Batf3+ DCs and the 4-1BB/4-1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy

The cellular source of positive signals that reinvigorate T cells within the tumor microenvironment (TME) for the therapeutic efficacy of programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) blockade has not been clearly defined. We now show that Batf3-lineage dendritic cells (DCs) are essential in this process. Flow cytometric analysis, gene-targeted mice, and blocking antibody studies revealed that 4-1BBL is a major positive co-stimulatory signal provided by these DCs within the TME that translates to CD8+ T cell functional reinvigoration and tumor regression. Immunofluorescence and spatial transcriptomics on human tumor samples revealed clustering of Batf3+ DCs and CD8+ T cells, which correlates with anti-PD-1 efficacy. In addition, proximity to Batf3+ DCs within the TME is associated with CD8+ T cell transcriptional states linked to anti-PD-1 response. Our results demonstrate that Batf3+ DCs within the TME are critical for PD-1/PD-L1 blockade efficacy and indicate a major role for the 4-1BB/4-1BB ligand (4-1BBL) axis during this process.

Synergistic innate immune activation and anti-tumor immunity through combined STING and TLR4 stimulation

Previous work has shown that innate immune sensing of tumors involves the host STING pathway, which leads to IFN-β production, dendritic cell (DC) activation, and T cell priming against tumor antigens. This observation has led to the development of STING agonists as a potential cancer therapeutic. However, despite promising results in mouse studies using transplantable tumor models, clinical testing of STING agonists has shown activity in only a minority of patients. Thus, further study of innate immune pathways in anti-tumor immunity is paramount. Innate immune activation in response to a pathogen rarely occurs through stimulation of only one signaling pathway, and activating multiple innate immune pathways similar to a natural infection is one possible strategy to improve the efficacy of STING agonists. To test this, we performed experiments with the STING agonist DMXAA alone or in combination with several TLR agonists. We found that LPS + DMXAA induced significantly greater IFN-β transcription than the sum of either agonist alone. To explain this synergy, we assayed each step of STING pathway signaling. LPS did not increase STING protein aggregation, IRF3 phosphorylation, or IRF3 nuclear translocation beyond what occurred with DMXAA alone. However, since the IFN-β promoter also includes NF-κB binding sites, we additionally examined the NF-κB pathway. In fact, LPS increased the phosphorylation and nuclear translocation of the NF-κB subunit p65, and NF-κB signaling was required for the observed synergy. Intratumoral injection of suboptimal doses of LPS + DMXAA resulted in significantly improved tumor control of B16 melanoma in vivo compared to either agonist alone. Our results suggest that combinatorial signaling through TLR4 and STING results in optimal innate signaling via co-involvement of NF-κB and IRF3, and that combined engagement of these two pathways has therapeutic potential.

Insights from a Rapidly Implemented COVID-19 Biobank Using Electronic Consent and Informatics Tools

Biobanking during the COVID-19 pandemic presented unique challenges regarding patient enrollment, sample collection, and experimental analysis. This report details the ways in which we rapidly overcame those challenges to create a robust database of clinical information and patient samples while maintaining clinician and researcher safety. We developed a pipeline using REDCap (Research Electronic Data Capture) to coordinate electronic informed consent, sample collection, immunological assay execution, and data analysis for biobanking samples from patients with COVID-19. We then integrated immunological assay data with clinical data extracted from the electronic health record to link study parameters with clinical readouts. Of the 193 inpatients who participated in this study, 138 consented electronically and 56 provided paper consent. We collected and banked blood samples to measure circulating cytokines and chemokines, peripheral immune cell composition and activation status, anti-COVID-19 antibodies, and germline gene polymorphisms. In addition, we collected DNA and RNA from nasopharyngeal swabs to assess viral titer and microbiome composition by 16S sequencing. The rapid spread and contagious nature of COVID-19 required special considerations and innovative solutions to biobank samples quickly while protecting researchers and clinicians. Overall, this workflow and computational pipeline allowed for comprehensive immune profiling of 193 inpatients infected with COVID-19, as well as 89 outpatients, 157 patients receiving curbside COVID-19 testing, and 86 healthy controls. We describe a novel electronic framework for biobanking and analyzing patient samples during COVID-19, and present insights and strategies that can be applied more broadly to other biobank studies.

