Reverse Translating Molecular Determinants of Anti-Programmed Death 1 Immunotherapy Response in Mouse Syngeneic Tumor Models

Targeting the programmed death 1/programmed death ligand 1 (PD-1/PD-L1) pathway with immunotherapy has revolutionized the treatment of many cancers. Somatic tumor mutational burden (TMB) and T-cell-inflamed gene expression profile (GEP) are clinically validated pan-tumor genomic biomarkers that can predict responsiveness to anti-PD-1/PD-L1 monotherapy in many tumor types. We analyzed the association between these biomarkers and the efficacy of PD-1 inhibitor in 11 commonly used preclinical syngeneic tumor mouse models using murinized rat anti-mouse PD-1 DX400 antibody muDX400, a surrogate for pembrolizumab. Response to muDX400 treatment was broadly classified into three categories: highly responsive, partially responsive, and intrinsically resistant to therapy. Molecular and cellular profiling validated differences in immune cell infiltration and activation in the tumor microenvironment of muDX400-responsive tumors. Baseline and on-treatment genomic analysis showed an association between TMB, murine T-cell-inflamed gene expression profile (murine-GEP), and response to muDX400 treatment. We extended our analysis to investigate a canonical set of cancer and immune biology-related gene signatures, including signatures of angiogenesis, myeloid-derived suppressor cells, and stromal/epithelial-to-mesenchymal transition/TGFβ biology previously shown to be inversely associated with the clinical efficacy of immune checkpoint blockade. Finally, we evaluated the association between murine-GEP and preclinical efficacy with standard-of-care chemotherapy or antiangiogenic agents that previously demonstrated promising clinical activity, in combination with muDX400. Our profiling studies begin to elucidate the underlying biological mechanisms of response and resistance to PD-1/PD-L1 blockade represented by these models, thereby providing insight into which models are most appropriate for the evaluation of orthogonal combination strategies.

Rational design of a SOCS1-edited tumor-infiltrating lymphocyte therapy using CRISPR/Cas9 screens

Cell therapies such as tumor-infiltrating lymphocyte (TIL) therapy have shown promise in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought. To identify targets capable of enhancing the antitumor activity of T cell therapies, large-scale in vitro and in vivo clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screens were performed, with the SOCS1 gene identified as a top T cell-enhancing target. In murine CD8+ T cell-therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of central memory T cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cells (Texprog) in tumors. A comprehensive CRISPR tiling screen of the SOCS1-coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with an sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9. KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo antitumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.

Abstract 1337: Functional genomic characterization of the USP1 inhibitor KSQ-4279 reveals a distinct mechanism of action and resistance profile relative to other DDR targeting drugs

Genomic instability is a hallmark of most cancers that enables tumor cells to adapt and evolve, but also creates vulnerabilities that can be therapeutically exploited. Cancer therapies that target the DNA Damage Response (DDR) have proven to be efficacious across a broad range of cancer types, but often present a narrow therapeutic window and limited duration of response due to the development of resistance. Through mining our proprietary CRISPRomics® Oncology dataset we identified the ubiquitin protease, USP1, as an attractive target with activity in ovarian and triple negative breast cancers (TNBC). USP1 facilitates DNA repair via its role regulating the Fanconi anemia complex and translesion synthesis. We developed a series of potent, selective USP1 inhibitors to investigate the therapeutic potential of targeting USP1 in tumor settings dependent on those DNA repair processes. When profiled across a broad range of cancer cell line models, the USP1-inhibitor KSQ-4279 showed anti-proliferative effects in a subset of cell lines, often characterized by the presence of homologous recombination deficiencies (HRD), including mutations in BRCA1/2. To better understand the mechanism of action of KSQ-4279, we employed large scale functional genomic screens using KSQ-4279, olaparib, and cisplatin, in combination with a DNA-repair focused CRISPR library, to identify genetic determinants of sensitivity and anticipate modes of drug resistance. In addition to recovering genetic associations between KSQ-4279 and genes that modify USP1's direct substrates, our screens identified genetic interactions of KSQ-4279 with multiple DNA repair pathways, including genes involved in ubiquitin-mediated signaling events that regulate the response to DNA damage and replication stress. These studies revealed that the profile of resistance to KSQ-4279 is distinct from, and in some cases complementary to, other DNA damaging agents, and provide a mechanistic rationale for the use of KSQ-4279 in combination with other agents that target DNA repair. Consistent with the largely non-overlapping resistance profile of USP1 and PARP inhibitors, we found that the combination of KSQ-4279 with olaparib was able to induce strong and durable regressions across a number of ovarian and TNBC PDX models.

