Early, precise, and safe clinical evaluation of the pharmacodynamic effects of novel agents in the intact human tumor microenvironment

Introduction: Drug development is systemically inefficient. Research and development costs for novel therapeutics average hundreds of millions to billions of dollars, with the overall likelihood of approval estimated to be as low as 6.7% for oncology drugs. Over half of these failures are due to a lack of drug efficacy. This pervasive and repeated low rate of success exemplifies how preclinical models fail to adequately replicate the complexity and heterogeneity of human cancer. Therefore, new methods of evaluation, early in the development trajectory, are essential both to rule-in and rule-out novel agents with more rigor and speed, but also to spare clinical trial patients from the potentially toxic sequelae (high risk) of testing investigational agents that have a low likelihood of producing a response (low benefit). Methods: The clinical in vivo oncology (CIVO®) platform was designed to change this drug development paradigm. CIVO precisely delivers microdose quantities of up to 8 drugs or combinations directly into patient tumors 4-96 h prior to planned surgical resection. Resected tissue is then analyzed for responses at each site of intratumoral drug exposure. Results: To date, CIVO has been used safely in 6 clinical trials, including 68 subjects, with 5 investigational and 17 approved agents. Resected tissues were analyzed initially using immunohistochemistry and in situ hybridization assays (115 biomarkers). As technology advanced, the platform was paired with spatial biology analysis platforms, to successfully track anti-neoplastic and immune-modulating activity of the injected agents in the intact tumor microenvironment. Discussion: Herein we provide a report of the use of CIVO technology in patients, a depiction of the robust analysis methods enabled by this platform, and a description of the operational and regulatory mechanisms used to deploy this approach in synergistic partnership with pharmaceutical partners. We further detail how use of the CIVO platform is a clinically safe and scientifically precise alternative or complement to preclinical efficacy modeling, with outputs that inform, streamline, and de-risk drug development.

Trackable Intratumor Microdosing and Spatial Profiling Provide Early Insights into Activity of Investigational Agents in the Intact Tumor Microenvironment

PURPOSE

Cancer drug development is currently limited by a paradigm of preclinical evaluation that does not adequately recapitulate the complexity of the intact human tumor microenvironment (TME). To overcome this, we combined trackable intratumor microdosing (CIVO) with spatial biology readouts to directly assess drug effects in patient tumors in situ.

EXPERIMENTAL DESIGN

In a first-of-its-kind phase 0 clinical trial, we explored the effects of an investigational stage SUMOylation-activating enzyme (SAE) inhibitor, subasumstat (TAK-981) in 12 patients with head and neck carcinoma (HNC). Patients scheduled for tumor resection received percutaneous intratumor injections of subasumstat and vehicle control 1 to 4 days before surgery, resulting in spatially localized and graded regions of drug exposure (∼1,000-2,000 μm in diameter). Drug-exposed (n = 214) and unexposed regions (n = 140) were compared by GeoMx Digital Spatial Profiler, with evaluation at single-cell resolution in a subset of these by CosMx Spatial Molecular Imager.

RESULTS

Localized regions of subasumstat exposure revealed SUMO pathway inhibition, elevation of type I IFN response, and inhibition of cell cycle across all tumor samples. Single-cell analysis by CosMx demonstrated cell-cycle inhibition specific to the tumor epithelium, and IFN pathway induction commensurate with a TME shift from immune-suppressive to immune-permissive.

CONCLUSIONS

Pairing CIVO with spatial profiling enabled detailed investigation of response to subasumstat across a diverse sampling of native and intact TME. We demonstrate that drug mechanism of action can be directly evaluated in a spatially precise manner in the most translationally relevant setting: an in situ human tumor.

