Abstract: Background: Multiple myeloma (MM) is an incurable disease with a heterogenous clinical course and genomic landscape. Autologous anti-BCMA chimeric antigen receptor (CAR) T-cells are a promising new therapy, but determinants of response and resistance are not well known. Cell-free DNA (cfDNA) is a useful tool to study MM as it allows for repeated, non-invasive tumor assessment. We apply a novel method for simultaneously tracking tumor mutations and CAR T-cells from cfDNA using Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq). Methods: We designed a 480kb CAPP-Seq hybrid capture panel to identify mutations, track tumor burden and minimal residual disease, and detect cfDNA derived from the CAR transgene (CAR-cfDNA) in patients receiving idecabtagene vicleucel (ide-cel). Flow cytometry (FC) for enumeration of CAR T-cells was performed from peripheral blood mononuclear cells (PBMCs) when available. Results: We profiled 153 biologic samples, including plasma, PBMCs, and bone marrow mononuclear cells, from 15 patients receiving ide-cel and 18 healthy controls. We observed a median of 84 SNVs (range 30-277) prior to therapy. Patients with prolonged responses ( & gt;90 days) had significantly lower circulating tumor DNA (ctDNA) at day 28 post-infusion than patients with early progression ( & lt;90 days) (0.6 vs. 4.6 log haploid genome equivalents (hGE)/mL; p=0.002). Additionally, higher ctDNA at D28 was prognostic for time to progression (TTP) (HR=1.67, p=0.019). We validated CAR-cfDNA detection by comparison with FC from PBMCs at matched timepoints (n=38), finding a significant correlation (rho=0.79, p=3E-09). CAR-cfDNA typically reached its peak level around D14 (median 332 hGE/mL), with ctDNA declining at the same time-point. Thus, CAR-cfDNA levels and ctDNA burden were inversely correlated (rho= -0.3, p=0.019). Surprisingly, peak CAR expansion was not associated with TTP (HR=1, p=0.463). However, lower CAR-cfDNA at D28 was prognostic for inferior TTP (HR=2.68, p=0.011). This suggests CAR persistence may play a more important role in clinical outcomes. Furthermore, among progressors, time until loss of detectable CAR-cfDNA correlated with TTP (rho=0.81, p=0.02). Patients who progressed before day 90 had a median CAR persistence of 28 days. In contrast, patients who progressed after day 90 had a median of 137 days and often had emergent copy number alterations in ctDNA at relapse. This included one case with emergent loss of chr16, where TNFRSF17 (BCMA), resides. This event was detected 36 days prior to clinical relapse; BCMA loss was validated via whole-genome sequencing and immunohistochemistry staining of the tumor. Conclusions: Cell-free DNA is a promising biomarker for mutational genotyping, disease monitoring, and tracking CAR T-cells in MM. The persistence of CAR-cfDNA has particular prognostic importance and novel strategies to increase CAR persistence should be explored. Citation Format: Mia Carleton, Hitomi Hosoya, Kailee L. Tanaka, Brian Sworder, Vanna Hovanky, Bita Sahaf, Matthew J. Frank, George E. Duran, Tian Y. Zhang, Sally Arai, David Iberri, Michaela Liedtke, David B. Miklos, Michael S. Khodadoust, Surbhi Sidana, David M. Kurtz. Tumor and immune determinants of response to anti-BCMA CAR T-cell therapy in multiple myeloma using cell-free DNA. [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 5707.