Citation Format: Sol Shenker, Hugh Gannon, Alyssa Carlson, Paula Grasberger, Pamela Sullivan, Chris Middleton, Anne Dodson, Caroline Bullock, Michael McGuire, Erica Tobin, Kerstin Sinkevicius, Mike Schlabach, Frank Stegmeier, Louise Cadzow, Andrew Wylie. Functional genomic characterization of the USP1 inhibitor KSQ-4279 reveals a distinct mechanism of action and resistance profile relative to other DDR targeting drugs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1337.

Abstract 699: Optimized dosing strategies resulting in prolonged pathway inhibition enhance dinaciclib anti-tumor activity in preclinical xenograft models

Dinaciclib is a novel CDK1, 2, 5, and 9 inhibitor currently in clinical development for CLL. Preclinical studies indicate that dinaciclib may have activity in a wide variety of indications including hematologic malignancies and solid tumors. Clinically, dinaciclib is administered by 2 hour intravenous (iv) infusion and achieves plasma concentrations above 100nM for ∼6 hours; a concentration and duration of treatment which in vitro provides complete target engagement and induces apoptosis. Pre-clinically, dinaciclib is administered by intraperitoneal (ip) bolus injections and achieves plasma concentrations above 100nM for less than 2 hours. To determine whether prolonged plasma concentrations would enhance dinaciclib activity, we administered dinaciclib to COLO-320DM tumor bearing mice either as a 40 mg/kg single dose, or as two doses of 20 mg/kg separated by 2 hours. This 20-20 split dosing resulted in prolonged target engagement, phospho-RNA-Polymerase-2 reduction, decreased MCL-1, and increased apoptosis relative to the 40mg/kg single dose. Comparing the in vivo anti-tumor activity of dinaciclib dosed at 40 mg/kg ip every 4 days (q4d) vs. 20 mg/kg bid separated by 2 hours q4d demonstrated that the 20-20 split dose increased the anti-tumor activity of dinaciclib (25% Tumor Growth Inhibition (TGI) versus 66% TGI). Dinaciclib single vs. split dosing was further evaluated in 8 lung cancer xenograft models, 5 of which were insensitive to dinaciclib single dose (TGI >50%) and 3 of which were sensitive. 20-20 split dosing resulted in increased anti-tumor activity in all models tested. Split dosing resulted in <50% TGI in 4 of 5 insensitive models. Split dosing also increased anti-tumor activities in all 3 sensitive models tested resulting in stasis in 2 models, and sustained complete regressions in one lung cancer xenograft model. Body weight measurements revealed that split dosing increased body weight loss indicating that prolonged pathway inhibition can affect both anti-tumor activity and tolerability. Taken together, these data suggest that dinaciclib dosing paradigms that prolong pathway inhibition enhanced anti-tumor activity in pre-clinical xenograft models.

Citation Format: Alwin Schuller, Robert Booher, Louise Cadzow, Minilik Angagaw, Lauren Harmonay, Xianlu Qu, Nathan Miselis, Vincenzo Pucci, Mark Ayers, Thorsten Graef, Ellie Im, Rebecca Blanchard, Brian Long, Leigh Zawel, peter strack. Optimized dosing strategies resulting in prolonged pathway inhibition enhance dinaciclib anti-tumor activity in preclinical xenograft models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 699. doi:10.1158/1538-7445.AM2013-699

Abstract C101: Comprehensive identification of novel therapeutic targets for treatment of PD-1 resistant solid tumors via a genome-scale CRISPR/Cas9 in vivo T-cell screen

Although immunotherapy with PD-1/PD-L1 antagonists has significantly advanced patient care, the majority of cancer patients currently do not benefit from checkpoint inhibitor therapies. To identify novel targets for the treatment of PD-1 insensitive cancers, we developed a novel Immune-CRISPRomicsTM platform that enabled genome-wide CRISPR/Cas9 screens in primary T cells in an in vivo setting. Notably, the screen identified clinically active molecules, such as PD-1 and also predicted recent clinical failures. In addition, we identified multiple targets that enhanced anti-tumor T-cell function similar to or better than PD-1 as a monotherapy. The anti-tumor activity of targets was assessed across a collection of PD-1 sensitive and PD-1 refractory syngeneic tumor models. One of the targets identified, IO-7, was found to possess robust activity across multiple PD-1 refractory models. We found that inhibition of IO-7 leads to long-term T-cell memory and prevents tumor growth upon re-challenge. Moreover, mechanistic follow-up studies demonstrate that IO-7 inhibition leads to an expansion of central memory T-cell subsets, which have been implicated in driving the durable clinical response of checkpoint inhibitors. We describe the first genome-wide in vivo T-cell CRISPR/Cas9 screen, which identified multiple therapeutic targets that present promising therapeutic opportunities for the treatment of PD-1 resistant solid tumors.