Abstract 3476: TAK-243 increases tumor immunogenicity enhancing systemic anti-tumor immune response and tumor regression in combination with immune checkpoint inhibition in a syngeneic model of lymphoma

Agents that induce a shift in the activity state of the immune tumor microenvironment (TME) from “cold-to-hot” may increase response to immune checkpoint inhibitors. Here we examined whether TAK-243, a small molecule inhibitor of the ubiquitin activating enzyme (UAE), could heighten tumor immunogenicity and increase response to checkpoint inhibition. Our hypothesis was based on previous studies showing that TAK-243 induces ER stress (Hyer et al.) a phenomenon that can influence the status of the immune TME. While TAK-243 has previously shown anti-tumor potential, these studies were largely performed in immune-deficient models of cancer leaving potential influence on immune response in question. We first examined this potential using multiplexed trackable intratumor microdosing (CIVOTM, Presage Biosciences) to introduce TAK-243 alone or in combination with an anti-PD1 antibody (RPM1-14) to distinct localized positions within in a syngeneic model of lymphoma (A20). Response to localized drug exposure was then evaluated by immunohistochemistry and in situ hybridization biomarker analysis. TAK-243 induced elevation of multiple immune response biomarkers including 1) dendritic cell enrichment, 2) chemokine elevation, 3) TNFa elevation, and 4) CD8/Granzyme B elevation. We next examined whether TAK-243 could act as an “in situ vaccine” upon intratumor delivery and increase response to systemically delivered anti-PD1. Consistent with this potential, intratumor injection of TAK-243 resulted in greater regression of tumors in a dual flanked A20 xenograft model (ie one tumor on each flank of the host) when combined with systemically delivered anti-PD1 compared to either TAK-243 or anti-PD1 treatment alone. Importantly clear abscopal effects were induced as tumor regression was observed in both TAK-243 injected and non-injected tumors from subjects treated with the combination of TAK-243 and anti-PD1, 60% of which showed complete loss of tumor. Inhibition of the anti-tumor response was observed upon introduction of the drug combination with a CD8-depleting antibody. Furthermore, re-inoculation of subjects that exhibited complete regression of tumor masses with A20 cells showed no growth of new tumors. Taken together, these data suggest that intratumor injection of TAK-243 has potential to act as an in situ vaccine which increases anti-tumor immunogenicity and primes tumors for response to ICIs.

Citation Format: Richard Klinghoffer, Connor Burns, Angela Merrell, Marc Grenley. TAK-243 increases tumor immunogenicity enhancing systemic anti-tumor immune response and tumor regression in combination with immune checkpoint inhibition in a syngeneic model of lymphoma [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 3476.

Abstract 3424: Deep mechanistic profiling of immune oncology (I-O) drug combinations in cancer patients with CIVO® intratumoral microdosing and NanoString GeoMx DSP

Despite over four thousand clinical trials investigating combinations of various anti-cancer agents with immune checkpoint inhibitors (CPI), few have demonstrated significant clinical improvement over CPI alone. This indicates a need for approaches that can guide development of complex (≥ 3 drug) I-O combination treatments by enabling far greater mechanistic understanding of response to drug exposure by components of the authentic tumor microenvironment (TME). Here we show how an approach based on two technologies, the Presage Comparative In Vivo Oncology (CIVO) Platform and the NanoString GeoMx Digital Spatial Profiler (GeoMx DSP), highlights drug synergies as well as mechanisms of resistance to drug exposure in the native and intact TME of cancer patients, providing a path to rapid identification of effective drug combinations. The CIVO platform enables trackable multiplexed intratumoral delivery of microdosed drugs, either as single agents or in combinations, allowing evaluation of the localized tumor response to drug candidates in the TME while capturing tumor heterogeneity and patient diversity. GeoMx DSP is a method for high-plex spatial profiling of mRNAs with rare-cell sensitivity. Combining these technologies in Phase 0 clinical studies in human soft tissue sarcoma patients we evaluated distinct tumor sites microdosed with either nivolumab (anti-PD1), aldesleukin (recombinant IL-2), the combination of nivolumab and aldesleukin, vehicle (no drug), or chemotherapy controls. Using the Nanostring Cancer Transcriptome Atlas we evaluated the effect of drug exposure on expression of over 1,800 genes simultaneously with spatial resolution across individual patient tumors. Synergistic elevation of multiple transcripts was observed at tumor sites exposed to the combination of aldesleukin and nivolumab. This included T-cell specific elevation of granzyme B, a classic biomarker of T-cell activation. Importantly, we show how events such as T-cell activation may be dampened by feedback loops involving immune suppressive responses including, but not limited to, elevation of IDO-1 in non-T-cell components of the TME. Results were observed across multiple patient tumors and were verified by conventional immuno-histochemistry or in situ hybridization. Performing these studies across different patients allows us to explore the inter-individual variation in drug responses. We believe this is an efficient and biologically relevant approach to better understanding feedback loops activated within the authentic TME and ultimately prioritizing drug combinations for clinical development.