Abstract: CD19 CAR T cells have revolutionized the treatment of relapsed and refractory (R/R) large B cell lymphomas (LBCL), mediating durable complete responses in approximately 40-50% of patients. Besides a loss or decrease in CD19 expression, no studies have identified tumor specific factors driving inherent or acquired resistance to CAR T cells in LBCL. Mutations in and loss of expression of LFA-3 (CD58) have been described in approximately 20% of cases of LBCL. As the ligand for CD2 on T cells, CD58 provides costimulation to T cells and CD58 loss or mutation has been linked to immune resistance in LBCL. We evaluated CD58 status in fifty-one R/R LBCL patients treated at Stanford with commercial axicabtagene ciloleucel (axi-cel) through immunohistochemistry (IHC) on tumor biopsy samples and/or deep sequencing of circulating tumor DNA by CAPP-Seq. We identified 12/51 (24%) patients with a CD58 aberration (lack of expression by IHC or mutation by CAPP-Seq). Progression-free survival (PFS) was significantly decreased in patients with a CD58 aberration (median PFS for CD58 aberration 3 months vs. not reached for CD58 intact, p & lt;0.0001). In fact, only 1/12 patients with a CD58 alteration achieved a durable, complete response to axi-cel, while the remaining 11 patients progressed, most commonly after a period of initial response. Partial responses were more common among patients with CD58 aberrations (58% for CD58 aberration vs 10% for CD58 intact, p & lt;0.001), and complete responses were less common (25% for CD58 aberration vs 82% for CD58 intact, p & lt;0.0001). To probe the biology of CAR T cell responses towards tumors lacking functional CD58, we generated a CD58 knockout Nalm6 model. CD19.CD28.ζ, CD19.4-1BB.ζ, and CD22.4-1BB.ζ CAR T cells demonstrated significantly reduced cytokine production and cytolytic activity in response to CD58 KO vs wildtype (WT) tumor cells. Additionally, while mice inoculated with WT Nalm6 and treated with any of the three CARs demonstrate complete responses and prolonged leukemia-free survival, mice inoculated with CD58KO Nalm6 demonstrated only partial responses, eventual tumor progression, and death from leukemia. CD2, the T cell ligand for CD58, plays both an adhesive role and a costimulatory role in T cells. CD2 knockout resulted in significantly reduced cytokine production after CAR stimulation. Re-expression of only the CD2 extracellular domain did not rescue CAR function, indicating that CD2 signaling is essential for full CAR activation. Additionally, when we stimulated CD19 CAR T cells with anti-idiotype antibody (CAR stimulation), soluble CD58 (CD2 stimulation), or both, we observed significantly enhanced phosphorylation of both CD3ζ and ERK by western blot in CAR T cells stimulated through both the CAR and CD2. Phosphorylation analysis by mass spectrometry revealed that CD2 stimulation enhances phosphorylation of proximal signaling molecules in the TCR pathway (LCK, LAT, CD3ε among others) and also mediators of actin-cytoskeletal rearrangement in CAR T cells, consistent with effects in natural T cell responses. To overcome CD58 loss in LBCL, we generated second- and third-generation CAR T cell constructs integrating CD2 costimulatory domains within the CAR molecule. While these cis constructs demonstrated increased potency against CD58KO cells in vitro, they were unable to ultimately overcome CD58 loss in vivo. However, when CARs were co-expressed with an additional CD2 receptor in trans, they mediated significant anti-tumor activity in vivo, overcoming CD58 knockout in tumor cells. In conclusion, we have identified that CD58 status is an important biomarker for durable response to CAR T cells in LBCL. We modeled the biologic basis for this finding and generated CAR T cells capable of overcoming CD58 loss in B cell malignancies. CD58 mutations have been reported in many cancers, including multiple myeloma and colon cancer, and are likely to play a role in immune evasion for CAR T cells as they are developed for additional histologies. These data provide rationale for investigating CD58 status for patients receiving CAR based therapeutics and devising next generation CARs capable of overcoming this newly discovered mechanism of resistance. Disclosures Majzner: Xyphos Biopharma: Consultancy; Zai Lab: Consultancy; Lyell Immunopharma: Consultancy; GammaDelta Therapeutics: Membership on an entity's Board of Directors or advisory committees; Aprotum Group: Consultancy; Illumina Radiopharmaceuticals: Consultancy. Kurtz:Roche: Consultancy; Genentech: Consultancy; Foresight Diagnostics: Other: Ownership. Sotillo:Lyell Immunopharma: Consultancy, Other: Consultancy. Alizadeh:Janssen: Consultancy; Genentech: Consultancy; Pharmacyclics: Consultancy; Chugai: Consultancy; Celgene: Consultancy; Gilead: Consultancy; Roche: Consultancy; Pfizer: Research Funding. Miklos:Miltenyi Biotec: Research Funding; Janssen: Consultancy, Other: Travel support; Pharmacyclics: Consultancy, Other: Travel support, Patents & Royalties, Research Funding; Novartis: Consultancy, Other: Travel support, Research Funding; Allogene Therapeutics Inc.: Research Funding; Juno-Celgene-Bristol-Myers Squibb: Consultancy, Other: Travel support, Research Funding; Kite-Gilead: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Research Funding; Adaptive Biotech: Consultancy, Other: Travel support, Research Funding. Mackall:BMS: Consultancy; Allogene: Current equity holder in publicly-traded company; Apricity Health: Consultancy, Current equity holder in private company; Nektar Therapeutics: Consultancy; NeoImmune Tech: Consultancy; Lyell Immunopharma: Consultancy, Current equity holder in private company.