Abstract 2100: Dendritic cell-intrinsic PTPN22 negatively regulates anti-tumor immunity

Checkpoint blockade immunotherapies have revolutionized cancer treatment; however, only a subset of patients benefit. Individuals with a loss-of-function single nucleotide polymorphism (SNP) in the gene encoding tyrosine-protein phosphatase non-receptor type 22 (PTPN22) are at increased risk for autoimmune disease and display a lower incidence of certain cancers. Studies in PTPN22 knockout (KO) mice have established it as a negative regulator of T cell responses in autoimmune and cancer models attributed to a hyperactive T cell response. However, these studies have not defined the cell lineage-intrinsic roles of PTPNN22 in distinct immune cell compartments, and the potential role of PTPN22 in myeloid cells remains undefined. Myeloid cells in general, and dendritic cells specifically, are critical modulators of antitumor T cell responses. We have developed a novel dendritic cell (DC) PTPN22 conditional KO (cKO) mouse model that enables deletion in CD11c+ cells. Deletion of PTPN22 in DCs resulted in augmented tumor control, evidenced by a significant reduction in tumor burden at endpoint. We found that at end point total CD8+ T cells, but not CD4+ T cells or Tregs, were increased in the tumors of CD11c+ PTPN22 cKO mice compared to control mice. The use of the syngeneic murine melanoma cell line B16.F10 expressing the model antigen “SIY” (B16.SIY) allowed for the tracking of endogenous tumor antigen-specific T cell responses. Indeed, CD8+ T cells demonstrated increased expression of both activation and memory markers at day 10 in the tumor draining lymph node (tdLN) and in day 27 tumor infiltrating lymphocytes. Depletion of CD8+ T cells with an anti-CD8β monoclonal antibody eliminated the tumor growth control in this model, suggesting a mechanism of action based on the DC-CD8+ T cell axis. To test precisely for increased antigen-specific T cell priming, we utilized IFN-γ ELISpot analysis on the tdLN and spleen of tumor bearing mice. We found an increased frequency of IFN-γ-producing T cells in the presence of tumor antigen SIY, but not irrelevant control antigen SIINFKL. Spectral analysis of tumor antigen-specific T cells in the tdLN at the same timepoint showed a significant increase in the number and percentage of CD8+ SIY+ T cells displaying elevated activation and memory markers. Lastly, analysis of DCs in the tdLN similarly revealed an increase in the quantity and percentage of DCs attributed to an increase of CD103+ DCs, but not CD11b+ DCs, displaying increased activation and proliferation markers. Thus, we show that deletion of PTPN22 in DCs is sufficient to drive a tumor antigen-specific T cell response resulting in enhanced tumor control. This work highlights the potential to modulate anti-tumor immunity through the manipulation of DCs.

Citation Format: Santiago Acero-Bedoya, Emily F. Higgs, Thomas F. Gajewski. Dendritic cell-intrinsic PTPN22 negatively regulates anti-tumor immunity [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 2100.

Wilms tumor reveals DNA repair gene hyperexpression is linked to lack of tumor immune infiltration

Background

A T cell-rich tumor microenvironment has been associated with improved clinical outcome and response to immune checkpoint blockade therapies in several adult cancers. Understanding the mechanisms for lack of immune cell infiltration in tumors is critical for expanding immunotherapy efficacy. To gain new insights into the mechanisms of poor tumor immunogenicity, we turned to pediatric cancers, which are generally unresponsive to checkpoint blockade.

Methods

RNA sequencing and clinical data were obtained for Wilms tumor, rhabdoid tumor, osteosarcoma, and neuroblastoma from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, and adult cancers from The Cancer Genome Atlas (TCGA). Using an 18-gene tumor inflammation signature (TIS) representing activated CD8⁺ T cells, we identified genes inversely correlated with the signature. Based on these results, adult tumors were also analyzed, and immunofluorescence was performed on metastatic melanoma samples to assess the MSH2 relationship to anti-programmed cell death protein-1 (PD-1) efficacy.

Results

Among the four pediatric cancers, we observed the lowest TIS scores in Wilms tumor. TIS scores were lower in Wilms tumors compared with matched normal kidney tissues, arguing for loss of endogenous T cell infiltration. Pathway analysis of genes upregulated in Wilms tumor and anti-correlated with TIS revealed activated pathways involved DNA repair. The majority of adult tumors in TCGA also showed high DNA repair scores associated with low TIS. Melanoma samples from an independent cohort revealed an inverse correlation between MSH2⁺ tumor cells and CD8⁺ T cells. Additionally, melanomas with high MSH2⁺ tumor cell numbers were largely non-responders to anti-PD-1 therapy.

