The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity

Immune checkpoint blockade is effective for some patients with cancer, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance1,2. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour cells or immune cells promotes anti-tumour immunity3-6. However, phosphatases are challenging drug targets; in particular, the active site has been considered undruggable. Here we present the discovery and characterization of ABBV-CLS-484 (AC484), a first-in-class, orally bioavailable, potent PTPN2 and PTPN1 active-site inhibitor. AC484 treatment in vitro amplifies the response to interferon and promotes the activation and function of several immune cell subsets. In mouse models of cancer resistant to PD-1 blockade, AC484 monotherapy generates potent anti-tumour immunity. We show that AC484 inflames the tumour microenvironment and promotes natural killer cell and CD8+ T cell function by enhancing JAK-STAT signalling and reducing T cell dysfunction. Inhibitors of PTPN2 and PTPN1 offer a promising new strategy for cancer immunotherapy and are currently being evaluated in patients with advanced solid tumours (ClinicalTrials.gov identifier NCT04777994 ). More broadly, our study shows that small-molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to or exceeding that of antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge, AC484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics that target this important class of enzymes.

Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis

Adult mammalian stem cells play critical roles in normal tissue homeostasis, as well as in tumor development, by contributing to cell heterogeneity, plasticity, and development of drug resistance. The relationship between different types of normal and cancer stem cells is highly controversial and poorly understood. Here, we carried out gene expression network analysis of normal and tumor samples from genetically heterogeneous mice to create network metagenes for visualization of stem-cell networks, rather than individual stem-cell markers, at the single-cell level during multistage carcinogenesis. We combined this approach with lineage tracing and single-cell RNASeq of stem cells and their progeny, identifying a previously unrecognized hierarchy in which Lgr6+ stem cells from tumors generate progeny that express a range of other stem-cell markers including Sox2, Pitx1, Foxa1, Klf5, and Cd44. Our data identify a convergence of multiple stem-cell and tumor-suppressor pathways in benign tumor cells expressing markers of lineage plasticity and oxidative stress. This same single-cell population expresses network metagenes corresponding to markers of cancer drug resistance in human tumors of the skin, lung and prostate. Treatment of mouse squamous carcinomas in vivo with the chemotherapeutic cis-platin resulted in elevated expression of the genes that mark this cell population. Our data have allowed us to create a simplified model of multistage carcinogenesis that identifies distinct stem-cell states at different stages of tumor progression, thereby identifying networks involved in lineage plasticity, drug resistance, and immune surveillance, providing a rich source of potential targets for cancer therapy.

iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-Cell RNAseq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration

The development of immune checkpoint-based immunotherapies has been a major advancement in the treatment of cancer, with a subset of patients exhibiting durable clinical responses. A predictive biomarker for immunotherapy response is the pre-existing T-cell infiltration in the tumor immune microenvironment (TIME). Bulk transcriptomics-based approaches can quantify the degree of T-cell infiltration using deconvolution methods and identify additional markers of inflamed/cold cancers at the bulk level. However, bulk techniques are unable to identify biomarkers of individual cell types. Although single-cell RNA sequencing (scRNAseq) assays are now being used to profile the TIME, to our knowledge there is no method of identifying patients with a T-cell inflamed TIME from scRNAseq data. Here, we describe a method, iBRIDGE, which integrates reference bulk RNAseq data with the malignant subset of scRNAseq datasets to identify patients with a T-cell inflamed TIME. Utilizing two datasets with matched bulk data, we show iBRIDGE results correlated highly with bulk assessments (0.85 and 0.9 correlation coefficients). Using iBRIDGE, we identified markers of inflamed phenotypes in malignant cells, myeloid cells, and fibroblasts, establishing type I and type II interferon pathways as dominant signals, especially in malignant and myeloid cells, and finding the TGFβ-driven mesenchymal phenotype not only in fibroblasts but also in malignant cells. Besides relative classification, per-patient average iBRIDGE scores and independent RNAScope quantifications were utilized for threshold-based absolute classification. Moreover, iBRIDGE can be applied to in vitro grown cancer cell lines and can identify the cell lines that are adapted from inflamed/cold patient tumors.