Citation Format: Isabelle Le Mercier, Jason J. Merkin, Sean Keegan, Conor Calnan, Anja F. Hohmann, Nick Colletti, Eric Fagerberg, Sol Shenker, Caroline Bullock, Chris Wrocklage, Noah Tubo, Tianlei Xu, Matt Noyes, Rami Rahal, Sean Arlauckas, Aria Pearlman Morales, Frank Stegmeier, Louise Cadzow, Mike Schlabach, Gregory Kryukov, Micah J. Benson. Comprehensive identification of novel therapeutic targets for treatment of PD-1 resistant solid tumors via a genome-scale CRISPR/Cas9 in vivo T-cell screen [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C101. doi:10.1158/1535-7163.TARG-19-C101

Abstract 1581: KSQ-4279, a first-in-class USP1 inhibitor shows strong combination activity with multiple PARP inhibitors in BRCA mutant cancers

Tumors harboring BRCA1/2 mutations and other homologous recombination deficiencies are sensitive to agents targeting pathways involved in DNA repair including poly (ADP-ribose) polymerase (PARP) inhibitors, which have been approved for the treatment of BRCA mutant cancers. Despite the clinical benefit with these drugs, many patients achieve incomplete disease control and often develop resistance. By employing our CRISPRomics® technology to screen over 600 cancer cell lines, we identified the deubiquitinating enzyme USP1 as one of the top targets that displays selective anti-tumor activity in ovarian and triple negative breast cancers with homologous recombination deficiencies. Subsequent drug discovery efforts identified KSQ-4279 as a potent and highly selective first-in-class small molecule USP1 inhibitor that is now in clinical development. In preclinical models, we previously demonstrated that KSQ-4279 shows therapeutic potential in combination with olaparib for treating patients who are either intrinsically resistant, or have developed acquired resistance to PARP inhibitors. We performed studies to investigate the therapeutic potential of combining KSQ-4279 across a variety of PARP inhibitors with different ‘PARP trapping’ potencies. Clonogenic assays demonstrated synergistic effects of KSQ-4279 across multiple PARP inhibitors regardless of their PARP trapping potency. Second generation PARP1 selective inhibitors such as AZD5305 are currently in clinical development and may provide a safety and efficacy advantage for patients. We have investigated the potential of combining KSQ-4279 with AZD5305 in a PARP refractory patient-derived triple negative breast cancer (TNBC) xenograft model by evaluating tolerability and anti-tumor efficacy. We observed significantly greater and more durable anti-tumor activity, including regressions, with the combination therapy compared to single agents. Our data supports the clinical testing of KSQ-4279 in combination with PARP inhibitors.

Citation Format: Erica Tobin, Pamela Sullivan, Morgan Murray, Hugh Gannon, Anne Dodson, Sol Shenker, Frank Stegmeier, Andrew Wylie, Louise Cadzow. KSQ-4279, a first-in-class USP1 inhibitor shows strong combination activity with multiple PARP inhibitors in BRCA mutant cancers [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 1581.

Pan-Cancer Analysis of Homologous Recombination Deficiency in Cell Lines

SIGNIFICANCE

HRD is common in cancer and can be exploited therapeutically, as it sensitizes cells to DNA-damaging agents. Here, we scored more than 1,300 cancer cell lines for HRD using two different bioinformatic approaches, thereby enabling large-scale analyses that provide insights into the etiology and features of HRD.