Conclusions

Increased tumor expression of DNA repair genes is associated with a less robust immune response in Wilms tumor and the majority of TCGA tumor types. Surprisingly, the negative relationship between DNA repair score and TIS remained strong across TCGA when correcting for mutation count, indicating a potential role for DNA repair genes outside of preventing the accumulation of mutations. While loss of DNA repair machinery has been associated with carcinogenesis and mutational antigen generation, our results suggest that hyperexpression of DNA repair genes might be prohibitive for antitumor immunity, arguing for pharmacologic targeting of DNA repair as a potential therapeutic strategy.

Severe COVID-19 infection is associated with aberrant cytokine production by infected lung epithelial cells rather than by systemic immune dysfunction

The mechanisms explaining progression to severe COVID-19 remain poorly understood. It has been proposed that immune system dysregulation/over-stimulation may be implicated, but it is not clear how such processes would lead to respiratory failure. We performed comprehensive multiparameter immune monitoring in a tightly controlled cohort of 128 COVID-19 patients, and used the ratio of oxygen saturation to fraction of inspired oxygen (SpO2 / FiO2) as a physiologic measure of disease severity. Machine learning algorithms integrating 139 parameters identified IL-6 and CCL2 as two factors predictive of severe disease, consistent with the therapeutic benefit observed with anti-IL6-R antibody treatment. However, transcripts encoding these cytokines were not detected among circulating immune cells. Rather, in situ analysis of lung specimens using RNAscope and immunofluorescent staining revealed that elevated IL-6 and CCL2 were dominantly produced by infected lung type II pneumocytes. Severe disease was not associated with higher viral load, deficient antibody responses, or dysfunctional T cell responses. These results refine our understanding of severe COVID-19 pathophysiology, indicating that aberrant cytokine production by infected lung epithelial cells is a major driver of immunopathology. We propose that these factors cause local immune regulation towards the benefit of the virus.

Immune cell and tumor cell-derived CXCL10 is indicative of immunotherapy response in metastatic melanoma

A T cell-inflamed tumor microenvironment is characterized by the accumulation and local activation of CD8⁺ T cells and Bat3-lineage dendritic cells, which together are associated with clinical response to anti-programmed cell death protein 1 (anti-PD-1)-based immunotherapy. Preclinical models have demonstrated a crucial role for the chemokine CXCL10 in the recruitment of effector CD8⁺ T cells into the tumor site, and a chemokine gene signature is also seen in T cell-inflamed tumors from patients. However, the cellular source of CXCL10 in human solid tumors is not known. To identify the cellular source of CXCL10 we analyzed 22 pretreatment biopsy samples of melanoma metastases from patients who subsequently underwent checkpoint blockade immunotherapy. We stained for CD45⁺ and Sox10⁺ cells with multiparameter immunofluorescence staining, and RNA in situ hybridization technology was used in concert to identify CXCL10 transcripts. The results were correlated with the expression levels of CXCL10 transcripts from bulk RNA sequencing and the best overall response to immune checkpoint inhibition (anti-PD-1 alone or with anti-CTLA-4) in the same patients. We identified CD45⁺ cells as the major cellular source for CXCL10 in human melanoma metastases, with additional CXCL10 production seen by Sox10⁺ cells. Up to 90% of CD45⁺ cells and up to 69% of Sox10⁺ cells produced CXCL10 transcripts. The CXCL10 staining result was consistent with the level of CXCL10 expression determined by bulk RNA sequencing. The percentages of CD45⁺ CXCL10⁺ cells and Sox10⁺ CXCL10⁺ cells independently predicted response (p<0.001). The average number of transcripts per cell correlated with the CD45⁺ cell infiltrate (R=0.37). Immune cells and melanoma cells produce CXCL10 in human melanoma metastases. Intratumoral CXCL10 is a positive prognostic factor for response to immunotherapy, and the RNAscope technique is achievable using paraffin tissue. Strategies that support effector T cell recruitment via induction of CXCL10 should be considered as a mechanism-based intervention to expand immunotherapy efficacy.

