 somatic mutations (range: 4-44) at baseline and 32 mutations (range: 15-81) at progression were identified. By comparing baseline and PD samples, we identified 88 PD-associated mutations. These specific mutations were tested for in a complete set of 13 patient samples; however, no recurrent progression-associated mutations were identified in more than 1 patient. In particular, no progression-associated mutations were identified in the PI3K signaling pathway or in any other related pathway.
Conclusion: Across 3 phase 3 studies in relapsed CLL, WES on 13 samples from patients with PD while on IDELA treatment were evaluated. This analysis detected no relapse-associated mutations in common across this patient set; in particular, no mutations were identified in the drug-binding site (ie, "gateway mutation") or in any other related signaling pathway. Based on these results, we conclude there is no common mutational mechanism of IDELA resistance in this patient group.

Disclosures
Ghia: Gilead: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Roche: Honoraria, Research Funding; Adaptive: Consultancy; Abbvie: Consultancy, Honoraria. Tausch:Gilead: Other: Travel support, Speakers Bureau; Celgene: Other: Travel support; Amgen: Other: Travel support. Owen:Roche: Honoraria, Research Funding; Pharmacyclics: Research Funding; Celgene: Honoraria, Research Funding; Abbvie: Honoraria; Lundbeck: Honoraria, Research Funding; Novartis: Honoraria; Janssen: Honoraria; Gilead: Honoraria, Research Funding. Barrientos:Gilead: Consultancy, Research Funding; Janssen: Consultancy; AbbVie: Consultancy, Research Funding. Munugalavadla:Gilead Sciences: Employment, Equity Ownership. Degenhardt:Gilead Sciences: Employment, Equity Ownership. Kim:Gilead Sciences: Employment, Equity Ownership. Dubowy:Gilead Sciences: Employment, Equity Ownership. Dreiling:Gilead Sciences: Employment, Equity Ownership. Rosenquist:Gilead Sciences: Speakers Bureau. Stilgenbauer:Hoffmann-La Roche: Consultancy, Honoraria, Other: Travel grants , Research Funding; AbbVie: Consultancy, Honoraria, Other: Travel grants, Research Funding; GSK: Consultancy, Honoraria, Other: Travel grants , Research Funding; Pharmacyclics: Consultancy, Honoraria, Other: Travel grants , Research Funding; Janssen: Consultancy, Honoraria, Other: Travel grants , Research Funding; Mundipharma: Consultancy, Honoraria, Other: Travel grants , Research Funding; Celgene: Consultancy, Honoraria, Other: Travel grants , Research Funding; Amgen: Consultancy, Honoraria, Other: Travel grants, Research Funding; Novartis: Consultancy, Honoraria, Other: Travel grants , Research Funding; Sanofi: Consultancy, Honoraria, Other: Travel grants , Research Funding; Genzyme: Consultancy, Honoraria, Other: Travel grants , Research Funding; Genentech: Consultancy, Honoraria, Other: Travel grants , Research Funding; Gilead: Consultancy, Honoraria, Other: Travel grants , Research Funding; Boehringer Ingelheim: Consultancy, Honoraria, Other: Travel grants , Research Funding.