Abstract: Chimeric antigen receptor (CAR) T-cell therapy targeting CD19 has significantly improved outcomes in the treatment of refractory or relapsed large B-cell lymphoma (LBCL). We evaluated the long-term course of hematologic recovery, immune reconstitution, and infectious complications in 41 patients with LBCL treated with axicabtagene ciloleucel (axi-cel) at a single center. Grade 3+ cytopenias occurred in 97.6% of patients within the first 28 days postinfusion, with most resolved by 6 months. Overall, 63.4% of patients received a red blood cell transfusion, 34.1% of patients received a platelet transfusion, 36.6% of patients received IV immunoglobulin, and 51.2% of patients received growth factor (granulocyte colony-stimulating factor) injections beyond the first 28 days postinfusion. Only 40% of patients had recovered detectable CD19+ B cells by 1 year, and 50% of patients had a CD4+ T-cell count & lt;200 cells per μL by 18 months postinfusion. Patients with durable responses to axi-cel had significantly longer durations of B-cell aplasia, and this duration correlated strongly with the recovery of CD4+ T-cell counts. There were significantly more infections within the first 28 days compared with any other period of follow-up, with the majority being mild-moderate in severity. Receipt of corticosteroids was the only factor that predicted risk of infection in a multivariate analysis (hazard ratio, 3.69; 95% confidence interval, 1.18-16.5). Opportunistic infections due to Pneumocystis jirovecii and varicella-zoster virus occurred up to 18 months postinfusion in patients who prematurely discontinued prophylaxis. These results support the use of comprehensive supportive care, including long-term monitoring and antimicrobial prophylaxis, beyond 12 months after axi-cel treatment.

Abstract: Introduction: Given similar overall survival (OS) seen in patients receiving delayed vs. early autologous stem cell transplant (ASCT) in multiple myeloma (MM), some patients are electing to proceed with transplant at relapse instead of with upfront therapy. However, there is limited data in the era of novel therapies on expected disease control and outcomes in MM when ASCT is done for relapsed disease. The objective of this single-center retrospective study was to evaluate the outcomes of ASCT in patients with relapsed MM. Methods: Between January 1, 2010, and November 31, 2019, 168 consecutive patients with relapsed MM received ASCT at our center and constitute the study cohort. Progression free survival (PFS) was estimated from start of therapy at relapse until progression or death. PFS-PRIOR represents PFS of the immediate prior line of therapy before current relapse for which ASCT was pursued. OS was estimated from start of therapy at relapse and also from diagnosis until death. Results: Of the 168 patients, the majority underwent transplant in first relapse (69%, n=116) and the majority had not received a prior transplant (80%, n=135). Baseline and treatment characteristics of the cohort are shown in Table 1. High-risk cytogenetics were seen in 27% and ISS stage III disease in 15%. Median PFS-PRIOR was 20 months (range 2-228). The induction regimen used before ASCT included a doublet in 32%, a triplet in 56%, a quadruplet in 1.5% and a chemotherapy-based regimen in 9% of patients. Stem cell collection was done after relapse in 72% of the cohort. Conditioning regimen included melphalan 200 mg/m2 in 90% patients, including melphalan 200 mg/m2+BCNU in 55%. Median time to neutrophil and platelet engraftment was 11 and 16 days, respectively. Response after ASCT was very good partial response or better in 82% (n=124) of patients. Maintenance therapy was given in 35% (n=56) of patients after ASCT, with 73% patients receiving IMiD maintenance and a median duration of maintenance of 7 months (range 1-41). Survival: Median follow-up of this cohort was 61 months. Median PFS from start of treatment was 28 months. Median OS from start of treatment was 69 months and from diagnosis was 118 months. Two patients (1%) died within the first 3 months of complications related to transplant. As expected, patients who received ASCT at first relapse had a longer PFS of 33 months compared to 22 months when the transplant was done at second or later relapse, p=0.003 (Fig. 1A). OS from treatment start in patients undergoing transplant at first relapse was 82 months and those undergoing ASCT at second or later relapse was 45 months, p=0.004 (Fig. 1B). However, there was no difference in OS from diagnosis in these two groups (118 vs 134 months, p=0.97). Subgroup analysis was done in patients undergoing transplant at first relapse. Patients who had a PFS-PRIOR of ≥36 months had OS of 91 months compared to 62 months for those who experienced a