Interoperability of phenome-wide multimorbidity patterns: a comparative study of two large-scale EHR systems

Background

Electronic health records (EHR) are increasingly used for studying multimorbidities. However, concerns about accuracy, completeness, and EHRs being primarily designed for billing and administration raise questions about the consistency and reproducibility of EHR-based multimorbidity research.

Methods

Utilizing phecodes to represent the disease phenome, we analyzed pairwise comorbidity strengths using a dual logistic regression approach and constructed multimorbidity as an undirected weighted graph. We assessed the consistency of the multimorbidity networks within and between two major EHR systems at local (nodes and edges), meso (neighboring patterns), and global (network statistics) scales. We present case studies to identify disease clusters and uncover clinically interpretable disease relationships. We provide an interactive web tool and a knowledge base combing data from multiple sources for online multimorbidity analysis.

Findings

Analyzing data from 500,000 patients across Vanderbilt University Medical Center and Mass General Brigham health systems, we observed a strong correlation in disease frequencies ( Kendall's τ = 0.643) and comorbidity strengths (Pearson ρ = 0.79). Consistent network statistics across EHRs suggest a similar structure of multimorbidity networks at various scales. Comorbidity strengths and similarities of multimorbidity connection patterns align with the disease genetic correlations. Graph-theoretic analyses revealed a consistent core-periphery structure, implying efficient network clustering through threshold graph construction. Using hydronephrosis as a case study, we demonstrated the network's ability to uncover clinically relevant disease relationships and provide novel insights.

Interpretation

Our findings demonstrate the robustness of large-scale EHR data for studying complex disease interactions. The alignment of multimorbidity patterns with genetic data suggests the potential utility for uncovering shared etiology of diseases. The consistent core-periphery network structure offers a strategic approach to analyze disease clusters. This work also sets the stage for advanced disease modeling, with implications for precision medicine.

Funding

VUMC Biostatistics Development Award, UL1 TR002243, R21DK127075, R01HL140074, P50GM115305, R01CA227481.

Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis

Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event of treatment with immune checkpoint inhibitors (ICI). We hypothesize that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) predisposes to IMC. In this study, we first develop a polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and then test these PRSs on IMC in a cohort of 1316 patients with ICI-treated non-small cell lung cancer and perform a replication in 873 ICI-treated pan-cancer patients. In a meta-analysis, the PRSUC predicts all-grade IMC (ORmeta=1.35 per standard deviation [SD], 95% CI = 1.12-1.64, P = 2×10-03) and severe IMC (ORmeta=1.49 per SD, 95% CI = 1.18-1.88, P = 9×10-04). PRSCD is not associated with IMC. Furthermore, PRSUC predicts severe IMC among patients treated with combination ICIs (ORmeta=2.20 per SD, 95% CI = 1.07-4.53, P = 0.03). Overall, PRSUC can identify patients receiving ICI at risk of developing IMC and may be useful to monitor patients and improve patient outcomes.

NKG2A Is a Therapeutic Vulnerability in Immunotherapy Resistant MHC-I Heterogeneous Triple-Negative Breast Cancer

Despite the success of immune checkpoint inhibition (ICI) in treating cancer, patients with triple-negative breast cancer (TNBC) often develop resistance to therapy, and the underlying mechanisms are unclear. MHC-I expression is essential for antigen presentation and T-cell-directed immunotherapy responses. This study demonstrates that TNBC patients display intratumor heterogeneity in regional MHC-I expression. In murine models, loss of MHC-I negates antitumor immunity and ICI response, whereas intratumor MHC-I heterogeneity leads to increased infiltration of natural killer (NK) cells in an IFNγ-dependent manner. Using spatial technologies, MHC-I heterogeneity is associated with clinical resistance to anti-programmed death (PD) L1 therapy and increased NK:T-cell ratios in human breast tumors. MHC-I heterogeneous tumors require NKG2A to suppress NK-cell function. Combining anti-NKG2A and anti-PD-L1 therapies restores complete response in heterogeneous MHC-I murine models, dependent on the presence of activated, tumor-infiltrating NK and CD8+ T cells. These results suggest that similar strategies may enhance patient benefit in clinical trials.

SIGNIFICANCE

Clinical resistance to immunotherapy is common in breast cancer, and many patients will likely require combination therapy to maximize immunotherapeutic benefit. This study demonstrates that heterogeneous MHC-I expression drives resistance to anti-PD-L1 therapy and exposes NKG2A on NK cells as a target to overcome resistance. This article is featured in Selected Articles from This Issue, p. 201.