Abstract B25: Development of a nanoparticle containing the PI3K/mTOR dual Inhibitor, gedatolisib, for cancer therapy

Gedatolisib, a PI3K/mTOR dual inhibitor delivered intravenously, is in early clinical trials in women with metastatic ER+ breast cancer. We reasoned that the therapeutic index could be further maximized by encapsulation of gedatolisib in nanoparticles (NP), thereby providing longer half-life, sustained release, blunting of Cmax and associated toxicity, asymmetric distribution to leaky tumor vasculature and the possibility of less frequent dosing. PF-07034663 is a polymeric NP encapsulating gedatolisib, targeted to prostate-specific membrane antigen (PSMA), a clinically validated tumor antigen expressed on prostate cancer cells and the neovasculature of some nonprostate solid tumors. Studies in mice, rats, and cynomolgus monkeys demonstrated that the terminal half-life of PF-07034663 following intravenous administration increased by ~1.5 fold and the Cmax of released gedatolisib from PF-07034663 decreased by ~75 fold compared to gedatolisib delivered by the same route. Gedatolisib released from PF-07034663 exhibited markedly enhanced intratumoral accumulation compared to gedatolisib (~40 fold), indicating enhanced tissue delivery and/or prolonged retention. In exploratory toxicology studies, PF-07034663 caused no hyper-insulinemic spike in rats, in contrast to gedatolisib. To evaluate the antitumor activity of PF-07034663, we performed tumor growth inhibition (TGI) studies in PSMA-positive C4-2 prostate and in PSMA-negative MDAMB361 ER+ breast and A549 lung xenograft tumor models. In the C4-2 model, PF-07034663 showed dose-dependent antitumor efficacy as a single agent, and, in combination with enzalutamide, exhibited enhanced activity leading to tumor regressions. PF 07034663 also exhibited prolonged, dose-dependent inhibition of phosphorylation of S6 (pS6) in the C4-2 model compared to gedatolisib. Interestingly, increased pharmacodynamics (PD) responses compared to gedatolisib were not restricted to PSMA-positive tumors. Moreover, TGI responses were increased in the PSMA-negative A549 lung cancer model, relative to those observed with gedatolisib. PF 07034663 treatment in spontaneous prostate tumors in PTENnullp53mut GEM mice and in subcutaneous allografts of these spontaneous tumors in wild-type mice showed that treatment of PF-07034663 caused similar pS6 inhibition in both models, suggesting that PD modulation is independent of tumor origin or milieu and is less likely due to altered enhanced permeability and retention (EPR) effect. Taken together, PF-07034663 exhibits potential for improved tolerability, sustained tumor PK, prolonged PD modulation, and less frequent dosing schedule compared to gedatolisib. These results support further exploration of gedatolisib in tumor-targeted or non-tumor-targeted nanoparticles in clinical trials as a promising vehicle for delivery of PI3K/mTOR inhibitors to advanced cancer patients.

Citation Format: Lianglin Zhang, Gabriel Troche, Ravi Visswanathan, Wenhu Huang, Young-Ho Song, Mary E. Spilker, Zhenxiong Wang, Hui Wang, Anand Giddabasappa, Louise Cadzow, Susan Low, Greg Troiano, Jennifer Lafontaine, Valeria Fantin, Robert T. Abraham, Shubha Bagrodia. Development of a nanoparticle containing the PI3K/mTOR dual Inhibitor, gedatolisib, for cancer therapy [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B25.

204 KSQ-004: Unbiased pair-wise discovery of SOCS1 and Regnase-1 as the top CRISPR/Cas9 dual-edit combination enhancing in vivo TIL potency against solid tumors

Background

The application of CRISPR/Cas9-gene-editing to enhance the anti-tumor activity of T cell Adoptive Cell Therapies (ACT) is a promising approach in the treatment of patients with solid tumors. We developed an in vivo CRISPR^2 screening approach and interrogated the top dual-edit combinations enhancing T cell anti-tumor function. We discovered that across all possible dual-edit combinations of T cell targets, inactivation of Regnase-1 and SOCS1 led to the greatest enhancement in anti-tumor T cell potency in vivo. We applied these findings to discover KSQ-004, a Regnase-1/SOCS1 dual-edited human CRISPR/Cas9-engineered TIL (eTIL) therapy currently under development for therapeutic use.

Methods

We generated randomly paired CRISPR guide libraries (CRISPR2) targeting top hits from previous single-gene Immune CRISPRomics® screens. CRISPR^2 libraries with over 1200 gene pairs were screened in primary mouse OT1 and PMEL-TCR-Tg-T cells in the relevant syngeneic tumor models. Top dual-edit combinations were then evaluated in the immunotherapy-refractory B16F10 metastatic lung tumor model. The efficacy of the top combo was further evaluated in a mouse TIL model wherein TIL from B16-Ova tumors were expanded and engineered ex vivo and adoptively transferred into tumor bearing hosts for efficacy assessment.