shorter PFS-PRIOR, p=0.03. PFS in the subgroup of patients without prior ASCT undergoing transplant in first relapse (N=96) was 30 months. Multivariate Cox proportional hazards analysis was done for PFS and OS incorporating the following covariates: high risk cytogenetics, Karnofsky performance status (KPS), relapse number, PFS-PRIOR ≥36 months, response at ASCT, and use of maintenance. ASCT in first relapse was associated with better PFS with a hazard ratio (HR) of 0.63 (95% CI 0.42-0.94, p=0.03) and OS (HR 0.59, 95% CI 0.35-0.99, p=0.04). Achieving a PFS-PRIOR of ≥36 months was associated with improved PFS (HR 0.62, 95% CI 0.39-0.99, p=0.04) and OS (HR 0.41, 95% CI 0.21-0.82, p=0.01). Better KPS was also associated with longer PFS (HR 0.61, 95% CI 0.41-0.91, p=0.01) and OS (HR 0.52, 95% CI 0.31-0.86, p=0.01). Progressive disease at transplant was, as expected, associated with worse PFS (HR 3.28, 95% CI 1.89-5.70, p & lt;0.001) and OS (HR 2.70, 95% CI 1.39-5.22, p=0.003). Conclusions: This study provides comprehensive data on expected outcomes and prognostic factors amongst patients with MM undergoing ASCT at relapse, with median PFS and OS being 28 and 69 months in a cohort where only a third of patients received maintenance therapy. Disease response at transplant, PFS-PRIOR and KPS were prognostic for survival. These data can serve as a guide when counseling patients undergoing ASCT for relapsed MM and also serve as benchmark in designing clinical trials of transplant and comparative novel therapies for relapsed MM. Disclosures Muffly: Amgen: Consultancy; Adaptive: Research Funding; Servier: Research Funding. Shiraz:Kite, a Gilead Company: Research Funding; ORCA BioSystems: Research Funding. Liedtke:Adaptive: Membership on an entity's Board of Directors or advisory committees; Pfizer: Honoraria; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; GSK: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Caelum: Membership on an entity's Board of Directors or advisory committees. Rezvani:Pharmacyclics: Research Funding. Meyer:Orca Bio: Research Funding. Shizuru:Jasper Therapeutics, Inc: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. Negrin:Biosource: Current equity holder in private company; Magenta Therapeutics: Consultancy, Current equity holder in publicly-traded company; BioEclipse Therapeutics: Current equity holder in private company; UpToDate: Honoraria; KUUR Therapeutics: Consultancy; Amgen: Consultancy. Miklos:Pharmacyclics: Consultancy, Other: Travel support, Patents & Royalties, Research Funding; Novartis: Consultancy, Other: Travel support, Research Funding; Allogene Therapeutics Inc.: Research Funding; Juno-Celgene-Bristol-Myers Squibb: Consultancy, Other: Travel support, Research Funding; Kite-Gilead: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Research Funding; Janssen: Consultancy, Other: Travel support; Miltenyi Biotec: Research Funding; Adaptive Biotech: Consultancy, Other: Travel support, Research Funding. Sidana:Janssen: Consultancy.

Abstract: Background: Characterization of T-cell receptor (TCR) diversity and dynamics is increasingly critical to understanding therapeutic immune responses targeting tumors. Current TCR profiling methods generally require invasive tissue biopsies that capture a single snapshot of immune activity or are limited by the sheer diversity of the circulating TCR repertoire. In theory, T-cells with the greatest turnover could best reflect pivotal immune dynamics from both circulating and tissue-derived compartments, including non-circulating tissue-resident memory T-cells (Trm). To noninvasively capture such responses in the blood, we developed and benchmarked a high-throughput TCR profiling approach using plasma, optimized for the fragmented nature of cfDNA and the non-templated nature of rearranged TCRs. We then applied this method for residual disease monitoring in mature T-cell lymphomas (TCL) without circulating disease and for characterizing immune dynamics after anti-CD19 chimeric antigen receptor (CAR19) T-cell therapy of B-cell lymphomas with axicabtagene ciloleucel. Methods: We developed SABER (Sequence Affinity capture & analysis By Enumeration of cell-free Receptors) as a technique for TCR enrichment and analysis of fragmented rearrangements shed in cfDNA and applied this method using Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq). We used SABER to profile a total of 381 samples (300 cfDNA and 81 PBMC samples) from 75 lymphoma patients and 18 healthy controls. After mapping sequencing reads (hg38) to identify candidate rearrangements within TCR loci, unique cfDNA fragments were resolved by a novel strategy to define consensus of unique molecular identifiers clustered by Levenshtein distances, followed by CDR3-anchoring for enumeration