Chemoradiation therapy alters the PD-L1 score in locoregional recurrent squamous cell carcinomas of the head and neck

PD-L1 testing guides therapeutic decision-making for head and neck squamous cell carcinoma (HNSCC). We sought to understand whether chemoradiation therapy (CRT) influences the PD-L1 combined positive score (CPS) and other biomarkers of response to immunotherapy. PD-L1 expression was assessed using immunohistochemistry, and bulk RNA sequencing was performed on 146 HNSCC patients (65 primary sites, 50 paired local recurrences, and 31 paired regional recurrences). PD-L1 was scored using the CPS of ≥1, ≥20, and ≥50. Overall, 98 %, 54 %, and 17 % of HNSCCs had a CPS ≥1, ≥20, and ≥50, respectively. When using a cut-off of ≥1, CRT did not significantly change CPS at the locoregional recurrent site. However, there were significant changes when using CPS ≥20 or ≥50. The CPS changed for 32 % of patients when using a CPS ≥20 (p < 0.001). When using a CPS ≥50, there was a 20-23 % (p = 0.0058-0.00067) discordance rate at the site of locoregional recurrence. Oral cavity cancers had a significantly higher discordant rate than other primary sites for CPS ≥50, 44 % (8/18, p = 0.0058) and 58 % (7/12, p = 0.00067) discordance at the site of local and regional recurrence, respectively. When evaluating the 18 gene IFN-ɣ signature predictive of response to anti-PD-1 blockade, there was a statistically significant increase in the IFN-ɣ signature in recurrent larynx cancer (p = 0.02). Our study demonstrates that when using a higher cut-off of CPS ≥20 and ≥50, a repeat biopsy may be warranted after CRT for local and regional recurrent HNSCCs.

Abstract ND06: ABBV-CLS-484: An active site PTPN2/N1 inhibitor that augments the immune response and sensitizes tumors to immune-mediated killing

Background: Pharmacologic inhibition of PTPN2 and PTPN1 (PTPN2/N1) represents a novel therapeutic approach in immuno-oncology that augments innate and adaptive immune responses in addition to enhancing tumor cell sensitivity to immune-mediated killing. PTPN2/N1 emerged as top hits in an in vivo CRISPR screen to identify tumor-intrinsic targets that enhance sensitivity and overcome resistance to anti-PD-1 treatment. PTPN2/N1 are phosphatases that act as negative regulators in numerous pathways including immune activation. While phosphatases have long been of interest, they are challenging drug targets, and the active site had been considered undruggable.

Results: Here we report the discovery of the highly selective, active site PTPN2/N1 small molecule inhibitor, ABBV-CLS-484. Highly optimized ligand-protein interactions have led to the design of sub-nanomolar PTPN2/N1 inhibitors, confirmed through x-ray crystallography. PTPN2/N1 inhibitors increase the activation and function of cytotoxic T cells as well as increase the pro-inflammatory properties of CD103+ dendritic cells and macrophages in vitro. However, they do not cause non-specific activation in the absence of stimulation; rather, they augment signaling in cells that are already activated. PTPN2/N1 inhibition also has effects directly on tumor cells, where it amplifies sensitivity to immune-mediated killing by enhancing the interferon response. ABBV-CLS-484 promotes anti-tumor immunity as monotherapy and in combination with anti-PD-1 leading to dramatic tumor regression, even in models resistant to anti-PD-1 treatment such as 4T1, or those with minimal inflammation such as EMT6. Single-cell RNAseq analyses of tumor-infiltrating immune cells confirmed activation of T cells and demonstrated switching of myeloid-derived suppressor cells towards a proinflammatory phenotype, thereby revealing a distinct mechanism of action of ABBV-CLS-484 compared with PD-1 blockade. Our results show that PTPN2/N1 inhibitors have complementary effects on the immune system and tumor microenvironment that act to promote effective tumor killing. Based on these robust preclinical data, phase I clinical trials of ABBV-CLS-484 alone and in combination with an anti-PD-1 agent have been initiated to establish the safety, tolerability, and efficacy in diverse solid tumor indications.