TBCRC 039: a phase II study of preoperative ruxolitinib with or without paclitaxel for triple-negative inflammatory breast cancer

BACKGROUND

Patients with inflammatory breast cancer (IBC) have overall poor clinical outcomes, with triple-negative IBC (TN-IBC) being associated with the worst survival, warranting the investigation of novel therapies. Preclinical studies implied that ruxolitinib (RUX), a JAK1/2 inhibitor, may be an effective therapy for TN-IBC.

METHODS

We conducted a randomized phase II study with nested window-of-opportunity in TN-IBC. Treatment-naïve patients received a 7-day run-in of RUX alone or RUX plus paclitaxel (PAC). After the run-in, those who received RUX alone proceeded to neoadjuvant therapy with either RUX + PAC or PAC alone for 12 weeks; those who had received RUX + PAC continued treatment for 12 weeks. All patients subsequently received 4 cycles of doxorubicin plus cyclophosphamide prior to surgery. Research tumor biopsies were performed at baseline (pre-run-in) and after run-in therapy. Tumors were evaluated for phosphorylated STAT3 (pSTAT3) by immunostaining, and a subset was also analyzed by RNA-seq. The primary endpoint was the percent of pSTAT3-positive pre-run-in tumors that became pSTAT3-negative. Secondary endpoints included pathologic complete response (pCR).

RESULTS

Overall, 23 patients were enrolled, of whom 21 completed preoperative therapy. Two patients achieved pCR (8.7%). pSTAT3 and IL-6/JAK/STAT3 signaling decreased in post-run-in biopsies of RUX-treated samples, while sustained treatment with RUX + PAC upregulated IL-6/JAK/STAT3 signaling compared to RUX alone. Both treatments decreased GZMB+ T cells implying immune suppression. RUX alone effectively inhibited JAK/STAT3 signaling but its combination with PAC led to incomplete inhibition. The immune suppressive effects of RUX alone and in combination may negate its growth inhibitory effects on cancer cells.

CONCLUSION

In summary, the use of RUX in TN-IBC was associated with a decrease in pSTAT3 levels despite lack of clinical benefit. Cancer cell-specific-targeting of JAK2/STAT3 or combinations with immunotherapy may be required for further evaluation of JAK2/STAT3 signaling as a cancer therapeutic target.

TRIAL REGISTRATION

www.

CLINICALTRIALS

gov , NCT02876302. Registered 23 August 2016.

Impact of BMI in Patients With Early Hormone Receptor-Positive Breast Cancer Receiving Endocrine Therapy With or Without Palbociclib in the PALLAS Trial

PURPOSE

BMI affects breast cancer risk and prognosis. In contrast to cytotoxic chemotherapy, CDK4/6 inhibitors are given at a fixed dose, irrespective of BMI or weight. This preplanned analysis of the global randomized PALLAS trial investigates the impact of BMI on the side-effect profile, treatment adherence, and efficacy of palbociclib.

METHODS

Patients were categorized at baseline according to WHO BMI categories. Neutropenia rates were assessed with univariable and multivariable logistic regression. Time to early discontinuation of palbociclib was analyzed with Fine and Gray competing risk models. Unstratified Cox models were used to investigate the association between BMI category and time to invasive disease-free survival (iDFS). 95% CIs were derived.

RESULTS

Of 5,698 patients included in this analysis, 68 (1.2%) were underweight, 2,082 (36.5%) normal weight, 1,818 (31.9%) overweight, and 1,730 (30.4%) obese at baseline. In the palbociclib arm, higher BMI was associated with a significant decrease in neutropenia (unadjusted odds ratio for 1-unit change, 0.93; 95% CI, 0.91 to 0.94; adjusted for age, race ethnicity, region, chemotherapy use, and Eastern Cooperative Oncology Group at baseline, 0.93; 95% CI, 0.92 to 0.95). This translated into a significant decrease in treatment discontinuation rate with higher BMI (adjusted hazard ratio [HR] for 10-unit change, 0.75; 95% CI, 0.67 to 0.83). There was no significant improvement in iDFS with the addition of palbociclib to ET in any weight category (normal weight HR, 0.84; 95% CI, 0.63 to 1.12; overweight HR, 1.10; 95% CI, 0.82 to 1.49; and obese HR, 0.95; 95% CI, 0.69 to 1.30) in this analysis early in follow-up (31 months).

CONCLUSION

This preplanned analysis of the PALLAS trial demonstrates a significant impact of BMI on side effects, dose reductions, early treatment discontinuation, and relative dose intensity. Additional long-term follow-up will further evaluate whether BMI ultimately affects outcome.

