Andy Conroy

. Here we developed a clinical-grade approach based on CRISPR-Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes TCRβ). We also inserted into the TRAC locus two chains of a neoantigen-specific TCR (neoTCR) isolated from circulating T cells of patients. The neoTCRs were isolated using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with different refractory solid cancers received up to three distinct neoTCR transgenic cell products. Each product expressed a patient-specific neoTCR and was administered in a cell-dose-escalation, first-in-human phase I clinical trial ( NCT03970382 ). One patient had grade 1 cytokine release syndrome and one patient had grade 3 encephalitis. All participants had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease and the other eleven had disease progression as the best response on the therapy. neoTCR transgenic T cells were detected in tumour biopsy samples after infusion at frequencies higher than the native TCRs before infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs that recognize mutational neoantigens. Moreover, simultaneous knockout of the endogenous TCR and knock-in of neoTCRs using single-step, non-viral precision genome-editing are achieved. The manufacture of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene-edited neoTCR T cell products and the ability of the transgenic T cells to traffic to the tumours of patients are also demonstrated.

<h3>Background</h3> NeoTCR-P1 is a personalized autologous T cell therapy for treatment of patients with solid tumors. Neoantigen-specific T cell receptors (neoTCRs) were isolated from the patients’ own circulating CD8 T cells using the imPACT Isolation Technology^®, followed by non-viral precision genome engineering into an autologous apheresis product for infusion back into the patient. <h3>Methods</h3> This phase 1 trial is a first-in-human, multi-center, dose-escalation study to evaluate the safety, tolerability, and manufacturing feasibility of NeoTCR-P1 alone or in combination with IL-2 in solid tumors. Patients with TCRs identified at screening and meeting eligibility criteria underwent apheresis to manufacture personalized NeoTCR-P1 cell product. Lymphodepleted patients received a single dose of up-to-three distinct NeoTCR cell products at dose levels of 0.4, 1.2, or 4×10⁹ NeoTCR-edited T cells. Pre- and post-treatment blood and biopsy samples were collected to evaluate NeoTCR-P1 pharmacokinetics, tumor trafficking, signs of T cell engagement or potential mechanisms of resistance. <h3>Results</h3> Sixteen patients were infused with NeoTCR-P1 T cells including patients with MSS-colorectal cancer (11), breast cancer (2), ovarian cancer (1), melanoma (1), or non-small cell lung cancer (1). Four of the sixteen patients were treated with NeoTCR-P1 + IL-2. Two patients experienced toxicities associated with NeoTCR-P1 cell infusions: a grade 1 CRS and a grade 2 ICANS. Five patients had stable disease as their best response at their first tumor assessment (day 28). NeoTCR+ T cells detected in the peripheral blood had an average peak of 3.6% (range 0.9-7.3%) for DL1, 11.7% (7.7-20.8%) for DL2, and 19.8% (12.0-37.3%) for DL3. Increases in NeoTCR T cells were observed at higher dose levels, stronger lymphodepletion, or higher gene editing rates of the infused product. Eight post-infusion biopsies were available for sequencing and imaging analysis; 17 of 22 neoTCR-T cells were detected in post-infusion biopsies with 12 neoTCRs among the top 4% of CDR3 sequences detected. The targeted neoantigens were detected in 7 of 8 post-treatment biopsies (15 of 22 targets), and personalized ctDNA confirmed targeting of a predicted sub-clonal mutation. An APOBEC signature and HLA-LOH were identified as potential mechanisms of resistance. By single-cell, spatial molecular imaging, neoTCR-T cells were visualized in post-treatment biopsies and found to differentially express potential markers of engagement. <h3>Conclusions</h3> This study demonstrates the feasibility of isolating and manufacturing NeoTCR-T cells using non-viral precision genome engineering, the safety of infusing up-to-three gene edited NeoTCR-T cell products, and T cell persistence and trafficking to a variety of solid tumors. <h3>Trial Registration</h3> NCT03970382 <h3>Ethics Approval</h3> Ethics approvals have been obtained from each clinical site enrolling patients: City of Hope, Duarte California; University of California Los Angeles, Los Angeles California; University of California, Irvine Medical Center, Orange, California; University of California, Davis, Sacramento California; University of California, San Francisco, San Francisco California; Northwestern University Medical Center, Chicago Illinois; Memorial Sloan Kettering Cancer Center, New York, New York; Tennessee Oncology, Nashville, Tennessee; and Fred Hutchinson Cancer Research Center, Seattle, Washington.