COVIDOSE: A Phase II Clinical Trial of Low-Dose Tocilizumab in the Treatment of Noncritical COVID-19 Pneumonia

Interleukin-6 (IL-6)-mediated hyperinflammation may contribute to the mortality of coronavirus disease 2019 (COVID-19). The IL-6 receptor-blocking monoclonal antibody tocilizumab has been repurposed for COVID-19, but prospective trials and dose-finding studies in COVID-19 have not yet fully reported. We conducted a single-arm phase II trial of low-dose tocilizumab in nonintubated hospitalized adult patients with COVID-19, radiographic pulmonary infiltrate, fever, and C-reactive protein (CRP) ≥ 40 mg/L. We hypothesized that doses significantly lower than the emerging standards of 400 mg or 8 mg/kg would resolve clinical and laboratory indicators of hyperinflammation. A dose range from 40 to 200 mg was evaluated, with allowance for one repeat dose at 24 to 48 hours. The primary objective was to assess the relationship of dose to fever resolution and CRP response. Thirty-two patients received low-dose tocilizumab, with the majority experiencing fever resolution (75%) and CRP decline consistent with IL-6 pathway abrogation (86%) in the 24-48 hours following drug administration. There was no evidence of a relationship between dose and fever resolution or CRP decline over the dose range of 40-200 mg. Within the 28-day follow-up, 5 (16%) patients died. For patients who recovered, median time to clinical recovery was 3 days (interquartile range, 2-5). Clinically presumed and/or cultured bacterial superinfections were reported in 5 (16%) patients. Low-dose tocilizumab was associated with rapid improvement in clinical and laboratory measures of hyperinflammation in hospitalized patients with COVID-19. Results of this trial provide rationale for a randomized, controlled trial of low-dose tocilizumab in COVID-19.

Abstract PO-067: Tissue banking from patients with SARS-CoV-2 (COVID-19) infection

The clinical spectrum of SARS-CoV-2 (COVID-19) infection ranges from asymptomatic infection to fatal pneumonia, but the determinants of outcome are not well understood. To characterize the immune response to COVID-19, we established a protocol to collect biologic specimens from patients with confirmed or suspected COVID-19. Between April 9th and June 8th, 2020, we enrolled 146 inpatients and 169 outpatients at the University of Chicago. We hypothesized that the complex interplay of viral, environmental, and host genetic factors may influence disease severity in patients with COVID-19. To probe for genetic predispositions that may influence outcomes, we collected germline DNA from 140 patients spanning the breadth of clinical severity, which will be sequenced for SNPs in genes previously implicated in immune responsiveness and ARDS. To determine whether a pattern of commensal bacteria correlates with disease severity, we will analyze the composition of airway microbiota from 226 nasopharyngeal swabs, using viral quantification and 16S sequencing. Longitudinal serum samples from 156 patients were obtained to probe for the presence of antibodies using an ELISA against the spike protein of SARS-CoV-2. In tandem, 36-color flow cytometry on PBMCs, from the same patients, will characterize immune cell phenotypes influenced by infection. We also hypothesized that by characterizing mechanisms of immune-hyperresponsiveness, we may elucidate key biologic pathways that inform the development of novel therapeutics. To determine if severity of disease and response to therapy correlates with soluble factors, we are performing 44-plex cytokine Luminex assays on serum samples. We will probe the adaptive immune response using an ELISA against the SARS-CoV-2 RBD domain, and by performing IFN-g ELISPOT analysis against peptide pools from SARS-CoV-2 proteins. We developed a bioinformatic pipeline to integrate clinical data with the results from the diverse data types and will adopt a machine learning approach to identify parameters contributing to disease severity, response to therapies, and outcomes. In establishing this protocol, there were significant biosafety considerations. To limit potential exposure and virus transmission, research coordinators contacted inpatients by phone for an informed consent discussion, and patients completed the consent form electronically using REDCap (n=61). Inpatients who were unable to navigate the electronic consent were visited with a paper consent (n= 85). Samples were processed in a BSL2 laboratory with enhanced biosafety precautions. Where feasible, samples were collected into reagents such as Zymo DNA/RNA shield to immediately inactivate the virus. Other safety measures included heat inactivation of some samples and use of a laminar flow washer to minimize aerosolization during FACS staining. In summary, we have established a biorepository of specimens from patients with COVID-19, including a subset with active cancer or a history of the disease (n=22).