Polycomb repressor complex 2 suppresses interferon-responsive MHC-II expression in melanoma cells and is associated with anti-PD-1 resistance

BACKGROUND

Despite the remarkable success of immunotherapy in treating melanoma, understanding of the underlying mechanisms of resistance remains limited. Emerging evidence suggests that upregulation of tumor-specific major histocompatibility complex-II (tsMHC-II) serves as a predictive marker for the response to anti-programmed death-1 (PD-1)/programmed death ligand 1 (PD-L1) therapy in various cancer types. The genetic and epigenetic pathways modulating tsMHC-II expression remain incompletely characterized. Here, we provide evidence that polycomb repressive complex 2 (PRC2)/EZH2 signaling and resulting H3K27 hypermethylation suppresses tsMHC-II.

METHODS

RNA sequencing data from tumor biopsies from patients with cutaneous melanoma treated with or without anti-PD-1, targeted inhibition assays, and assays for transposase-accessible chromatin with sequencing were used to observe the relationship between EZH2 inhibition and interferon (IFN)-γ inducibility within the MHC-II pathway.

RESULTS

We find that increased EZH2 pathway messenger RNA (mRNA) expression correlates with reduced mRNA expression of both presentation and T-cell genes. Notably, targeted inhibition assays revealed that inhibition of EZH2 influences the expression dynamics and inducibility of the MHC-II pathway following IFN-γ stimulation. Additionally, our analysis of patients with metastatic melanoma revealed a significant inverse association between PRC2-related gene expression and response to anti-PD-1 therapy.

CONCLUSIONS

Collectively, our findings demonstrate that EZH2 inhibition leads to enhanced MHC-II expression potentially resulting from improved chromatin accessibility at CIITA, the master regulator of MHC-II. These insights shed light on the molecular mechanisms involved in tsMHC-II suppression and highlight the potential of targeting EZH2 as a therapeutic strategy to improve immunotherapy efficacy.

Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis

Immune checkpoint inhibitors (ICIs) are a remarkable advancement in cancer therapeutics; however, a substantial proportion of patients develop severe immune-related adverse events (irAEs). Understanding and predicting irAEs is a key to advancing precision immuno-oncology. Immune checkpoint inhibitor-mediated colitis (IMC) is a significant complication from ICI and can have life-threatening consequences. Based on clinical presentation, IMC mimics inflammatory bowel disease, however the link is poorly understood. We hypothesized that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) may predispose to IMC. We developed and validated polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and assessed the role of each of these PRSs on IMC in a cohort of 1,316 patients with non-small cell lung cancer who received ICIs. Prevalence of all-grade IMC in our cohort was 4% (55 cases), and for severe IMC, 2.5% (32 cases). The PRSUC predicted the development of all-grade IMC (HR=1.34 per standard deviation [SD], 95% CI=1.02-1.76, P=0.04) and severe IMC (HR=1.62 per SD, 95% CI=1.12-2.35, P=0.01). PRSCD was not associated with IMC or severe IMC. The association between PRSUC and IMC (all-grade and severe) was consistent in an independent pan-cancer cohort of patients treated with ICIs. Furthermore, PRSUC predicted severe IMC among patients treated with combination ICIs (OR = 2.20 per SD, 95% CI = 1.07-4.53, P=0.03). This is the first study to demonstrate the potential clinical utility of a PRS for ulcerative colitis in identifying patients receiving ICI at high risk of developing IMC, where risk reduction and close monitoring strategies could help improve overall patient outcomes.

Biomarkers of immune checkpoint inhibitor response and toxicity: Challenges and opportunities

Immune checkpoint inhibitors have transformed cancer therapy, but their optimal use is still constrained by lack of response and toxicity. Biomarkers of response may facilitate drug development by allowing appropriate therapy selection and focusing clinical trial enrollment. However, aside from PD-L1 staining in a subset of tumors and rarely mismatch repair deficiency, no biomarkers are routinely used in the clinic. In addition, severe toxicities may cause severe morbidity, therapy discontinuation, and even death. Here, we review the state of the field with a focus on our research in therapeutic biomarkers and toxicities from immune checkpoint inhibitors.