Results

Of the 1200+ combinations tested in the CRISPR^2 screens, the Regnase-1/SOCS1 combination ranked amongst the top dual-edits, with this combination enhancing T cell infiltration into tumors >3500-fold in comparison to controls. Studies conducted in the checkpoint therapy refractory B16F10 lung metastasis model revealed that Regnase-1/SOCS1 dual-edited PMEL-TCR-Tg-T cells conferred remarkable survival benefit relative to controls, significantly extending median survival of animals from 21 days to 53 days. Furthermore, Regnase-1+SOCS1-edited mouse TIL isolated and expanded from B16-Ova tumors exerted complete control of tumors upon re-infusion into hosts, suggesting rejuvenation of tumor-experienced TILs by this edit combination. To apply these insights for therapeutic use, we discovered KSQ-004, a human Regnase-1/SOCS1 dual-edited CRISPR/Cas9-engineered TIL (eTIL). Methods were developed to manufacture KSQ-004 from melanoma and NSCLC tumor samples, with eTIL demonstrating robust expansion and viability comparable to unedited control TIL with over 90% knockout of both targets. Importantly, KSQ-004 produced elevated IFNγ upon autologous tumor stimulation and exerted greater control of tumor spheroids in vitro.

Conclusions

We used a novel CRISPR^2 screen approach to identify Regnase-1/SOCS1 as the top dual edit combination enhancing T cell function in the tumor microenvironment. We translated these findings to therapeutic use with the discovery of KSQ-004, a dual-edited eTIL therapy engineered that possesses enhanced anti-tumor potency and persistence against solid tumors.

The USP1 Inhibitor KSQ-4279 Overcomes PARP Inhibitor Resistance in Homologous Recombination-Deficient Tumors

Defects in DNA repair pathways play a pivotal role in tumor evolution and resistance to therapy. At the same time, they create vulnerabilities that render tumors dependent on the remaining DNA repair processes. This phenomenon is exemplified by the clinical activity of PARP inhibitors in tumors with homologous recombination (HR) repair defects, such as tumors with inactivating mutations in BRCA1 or BRCA2. However, the development of resistance to PARP inhibitors in BRCA-mutant tumors represents a high unmet clinical need. In this study, we identified deubiquitinase ubiquitin-specific peptidase-1 (USP1) as a critical dependency in tumors with BRCA mutations or other forms of HR deficiency and developed KSQ-4279, the first potent and selective USP1 inhibitor to enter clinical testing. The combination of KSQ-4279 with a PARP inhibitor was well tolerated and induced durable tumor regression across several patient-derived PARP-resistant models. These findings indicate that USP1 inhibitors represent a promising therapeutic strategy for overcoming PARP inhibitor resistance in patients with BRCA-mutant/HR-deficient tumors and support continued testing in clinical trials. Significance: KSQ-4279 is a potent and selective inhibitor of USP1 that induces regression of PARP inhibitor-resistant tumors when dosed in combination with PARP inhibitors, addressing an unmet clinical need for BRCA-mutant tumors.

Abstract ND01: KSQ-4279: A first-in-class USP1 inhibitor for the treatment of cancers with homologous recombination deficiencies

Tumors with BRCA1/2 mutations and other homologous repair deficiencies (HRD) are vulnerable to agents that target the remaining DNA repair pathways, including platinum-containing chemotherapy agents and molecules targeting poly (ADP-ribose) polymerase-1 (PARP1). Despite the clinical benefit achieved with these drugs, many patients achieve incomplete disease control and resistance often emerges. With the goal of addressing this clinical need, we applied our proprietary CRISPRomics technology to identify novel targets in cancer indications characterized by defects in DNA repair pathways. One of the top ranked targets was the deubiquitinating enzyme USP1. USP1 has established roles in DNA damage repair processes including Translesion Synthesis and the Fanconi Anemia pathway. We developed KSQ-4279, a potent, highly selective inhibitor of USP1. KSQ-4279 was active in cells, leading to the accumulation of mono-ubiquitinated substrates of USP1 and inhibited the proliferation of cancer cell lines with BRCA mutations or other HRD alterations. Studies investigating the effect of combining KSQ-4279 with PARP inhibitors revealed clear evidence of synergy in cell lines with partial or no sensitivity to each agent alone. To investigate how the distinct mechanisms of action of KSQ-4279 and PARP inhibitors would be reflected in their resistance profiles, we used our CRISPRomics technology to perform functional genomic resistance screens. The top scoring resistance genes for KSQ-4279 were distinct from those identified for PARP inhibitors, which raised the possibility that combining PARP and USP1 inhibitors may provide more durable disease control by reducing the emergence of resistance. Evaluation of KSQ-4279 in patient-derived ovarian and triple-negative breast cancer xenograft models demonstrated dose-dependent tumor growth inhibition as a single agent and in combination with PARP inhibitors. In xenograft models that were insensitive or only partially sensitive to PARP inhibitors, the combination of KSQ-4279 and Olaparib led to tumor regressions and durable tumor control. This data supports the ongoing clinical trial of KSQ-4279 in patients with tumors harboring BRCA1/2 or other HRD mutations, both as a single agent and in combination with PARP inhibitors.