of final receptor clonotypes. SABER thus leverages information from fragmented TCRs, a critical requirement for cfDNA, to make V gene, CDR3, and J gene assignments after deduplication-mediated error-correction. We benchmarked SABER against established amplicon-based TCR-β targeted sequencing (LymphoTrack, Invivoscribe) and repertoire analysis methods (MiXCR; Bolotin et al, 2015 Nature Methods) when considering both cfDNA and PBMC samples from healthy adults and TCL patients. We assessed SABER performance for tracking clonal molecular disease in patients with mature TCLs from both cellular and cell-free circulating compartments (n=9). Malignant TCL clonotypes were identified in tumor specimens using clonoSEQ (Adaptive Biotechnologies). Finally, we evaluated TCR repertoire dynamics over time in 66 DLBCL patients after CAR19 T-cell therapy. Results: SABER demonstrated superior recovery of TCR clonotypes from cfDNA compared to both amplicon sequencing (LymphoTrack, Invivoscribe) and hybrid-capture methods when enumerating receptors using MiXCR (Fig. 1A). When applied to blood samples from TCL patients, SABER identified the malignant clonal TCR-β rearrangement in 8/9 (88.9%) cases, with significantly improved detection in cfDNA (p=0.015, Fig. 1B). Specifically, tumoral TCR clonotype was detectable only in cfDNA in 6 cases (75%), cfDNA-enriched in 1 case (12.5%), and detectable only in PBMCs in 1 case (12.5%). We applied SABER to monitor TCR repertoire dynamics in cfDNA after CAR T-cell therapy of patients with relapsed/refractory DLBCL and observed increased T-cell turnover and repertoire expansion (greater total TCR-β clonotypes) (Fig. 1C). As early as 1-week after CAR19 infusion, TCR repertoire size was significantly correlated both with cellular CAR19 T-cell levels by flow cytometry (p=0.008) as well as with retroviral CAR19 levels in cfDNA (p=2.20e-07) suggesting faithful monitoring of CAR T-cell activity (Fig. 1D). TCR repertoire size one month after infusion was significantly associated with longer progression-free survival (HR 0.246, 95% CI 0.080-0.754, p=0.014). Conclusions: SABER has a favorable profile for cfDNA TCR repertoire capture when compared to existing methods and could thus have potential broad applicability to diverse disease contexts. Given the higher abundance of lymphoma-derived TCRs in cfDNA than intact circulating leukocytes, SABER holds promise for monitoring minimal residual disease in T-cell lymphomas. This approach also holds promise for monitoring T-cell repertoire changes including after CAR T-cell therapy and for predicting therapeutic responses. Disclosures Kurtz: Genentech: Consultancy; Foresight Diagnostics: Other: Ownership; Roche: Consultancy. Kim:Corvus: Research Funding; Eisai: Membership on an entity's Board of Directors or advisory committees, Research Funding; Elorac: Research Funding; Forty Seven Inc: Research Funding; Galderma: Membership on an entity's Board of Directors or advisory committees, Research Funding; Horizon Pharma: Consultancy, Research Funding; Innate Pharma: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Kyowa-Kirin Pharma: Research Funding; Medivir: Membership on an entity's Board of Directors or advisory committees; Merck: Research Funding; miRagen: Research Funding; Neumedicine: Consultancy, Research Funding; Portola: Research Funding; Seattle Genetics: Membership on an entity's Board of Directors or advisory committees; Solingenix: Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Trillium: Research Funding. Mackall:Lyell Immunopharma: Consultancy, Current equity holder in private company; BMS: Consultancy; Allogene: Current equity holder in publicly-traded company; Apricity Health: Consultancy, Current equity holder in private company; Nektar Therapeutics: Consultancy; NeoImmune Tech: Consultancy. Miklos:Kite-Gilead: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Research Funding; Adaptive Biotech: Consultancy, Other: Travel support, Research Funding; Juno-Celgene-Bristol-Myers Squibb: Consultancy, Other: Travel support, Research Funding; Novartis: Consultancy, Other: Travel support, Research Funding; Allogene Therapeutics Inc.: Research Funding; Pharmacyclics: Consultancy, Other: Travel support, Patents & Royalties, Research Funding; Janssen: Consultancy, Other: Travel support; Miltenyi Biotec: Research Funding. Diehn:Varian Medical Systems: Research Funding; Illumina: Research Funding; Roche: Consultancy; AstraZeneca: Consultancy; RefleXion: Consultancy; BioNTech: Consultancy. Khodadoust:Seattle Genetics: Consultancy; Kyowa Kirin: Consultancy. Alizadeh:Janssen: Consultancy; Genentech: Consultancy; Pharmacyclics: Consultancy; Chugai: Consultancy; Celgene: Consultancy; Gilead: Consultancy; Roche: Consultancy; Pfizer: Research Funding.