Citation Format: Jason P. Frazier, Kenneth R. Gundle, Marc Grenley, Gloria Kung, Kimberly Sottero, Kirsten Anderson, Richard Klinghoffer, Jonathan M. Derry. Deep mechanistic profiling of immune oncology (I-O) drug combinations in cancer patients with CIVO® intratumoral microdosing and NanoString GeoMx DSP [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 3424.

Abstract 620: Intratumoral microdosing via the CIVO® Platform reveals anti-tumor immune responses induced by the STING Agonist TAK-676 alone and in combination with chemotherapies

Purpose/Objectives: Individual tumor complexity and the emergence of treatment resistance mechanisms have proven challenging for oncology drug development, and methods for prioritizing combination therapy approaches are needed. The CIVO (Comparative In Vivo Oncology) platform can simultaneously deliver up to 8 drugs and combinations in microdose amounts to distinct, trackable regions within a single intact tumor, enabling studies that can assess multiple drugs and combinations directly in patients during early drug development. This study employed CIVO to assess two combination strategies incorporating the STING (Stimulator of Interferon Genes) agonist TAK-676 and chemotherapies capable of inducing immunogenic cell death. We evaluated TAK-676’s ability to elicit pharmacodynamic (PD) changes suggestive of anti-tumor immune activation within the tumor microenvironment (TME) in a syngeneic mouse model, both as monotherapy and in combination with cisplatin and 5-FU or cisplatin and paclitaxel chemotherapy doublets.

Materials/Methods: TAK-676 and chemotherapy combinations were simultaneously microdosed via CIVO in a syngeneic mouse melanoma model (YUMM1.7). Successful injections were visualized after administration, during sample processing, and in biomarker-stained tissue sections via a fluorescent tracking marker co-injected through each needle, and PD responses were assessed via immunohistochemistry and in situ hybridization following tumor resection.

Results: Drug mechanism of action-specific biomarker activity was evident as early as 4 hours after injection. TAK-676 induced robust elevation of pIRF3 and CXCL10 along with IFNγ from both T and NK cell compartments, indicating STING pathway activation. Phospho-histone H3 accumulation was noted in response to paclitaxel-induced mitotic arrest. 5-FU and cisplatin induced localized DNA damage, visible via elevated phospho-histone H2AX-positive nuclei. Cytotoxic T lymphocyte (CTL) accumulation was detected around TAK-676 injection sites, likely recruited from the local TME via induction of chemokines such as CXCL10. Early tumor cell apoptosis and induction of pro-inflammatory cytokines such as CXCL10 were detected in response to both triplet combinations. CTL activation was enhanced in response to both triplet combinations by 24 hours, whereas CTL enrichment at levels greater than induced by TAK-676 alone was noted specifically in response to the triplet combination with cisplatin and paclitaxel by 72 hours.

Conclusion: These studies highlight TAK-676’s potential to promote anti-tumor immunity and the utility of the CIVO platform to reveal and characterize combination-specific responses. This application of CIVO is being further evaluated in an ongoing Phase 0 trial in patients with head and neck squamous cell carcinoma (NCT04541108).

Citation Format: Beryl A. Hatton, Marc Grenley, Sally Ditzler, Richard A. Klinghoffer, Allison J. Berger, Karim S. Malek, Richard C. Gregory, Neil B. Lineberry. Intratumoral microdosing via the CIVO® Platform reveals anti-tumor immune responses induced by the STING Agonist TAK-676 alone and in combination with chemotherapies [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 620.

Abstract A39: A platform to assess multiple therapy options simultaneously in a patient's own tumor

Assessment of anti-cancer drug efficacy is an imprecise and challenging undertaking. Early candidate selection is typically based on results from systemically treated animal models and later by performance in human trials where patients are exposed to often toxic levels of drug, prior to obtaining readouts of tumor response. In both of these testing models, only one drug can be tested at a time. Using these methods, over 90% of candidate new oncology drugs fail to provide benefit for patients in human clinical trials.