Citation Format: Emily F. Higgs, Blake A. Flood, Athalia R. Pyzer, Sherin J. Rouhani, Jonathan A. Trujillo, Kyle R. Cron, Alexandra Cabanov, Jessica Fessler, Jeffrey Bloodworth, Kathleen Beavis, Kiang-Teck J Yeo, Randy F. Sweis, Yuanyuan Zha, Thomas F. Gajewski. Tissue banking from patients with SARS-CoV-2 (COVID-19) infection [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr PO-067.

COVIDOSE: Low-dose tocilizumab in the treatment of Covid-19

Background Interleukin-6 (IL-6)-mediated hyperinflammation may contribute to the high mortality of coronavirus disease 2019 (Covid-19). Tocilizumab, an IL-6 receptor blocking monoclonal antibody, has been repurposed for Covid-19, but prospective trials and dose-finding studies in Covid-19 are lacking. Methods We conducted a phase 2 trial of low-dose tocilizumab in hospitalized adult patients with Covid-19, radiographic pulmonary infiltrate, fever, and C-reactive protein (CRP) >= 40 mg/L who did not require mechanical ventilation. Dose cohorts were determined by a trial Operations Committee, stratified by CRP and epidemiologic risk factors. A range of doses from 40 to 200 mg (low-dose tocilizumab) was evaluated, with allowance for one repeat dose at 24-48 hours. The primary objective was to assess the relationship of dose to fever resolution and CRP response. Outcomes were compared with retrospective controls with Covid-19. Correlative studies evaluating host antibody response were performed in parallel. Findings A total of 32 patients received low-dose tocilizumab. This cohort had improved fever resolution (75.0% vs. 34.2%, p = 0.001) and CRP decline (86.2% vs. 14.3%, p < 0.001) in the 24-48 hours following drug administration, as compared to the retrospective controls (N=41). The probabilities of fever resolution or CRP decline did not appear to be dose-related in this small study (p=0.80 and p=0.10, respectively). Within the 28-day follow-up, 5 (15.6%) patients died. For patients who recovered, median time to clinical recovery was 3 days (IQR, 2-5). Clinically presumed and/or cultured bacterial superinfections were reported in 5 (15.6%) patients. Correlative biological studies demonstrated that tocilizumab-treated patients produced anti-SARS-CoV-2 antibodies comparable to controls. Interpretation Low-dose tocilizumab was associated with rapid improvement in clinical and laboratory measures of hyperinflammation in hospitalized patients with Covid-19. Results of this trial and its correlative biological studies provide rationale for a randomized, controlled trial of low-dose tocilizumab in Covid-19.

Tumor heterogeneity and clonal cooperation influence the immune selection of IFN-γ-signaling mutant cancer cells

PD-1/PD-L1 blockade can promote robust tumor regression yet secondary resistance often occurs as immune selective pressure drives outgrowth of resistant tumor clones. Here using a genome-wide CRISPR screen in B16.SIY melanoma cells, we confirm Ifngr2 and Jak1 as important genes conferring sensitivity to T cell-mediated killing in vitro. However, when implanted into mice, these Ifngr2- and Jak1-deficient tumors paradoxically are better controlled immunologically. This phenotype maps to defective PD-L1 upregulation on mutant tumor cells, which improves anti-tumor efficacy of CD8+ T cells. To reconcile these observations with clinical reports of anti-PD-1 resistance linked to emergence of IFN-γ signaling mutants, we show that when mixed with wild-type tumor cells, IFN-γ-insensitive tumor cells indeed grow out, which depends upon PD-L1 expression by wild-type cells. Our results illustrate the complexity of functions for IFN-γ in anti-tumor immunity and demonstrate that intratumor heterogeneity and clonal cooperation can contribute to immunotherapy resistance.

STING pathway agonism as a cancer therapeutic

The fact that a subset of human cancers showed evidence for a spontaneous adaptive immune response as reflected by the T cell-inflamed tumor microenvironment phenotype led to the search for candidate innate immune pathways that might be driving such endogenous responses. Preclinical studies indicated a major role for the host STING pathway, a cytosolic DNA sensing pathway, as a proximal event required for optimal type I interferon production, dendritic cell activation, and priming of CD8⁺ T cells against tumor-associated antigens. STING agonists are therefore being developed as a novel cancer therapeutic, and a greater understanding of STING pathway regulation is leading to a broadened list of candidate immune regulatory targets. Early phase clinical trials of intratumoral STING agonists are already showing promise, alone and in combination with checkpoint blockade. Further advancement will derive from a deeper understanding of STING pathway biology as well as mechanisms of response vs resistance in individual cancer patients.