Corticosteroids and Cancer Immunotherapy

Despite revolutionizing cancer management, immunotherapies dysregulate the immune system, leading to immune-mediated adverse events. These common and potentially dangerous toxicities are often treated with corticosteroids, which are among the most prescribed drugs in oncology for a wide range of cancer and noncancer indications. While steroids exert several mechanisms to reduce immune activity, immunotherapies, such as immune checkpoint inhibitors (ICI), are designed to enhance the immune system's inherent antitumor activity. Because ICI requires an intact and robust immune response, the immunosuppressive properties of steroids have led to a widespread concern that they may interfere with antitumor responses. However, the existing data of the effect of systemic steroids on immunotherapy efficacy remain somewhat conflicted and unclear. To inform clinical decision-making and improve outcomes, we review the impact of steroids on antitumor immunity, recent advances in the knowledge of their impact on ICI efficacy in unique populations and settings, associated precautions, and steroid-sparing treatment approaches.

STING-activating nanoparticles normalize the vascular-immune interface to potentiate cancer immunotherapy

The tumor-associated vasculature imposes major structural and biochemical barriers to the infiltration of effector T cells and effective tumor control. Correlations between stimulator of interferon genes (STING) pathway activation and spontaneous T cell infiltration in human cancers led us to evaluate the effect of STING-activating nanoparticles (STANs), which are a polymersome-based platform for the delivery of a cyclic dinucleotide STING agonist, on the tumor vasculature and attendant effects on T cell infiltration and antitumor function. In multiple mouse tumor models, intravenous administration of STANs promoted vascular normalization, evidenced by improved vascular integrity, reduced tumor hypoxia, and increased endothelial cell expression of T cell adhesion molecules. STAN-mediated vascular reprogramming enhanced the infiltration, proliferation, and function of antitumor T cells and potentiated the response to immune checkpoint inhibitors and adoptive T cell therapy. We present STANs as a multimodal platform that activates and normalizes the tumor microenvironment to enhance T cell infiltration and function and augments responses to immunotherapy.

Abstract 4152: Longitudinal local and peripheral immunologic changes associated with PD-L1 response in a murine breast cancer model

Immune checkpoint inhibitors (ICI) have significantly enhanced patient survival in many cancers but yield limited success in breast cancer. ICIs activate anti-tumor immunity by overriding the inhibition of tumor infiltrating lymphocytes (TILs). Clinical trials in triple negative breast cancer (TNBC) patients, who harbor TILs within tumor stroma, have demonstrated increased survival (IMpassion130) and pathologic complete response (KEYNOTE-522) to ICI leading to FDA-approval of ICI and chemotherapy combinations in metastatic TNBC. However, ICI benefit is heterogeneous among patients. We sought to model ICI response in vivo to evaluate therapeutic resistance and response heterogeneity and to ascertain predictive biomarkers for favorable ICI outcomes. An immunocompetent EMT6 orthotopic mammary tumor model was used to investigate the efficacy of anti-PD-L1. Matched longitudinal samples of the tumor microenvironment (TME) (collected by fine-needle aspiration) and peripheral blood (PBMC) from mice were profiled by bulk RNA and T-cell receptor sequencing.

Anti-PD-L1 robustly suppressed primary tumor growth and extended survival beyond the control group. The addition of chemotherapy demonstrated moderate therapeutic efficacy but failed to enhance ICI benefit. Phenotypic profiling of the TME revealed increased T cells, DCs, and NK cells in anti-PD-L1 only and chemotherapy combination groups. Despite using a genetically identical tumor model and host, PD-L1 blockade induced heterogeneous responses, like clinical outcomes in TNBC patients, ranging from complete response (CR) to intrinsic resistance (IR). The primary TME showed upregulated signatures of cytotoxic T cell response and activation, specifically inflammatory interferon signaling (both prior to and post ICI administration) that corresponded to favorable outcomes to anti-PD-L1 in individual mice. Longitudinal analysis of the peripheral blood identified modest changes among mice at baseline that progressively deviated by response type (IR-vs-CR). Mice harbored enriched myeloid signatures and clonal T cell expansion during therapy corresponding to ICI resistance and response, respectively. Further investigations of matched peripheral blood and the primary TME signatures may identify systemic biomarkers and tumor antigen-specific T cell clones to accurately predict ICI response in patients and uncover mechanisms for sensitizing tumors refractory to ICI.

Thus, we identify an in vivo model that emulates TNBC patient heterogeneous outcomes to ICI combinatorial approaches. We describe host-specific signatures, specifically from myeloid cells, that correlate with differential responses to ICI, which may serve as a basis for peripheral blood tracking of breast cancer patient responses.

Citation Format: Ann Hanna, Xiaopeng Sun, Emily Tran, Quanhu Sheng, Brandie C. Taylor, Susan R. Opalenik, Justin M. Balko. Longitudinal local and peripheral immunologic changes associated with PD-L1 response in a murine breast cancer model. [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 4152.