Abstract The specific functions of phenotypically defined B cell subsets in the regulation of protective immune responses and the pathogenesis of immune-mediated diseases is incompletely understood. SCNP is a multi-parametric flow cytometry based approach that simultaneously measures intracellular signaling in multiple cell subsets in heterogeneous tissues. In this study, SCNP was applied to examine 34 signaling nodes (paired modulator/intracellular readout) in B cell subsets (CD27-IgM+IgD+ naïve B cells, total CD27+ memory B cells, CD27+IgM-IgD- switched memory B cells, CD27+IgM+IgD+ IgM memory B cells) in peripheral blood mononuclear cells from 6 healthy donors. Signaling responses in B cell subsets were masked when the total B cell population was analyzed. Specifically, a higher responsiveness was observed in the memory B cell subset relative to the naïve; 14 signaling nodes showed statistically significant differences between these subsets (p&amp;lt;.05, paired Wilcoxon test) of which 12 displayed stronger activation in response to CD40L, SDF1α, PMA, IFNα, IFNγ, IL10 and IL27 modulation in the memory B cells. 11 signaling nodes differed significantly in IgM memory vs. switched memory B cells (p&amp;lt;.05, paired Wilcoxon test); 7/11 displayed stronger activation in response to CpG, R848, thapsigargin, IFNγ and IL10 modulation in IgM memory B cells. An increased understanding of B cell subset signaling may allow for the development of more effective B cell targeted therapies.

Abstract Experimental data and clinical observations indicate that local radiation therapy (RT) converts the irradiated tumor into an in situ vaccine and improves responses to immunotherapy. Preclinical breast cancer models show that TGFb neutralization was required to achieve CD8+ T cell priming specific for multiple tumor antigens, and rejection of the irradiated tumor and non-irradiated metastases (Vanpouille-Box et al., Cancer Res 2015). Tumor response and survival were improved by PD-1 blockade. We explored the role of the PD-1/PDL-1 pathway in resistance to combined RT + TGFβ neutralizing antibody (fresolimumab) in metastatic breast cancer patients (pts). 22 pts were treated in a prospective trial at NYU and UCLA (NCT01401062, supported by DOD MTA BC100481). Pts were randomly assigned to 2 doses of fresolimumab (freso) (1mg/kg and 10 mg/kg, q 3 weeks). Image guided RT was delivered to one metastasis on weeks 2 and 7, 7.5 GyX3. 1 pt achieved objective response, with 28% reduction of tumor burden. The response lasted 11 months, anthracycline-induced acute myelogenous leukemia developed. Pts randomized to the higher freso dose had a hazard ratio of 2.17 (95% CI: 0.753-6.272) for risk of death at 1 year follow up. Currently, at a median follow up of 2 years, 20/22 pts have died. To explore reasons for the limited response, peripheral blood mononuclear cells collected at baseline, 5 and 15 weeks into treatment, were analyzed. Responses to survivin, as a tumor antigen, were assessed using tetramers. Single cell network profiling (SCNP) was used to evaluate expression of 6 immunomodulatory receptors plus immune signaling in T cells collected from 7 healthy donors (HD) and 15 breast cancer pts (6 at 1mg/kg, 9 at 10mg/kg fresolimumab). In vitro activation of p-AKT and p-Erk was quantified following in vitro T cell receptor (TCR) modulation with anti-CD3/αnti-CD28. 6/12 HLA-A2.1+ pts had pre-existing survivin-specific CD8+ T cells, and 3 showed an increase over time. 2 pts who were negative generated modest responses after RT and 10 mg/kg freso. Prior to treatment, PDL-1 expression was increased in monocytes (p = 0.01) and CD4+ T cells (p = 0.037) compared to HD. Elevated PD-1 (p = 0.054) and OX-40 (p = 0.014) expression were identified on CD4+ T cells of pts. Upon TCR modulation, CD4+ and CD8+ T cells from pts showed reduced signaling through p-AKT and, to a lesser extent, p-Erk, compared to HD. Signaling was lower in PD-1+ vs PD-1- CD8+ and CD4+ T cells. Addition of anti-PD-1 pembrolizumab partially restored TCR-mediated signaling through p-AKT and p-Erk in PD-1+ but not PD-1- T cells. Overall, data indicate impaired T cell signaling in PD-1+ T cells of metastatic breast cancer pts, which may explain the inability to respond to RT + TGFβ blockade. In vitro addition of anti-PD-1 improved T cell signaling through p-AKT and p-Erk. Together with the preclinical data, this supports adding anti-PD-1 to the combination of RT +TGFβ blockade. Citation Format: Sandra Demaria, Claire Vanpouille-Box, Rachael E. Hawtin, Christie Fanton, Andy Conroy, Erik Evensen, Neha Dixit, Alan Barber, Dorthe Schaue, William H. McBride, Mary Helen Barcellos-Hoff, Silvia C. Formenti. Role of the PD-1/PDL-1 pathway in resistance of patients with metastatic breast cancer to treatment with radiotherapy and TGFβ neutralization. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4987.