Conclusions: We have discovered a first-in-class PTPN2/N1 inhibitor, which represents a promising novel immunotherapy that both enhances the immune response and increases tumor sensitivity to immune-mediated killing. ABBV-CLS-484 is currently being evaluated in phase I clinical trials in patients with advanced solid tumors, as a monotherapy or in combination with a PD-1 targeting agent (NCT04777994).

Citation Format: Christina K. Baumgartner, Marcia N. Paddock, Jennifer M. Frost, Keith M. Hamel, Kathleen A. McGuire, Kyle Halliwill, Zhaoming Xiong, Liang Mu, Kelly Klinge, Prasanthi Geda, Jaqueline Aguado, Marinka Bulic, Elliot P. Farney, Kathleen B. Yates, Robert T. Manguso, Clay Beauregard, Philip R. Kym. ABBV-CLS-484: An active site PTPN2/N1 inhibitor that augments the immune response and sensitizes tumors to immune-mediated killing [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 ND06.

Abstract 2198: The impact of carcinogens, obesity, and chronic inflammatory processes on mutational signatures and cancer risk in mouse tumor models

An estimated 40% of all human cancers are suspected to be a result of modifiable risk factors such as obesity, high fat diet and chronic inflammation. Whole genome sequencing (WGS) of thousands of human tumors have revealed “mutational signatures” that provide a molecular footprint of cancer origins. Whether such signatures exist for modifiable cancer risk factors remains unclear. We studied the impact of lifestyle risk factors using a compendium of 107 mouse tumors that model obesity, high fat diet, wounding, chronic inflammation, or chemotherapy. We used a well-established 2-step skin carcinogenesis model composed of exposure to mutagen DMBA followed by tumor promoter TPA, generating squamous carcinomas that were analysed by WGS for identification of mutational signatures. In addition to recapitulating many COSMIC human signatures, we identified a novel SNV signature induced by a single treatment with DMBA (SBS.DMBA) which explains the majority of all detected mutations. While a single exposure of normal skin to DMBA induces a highly variable number of carcinogen-specific mutations, a very high mutation burden is insufficient for tumorigenesis. SNVs attributable to reactive oxygen species (ROS) are broadly found in about 25% of all mouse tumors, but are most prominent in tumors from mice that are exposed to DMBA in utero, suggesting that the developmental age of mutagen exposure may impact the repair of ROS generated mutations and that the timing of exposure is a poorly understudied component of carcinogenesis. In mouse tumor models of genetic and dietary obesity, the total mutational load and mutational signatures in tumors from obese mice were indistinguishable from those of lean mice despite dramatic differences in tumor latency and progression as well transcriptomic differences in immune activation. We found an enrichment in deleterious Tgfrb2 mutations in tumors from mice with low compared to high body mass index (BMI) (p&lt;0.016). Using a conditionally activated RAS mouse model, we also show that a non-mutagenic inflammatory signal such as a chronic wound can act as the rate-limiting step for full tumor development. Surprisingly these tumors can be evoked even in somatic genomes with very few mutations apart from the initiating Ras driver. Finally, together with the Riva et al study, these chemically induced mouse tumors recapitulate &gt;50% of established human cancer driver genes. DMBA caused 91% of all Hras/Kras mutations, but only a minority of other recurrent driver mutations in genes such as Trp53 and Tert, suggesting that these occur later during the process of carcinogenesis. Taken together, we have analyzed the largest compendium of WGS data from nearly 300 mouse tumors, showing that while exogenous promotional factors do not increase mutation burden or induce novel mutational patterns, they have a major rate-limiting role in determining cancer risk.

Citation Format: Yun Rose Li, Kyle Halliwill, Eve Kandyba, Reyno Delrosario, Quan Tran, Nora Bayani, Di Wu, Olga Mirzoeva, Melissa McCreery Reeves, Mishu Islam, Laura Riva, Eric Bergstrom, John Digiovanni, Ludmil Alexandrov, Allan Balmain. The impact of carcinogens, obesity, and chronic inflammatory processes on mutational signatures and cancer risk in mouse tumor models [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 2198.