To improve the predictive value of preclinical candidate selection in animal models and enable a new type of pre-Phase 1 toxicity-sparing comparative drug efficacy study in humans, amenable for use in the solid tumor clinic, we have developed a technology platform called CIVO™. This platform allows for simultaneous assessment of multiple drugs or drug combinations directly in a single solid tumor to assess efficacy, resistance and drug synergies.

In this study, precise, controlled delivery of classic chemotherapy drugs vincristine and doxorubicin induced spatially defined (ranging 0.3 – 2.0 mm in diameter), readily detectable, and mechanism-specific cellular changes around sites of tumor microinjection across three xenograft models of lymphoma. The extent of apoptosis induced via CIVO™ microdosing of each drug (<1/100th the effective dose used to treat human patients) correlated with drug effect on tumor growth mediated by conventional systemic drug dosing. Consistent with utility for detecting pre-existing tumor resistance to certain drugs, CIVO™ microdosing predicted diminished responses to both vincristine and doxorubicin in tumors derived from cells that had previously acquired resistance to doxorubicin. This lack of efficacy was confirmed by systemic treatment of the resistant tumors. The CIVO™ platform is concurrently being evaluated for correlation to systemic treatment in immune-intact canine patients with autochthonous tumors.

The data presented here generated in drug-responsive and non-responsive solid tumors in the preclinical setting sets the stage for future application of this technology to demonstrate tumor responsiveness to novel drug candidates in the context of human patients.

Citation Format: Richard Klinghoffer, Alicia Moreno-Gonzalez, Michael Carleton, Marc Grenley, Beryl Hatton, Jason Frazier, William Kerwin, Ilona Tretyak, Nathan Hedin, Joyoti Dey, Joseph Casalini, Sally Ditzler, James Olson, Nathan Caffo. A platform to assess multiple therapy options simultaneously in a patient's own tumor. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A39.

Abstract 3129: A platform to assess multiple therapy options simultaneously in a patient's own tumor

Proper selection of anti-cancer agents at the earliest stage of patient treatment following diagnosis of disease relapse is expected to substantially impact clinical response to treatment. Currently, genomic approaches to personalized cancer treatments have been yielded mixed results, while empirical tests to assess tumor responsiveness have been limited to ex vivo systems that disrupt the native tumor microenvironment and show limited predictive value. To address the need for multiplexed in vivo chemosensitivity testing, we have developed a technology that allows simultaneous assessment of multiple cancer therapeutics directly in a patient's tumor. This technology could provide a valuable decision-making tool to prioritize effective treatments in the oncology clinic. Data herein highlight how this technology enables controlled and reliable microinjection of multiple drugs simultaneously in preclinical tumor models, canine lymphoma, and human lymphoma patients. Consistent with the controlled drug delivery of this system, spatially localized, readily detectable, and mechanism-specific cellular changes were observed around sites of microinjection in response to classic chemotherapy drugs (vincristine and doxorubicin) as well as to a small molecule inhibitor of TOR kinase. Importantly, localized response (or lack thereof) to individual components of CHOP combination therapy correlated with response to long-term systemic drug administration across multiple cell line and patient-derived xenograft models of lymphoma. Underscoring the importance of assessing drug efficacy in the context of an intact in vivo system, tumor responses to vincristine were impacted by the local tumor microenvironment. Our results also emphasize the importance of selecting effective therapies early in the course of treatment, as drug resistance mechanisms induced cross-resistance to otherwise efficacious drugs. These studies set the stage for use of this platform in oncology drug development, where the ability to more rapidly assess drug efficacy using clinically relevant in vivo tumors may decrease the current reliance on in vitro cell-based models of cancer and possibly increase the likelihood of clinical success. This platform may thus be useful a clinical decision-making tool for selection of patient-specific anti-cancer therapies.