Citation Format: Louise Cadzow, Erica Tobin, Pamela Sullivan, Sol Shenker, Sumeet Nayak, Janid Ali, Hugh Gannon, Anne Dodson, Paula Grasberger, Alyssa Carlson, Michael McGuire, Jehrod Brenneman, Hanlan Liu, Andrew Olaharski, Kerstin Sinkevicius, Jeff Hixon, Elsa Krall, Mike Schlabach, Matt Goulet, Jeremy Wilt, Patricia Harris, Frank Stegmeier, Andrew Wylie. KSQ-4279: A first-in-class USP1 inhibitor for the treatment of cancers with homologous recombination deficiencies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr ND01.

186 Development of KSQ-001, an engineered TIL (eTIL) therapy for solid tumors through CRISPR/Cas9-mediated editing of SOCS1

Background

Adoptive cell therapy with ex vivo expanded tumor infiltrating lymphocytes (TIL) offers a potentially curative treatment for cancer. However, the immunosuppressive tumor microenvironment limits the effectiveness of TIL therapy. To address this medical need, we used our Immune-CRISPRomics® Platform to perform a series of genome-wide CRISPR/Cas9 screens to identify targets enhancing the ability of T cells to infiltrate and kill solid tumors in an in vivo setting. These screens identified SOCS1 as a top target that restrains T cell anti-tumor immunity. Based on these findings, we developed KSQ-001, an engineered TIL (eTIL) therapy created via CRISPR/Cas9-mediated editing of SOCS1 for the treatment of solid tumors.

Methods

Genome-wide CRISPR/Cas9 screens were conducted in in vitro primary human T cells and TIL cultures and in in vivo primary mouse OT1 and PMEL-TCR-Tg T cells in syngeneic tumor models. The efficacy of surrogate murine KSQ-001 (mKSQ-001), in which the SOCS1 gene is inactivated by CRISPR/Cas9 in OT1 or PMEL-TCR-Tg T cells, was evaluated in both the B16-Ova and CRC-gp100 syngeneic tumor models, with memory formation and efficacy evaluated both in the presence and absence of cyclophosphamide-mediated lymphodepletion. KSQ-001 was manufactured from human TIL using SOCS1-targeting sgRNAs selected for therapeutic use based on potency and selectivity, with KSQ-001 characterized for in vitro function and in vivo anti-tumor efficacy.

Results

Upon adoptive transfer of a single dose into solid tumor-bearing hosts, mKSQ-001 was found to robustly enhance anti-tumor efficacy and eradicate tumors in 7/10 mice in the PD1-sensitive OT1/B16-Ova model and to drive responses in the PD-1 refractory PMEL/CRC-gp100 syngeneic tumor model. mKSQ-001 also showed a ten-fold increase in anti-tumor potency in vivo compared to unengineered T-cell product and established durable anti-tumor memory by persisting in the form of T central memory cells detectable at high frequency in the peripheral blood of complete responder mice. In the setting of lymphodepletion, mKSQ-001 also displayed heightened anti-tumor potency, accumulation, and memory formation in comparison to inactivation of PD-1. Importantly, human KSQ-001 displayed a transcriptional signature indicative of increased anti-tumor function, produced increased amounts of pro-inflammatory cytokines, exhibited a hypersensitivity to IL-12 signaling, and demonstrated increased anti-tumor function both in vitro and in vivo solid tumor models.

Conclusions

Based on insights from our Immune-CRISPRomics® platform and demonstrated efficacy across multiple preclinical tumor models, we have developed KSQ-001, a novel eTIL therapy. These preclinical data support clinical testing of KSQ-001 in a variety of solid tumor indications.