A balance score between immune stimulatory and suppressive microenvironments identifies mediators of tumour immunity and predicts pan-cancer survival

BACKGROUND

The balance between immune-stimulatory and immune-suppressive mechanisms in the tumour microenvironment is associated with tumour rejection and can predict the efficacy of immune checkpoint-inhibition therapies.

METHODS

We consider the observed differences between the transcriptional programmes associated with cancer types where the levels of immune infiltration predict a favourable prognosis versus those in which the immune infiltration predicts an unfavourable prognosis and defined a score named Mediators of Immune Response Against Cancer in soLid microEnvironments (MIRACLE). MIRACLE deconvolves T cell infiltration, from inhibitory mechanisms, such as TGFβ, EMT and PI3Kγ signatures.

RESULTS

Our score outperforms current state-of-the-art immune signatures as a predictive marker of survival in TCGA (n = 9305, HR: 0.043, p value: 6.7 × 10^-36). In a validation cohort (n = 7623), MIRACLE predicts better survival compared to other immune metrics (HR: 0.1985, p value: 2.73 × 10^-38). MIRACLE also predicts response to checkpoint-inhibitor therapies (n = 333). The tumour-intrinsic factors inversely associated with the reported score such as EGFR, PRKAR1A and MAP3K1 are frequently associated with immune-suppressive phenotypes.

CONCLUSIONS

The association of cancer outcome with the level of infiltrating immune cells is mediated by the balance of activatory and suppressive factors. MIRACLE accounts for this balance and predicts favourable cancer outcomes.

Oncogenic states dictate the prognostic and predictive connotations of intratumoral immune response

BACKGROUND

An immune active cancer phenotype typified by a T helper 1 (Th-1) immune response has been associated with increased responsiveness to immunotherapy and favorable prognosis in some but not all cancer types. The reason of this differential prognostic connotation remains unknown.

METHODS

To explore the contextual prognostic value of cancer immune phenotypes, we applied a multimodal pan-cancer analysis among 31 different histologies (9282 patients), encompassing immune and oncogenic transcriptomic analysis, mutational and neoantigen load and copy number variations.

RESULTS

We demonstrated that the favorable prognostic connotation conferred by the presence of a Th-1 immune response was abolished in tumors displaying specific tumor-cell intrinsic attributes such as high transforming growth factor-beta (TGF-β) signaling and low proliferation capacity. This observation was independent of mutation rate. We validated this observation in the context of immune checkpoint inhibition. WNT-β catenin, barrier molecules, Notch, hedgehog, mismatch repair, telomerase activity and AMPK signaling were the pathways most coherently associated with an immune silent phenotype together with mutations of driver genes including IDH1/2, FOXA2, HDAC3, PSIP1, MAP3K1, KRAS, NRAS, EGFR, FGFR3, WNT5A and IRF7.

CONCLUSIONS

This is the first systematic study demonstrating that the prognostic and predictive role of a bona fide favorable intratumoral immune response is dependent on the disposition of specific oncogenic pathways. This information could be used to refine stratification algorithms and prioritize hierarchically relevant targets for combination therapies.

Lgr6 is a stem cell marker in mouse skin squamous cell carcinoma

The G-protein-coupled receptors Lgr4/5/6 are Wnt signalling mediators, but their functions in squamous carcinomas (SCCs) are unclear. Using lineage tracing in Lgr5-EGFP-CreERT2- and Lgr6-EGFP-CreERT2- Rosa26/Tomato reporter mice, we demonstrate that Lgr6, but not Lgr5, acts as an epithelial stem cell marker in vivo in SCCs. We identify, by single molecule in situ hybridisation and cell sorting, rare Lgr6-positive cells in immortalised keratinocytes, and show that their frequency increases in advanced SCCs. Lgr6 expression is enriched in cells with stem cell characteristics, and Lgr6 downregulation in vivo causes increased epidermal proliferation, with expanded lineage tracing from Lgr6⁺ epidermal stem cells. Surprisingly, Lgr6 germline knockout mice are predisposed to SCC development, by a mechanism that includes compensatory upregulation of Lgr5. These data provide a model for human patients with germline loss of function mutations in WNT pathway genes RSPO1 or LGR4, who show increased susceptibility to squamous tumour development.

The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes

Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.