Citation Format: Richard Klinghoffer, Alicia Moreno-Gonzalez, Michael Carleton, Jason Frazier, Marc Grenley, Ilona Tretyak, Nathan Hedin, Joyoti Dey, Joseph Casalini, Beryl Hatton, Sally Ditzler, James Olson, Daniel Pierce, Ellen Filvaroff, Nathan Caffo. A platform to assess multiple therapy options simultaneously in a patient's own tumor. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3129. doi:10.1158/1538-7445.AM2014-3129

Abstract 4153: Arrayed microinjection of a ubiquitin activating enzyme inhibitor induces PD biomarker effects predictive of in vivo tumor responses to systemic drug delivery

Presage technology enables simultaneous analysis of multiple cancer drug candidates, drug concentrations, and drug combinations within a single living tumor. The platform employs arrayed tumor microinjection technology that delivers multiple spatially defined “threads” of drug directly into discreet portions of a tumor. This enables rapid, reliable, and internally controlled cross comparisons of multiple cancer therapeutics using screening quantities of drug in an in vivo setting in which the local tumor microenvironment is maintained. Here, as an example, we apply the platform to investigate tumor responsiveness to an inhibitor of the ubiquitin activating enzyme UBA1 from Millennium Pharmaceuticals.

The ubiquitin activating enzyme UBA1 regulates ubiquitin activation and subsequent polyubiquitination of proteins necessary for their degradation by the proteasome, and functionally impacts cell signaling, DNA damage repair and cell cycle progression. In vivo tumor responses were evaluated in two human xenograft models, WSU-DLCL2 and MCF-7, grown as flank tumors in immune-compromised mice. Microdosing of multiple concentrations of the UBA1 inhibitor (UBAi) into both models led to localized, easily detectable, and drug concentration-dependent biomarker changes indicative of ubiquitin pathway perturbation in the area proximal to injected drug. This included loss of poly-ubiquitin, accompanied by the expected accumulation of cMyc in tumor regions exposed to the UBAi. Localized time-dependent tumor cell death responses were observed following pathway perturbation as quantified by staining for cleaved caspase-3 and gamma-H2AX staining. Furthermore, pathological evidence of UBAi-induced cell death was clearly visible in both tumor models upon histological examination of H&E stained slides. These results highlight the capacity of the Presage platform to perform multiplexed drug studies in live tumor models. This capability could readily be expanded for use in validating additional biomarker hypotheses, indication finding studies, or for efficient identification of novel drug combinations.

Citation Format: Beryl A. Hatton, Marc Grenley, Nathan Hedin, Nathan Caffo, Marc L. Hyer, Mark Manfredi, Stephen Blakemore, Richard A. Klinghoffer, Neil Bence. Arrayed microinjection of a ubiquitin activating enzyme inhibitor induces PD biomarker effects predictive of in vivo tumor responses to systemic drug delivery. [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 4153. doi:10.1158/1538-7445.AM2013-4153

Abstract 5116: Identification and rapid in vivo validation of a novel drug combination for treating melanoma

The well-established capability of tumors to resist single agent chemotherapies underscores the need to identify novel synergistic drug combinations to treat patients with cancer. Here we use an innovative arrayed needle technology to provide rapid in vivo validation of findings from a genome scale RNAi screen and reveal the potential of an unexpected drug combination to treat patients with melanoma. Our efforts focused on the β-catenin pathway. The β-catenin pathway impacts cancer progression in a context dependent manner. In some malignancies such as colon cancer, increased β-catenin activity drives oncogenesis. In contrast activation of β-catenin has been associated with decreased tumor proliferation and improved prognosis in patients with melanoma. A screen with an arrayed library of 14,000 lentiviral shRNA vectors revealed that silencing of dihydrofolate reductase, the target of the classic chemotherapeutic methotrexate, led to synergistic activation of the β-catenin pathway when combined with an inhibitor of GSK3. We therefore explored whether combination therapy, consisting of a GSK3 inhibitor and methotrexate could represent a potential treatment for melanoma patients. Two distinct small molecule inhibitors of GSK3, 6-bromoindirubin-3αoxime (BIO) and Chiron 99021, demonstrated synergy with methotrexate to activate β-catenin signaling in the melanoma cell line A375. To rapidly assess whether the observed synergy translates to the context of a living tumor, precision multiplexed microinjection using Presage technology was performed on mice harboring flank melanoma tumors. Discreet positions on each tumor were injected with either vehicle control, methotexate as a single agent, Chiron 99021 as a single agent, or the combination of the two agents. Analysis of the activation of beta-catenin and histology for markers of cellular proliferation, death, and differentiation allowed us to rapidly evaluate the efficacy of this drug combination. This rapid in vivo validation approach sets the stage for full preclinical evaluation of combined methotrexate and GSK3 inhibitor therapy using advanced co-clinical models of melanoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5116. doi:1538-7445.AM2012-5116