Clonal Evolution of a Mutation in PTPRA As a Potential Cause for Resistance Against Anti-CD19 Directed Chimeric Antigen Receptor T-Cell (CAR-T) Therapy with CTL019 in DLBCL Patients

Introduction:

Anti-CD 19 directed CAR-T cell therapy has shown very promising effects in treatment of diffuse-large B-cell lymphoma (DLBCL). However, a substantial fraction of patients does not respond to treatment or relapses after approximately three to six months [Schuster, NEJM, 2017; Neelapu, NEJM, 2017]. Resistance mechanisms against anti-CD19 directed CAR-T cell therapy have so far only been described in B-cell acute lymphoblastic leukemia (B-ALL) and involve mutations, splice variants or even loss of CD19 [Sotillo, Cancer Discovery, 2015]. To further elucidate mechanisms of acquired resistance in DLBCL, we obtained matched pair tumor samples from four patients before and after treatment with CTL019 treated within the phase II JULIET trial.

Methods:

We performed whole exome sequencing in one patient (#UKK2) employing one matched normal sample that has been sequenced at a coverage of 130x and one pre-treatment as well as two post-treatment samples that were all sequenced at a coverage of 160x. Whole exome sequencing data were used to reconstruct clonal evolution of DLBCL after treatment with CTL019 as has been described previously [Herling, Nature Communications, 2018]. Furthermore, we obtained biopsies at relapse or disease progression including matched normal samples from three more patients. Whole exome sequencing from the three missing patients as well as 3´RNA sequencing from all four patients' samples are ongoing and results will be updated for presentation at the meeting.

Results:

The first analyzed patient, #UKK2, is a 67 year old male patient, who had chemotherapy refractory disease after treatment with R-CHOP, R-DHAP and Pixantrone. He showed predominantly pelvic lesions including infiltration of the iliopsoas muscle. The patient achieved a complete response at month 3 (Figure 1A) after CTL019 transfusion. At month 5 he developed new cutaneous lesions on his left thigh (Figure 1B, posttreatment sample 1) as well as new muscle infiltrations on his right quadriceps femoris muscle (posttreatment sample 2) and rectus abdominis muscle. Pathological examination confirmed relapse of CD19 positive DLBCL in both posttreatment samples. Whole exome sequencing from a biopsy obtained before study entry and the above mentioned posttreament biopsies showed clonal evolution of a single missense mutation in PTPRA (N297D). PTPRA encodes for the receptor protein-tyrosine phosphatase alpha, a receptor phosphatase involved in activation of c-Src via dephosphorylation of an inhibitory tyrosine at position 530 (Y530) [Mustelin, Science Signaling, 2002 and Gut, International Journal of Oncology, 2017]. On the other hand, c-Src is an onco-protein known to cause an invasive phenotype and metastasis in different tumor entities [Ishizawar, Cancer Cell, 2004]. All other mutations observed were either already clonal before CTL019 treatment or gained clonality in only one posttreatment biopsy (Figure 1C).

Conclusion:

To our knowledge, this is the first report identifying clonal evolution during CD19 redirected CAR-T cell therapy in r/r DLBCL involving PTPRA. We hypothesize that this PTPRA mutation contributes to an invasive phenotype and extranodal lymphoma growth pattern allowing the lymphoma to escape from the pattern allowing the lymphoma to escape from the CAR-T cell attack. Genomic workup of patients with pre- and posttreatment biopsies and functional investigation of this hypothesis is ongoing and will be presented.

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