Convolutional neural network for biomarker discovery for triple negative breast cancer with RNA sequencing data

Triple negative breast cancers (TNBCs) are tumors with a poor treatment response and prognosis. In this study, we propose a new approach, candidate extraction from convolutional neural network (CNN) elements (CECE), for discovery of biomarkers for TNBCs. We used the GSE96058 and GSE81538 datasets to build a CNN model to classify TNBCs and non-TNBCs and used the model to make TNBC predictions for two additional datasets, the cancer genome atlas (TCGA) breast cancer RNA sequencing data and the data from Fudan University Shanghai Cancer Center (FUSCC). Using correctly predicted TNBCs from the GSE96058 and TCGA datasets, we calculated saliency maps for these subjects and extracted the genes that the CNN model used to separate TNBCs from non-TNBCs. Among the TNBC signature patterns that the CNN models learned from the training data, we found a set of 21 genes that can classify TNBCs into two major classes, or CECE subtypes, with distinct overall survival rates (P = 0.0074). We replicated this subtype classification in the FUSCC dataset using the same 21 genes, and the two subtypes had similar differential overall survival rates (P = 0.0490). When all TNBCs were combined from the 3 datasets, the CECE II subtype had a hazard ratio of 1.94 (95% CI, 1.25-3.01; P = 0.0032). The results demonstrate that the spatial patterns learned by the CNN models can be utilized to discover interacting biomarkers otherwise unlikely to be identified by traditional approaches.

No rest for the wicked: Tumor cell senescence reshapes the immune microenvironment

Senescence induces key phenotypic changes that can modulate immune responses. Four recent publications in Cancer Discovery, Nature, and Nature Cancer highlight how senescent cells (aged normal or chemotherapy-treated cells) express antigen presentation machinery, present antigens, and interact with T cells and dendritic cells to robustly activate the immune system and promote anti-tumor immunity.

Efficacy and safety of immune checkpoint inhibitors in young adults with metastatic melanoma

BACKGROUND

The integration of immune checkpoint inhibitors (ICI) for the treatment of melanoma has resulted in remarkable and durable responses. Given the potential role of immunosenescence, age may contribute to differential ICI efficacy and toxicity. While older patients have been studied in detail, outcomes from ICI in young patients (≤40 years) are not well characterised.

METHODS

We performed a multi-institutional, retrospective study of patients with advanced melanoma treated with anti-PD-1 monotherapy or ICI combination (ipilimumab and anti-PD-1). Response rates, survival, and toxicities were examined based on age comparing those under 40 years of age with older patients (age 41-70 and ≥ 71 years).

RESULTS

A total of 676 patients were included: 190 patients (28%) aged ≤40 years, 313 (46%) between ages 41-70, and 173 patients (26%) aged ≥71. Patients ≤40 years had higher response rates (53% vs 38%, p = 0.035) and improved progression-free survival (median 13.7 vs 4.0 months, p = 0.032) with combination ICI compared to monotherapy. Progression-free survival was similar among groups while overall survival was inferior in patients >70 years, who had low response rates to combination therapy (28%). ICIs had a similar incidence of severe toxicities, though hepatotoxicity was particularly common in younger patients vs. patients >40 with monotherapy (9% vs. 2%, p = 0.007) or combination ICI (37% vs. 10%, p < 0.001).

CONCLUSIONS

ICIs had comparable efficacy between younger and older patients, although outcomes were superior with combination ICI compared to monotherapy in patients aged ≤40 years. Toxicity incidence was similar across age groups, though organs affected were substantially different.

Peripheral T-cell receptor repertoire dynamics in small cell lung cancer

Background

Identifying a circulating biomarker predictive of immune checkpoint inhibitor (ICI) benefit in patients with small cell lung cancer (SCLC) remains an unmet need. Characteristics of peripheral and intratumoral T-cell receptor (TCR) repertoires have been shown to predict clinical outcomes in non-small cell lung cancer (NSCLC). Recognizing a knowledge gap, we sought to characterize circulating TCR repertoires and their relationship with clinical outcomes in SCLC.

Methods

SCLC patients with limited (n=4) and extensive (n=10) stage disease were prospectively enrolled for blood collection and chart review. Targeted next-generation sequencing of TCR beta and alpha chains of peripheral blood samples was performed. Unique TCR clonotypes were defined by identical CDR3, V gene, and J gene nucleotide sequences of the beta chain and subsequently used to calculate TCR diversity indices.

Results

Patients with stable versus progressive and limited versus extensive stage disease did not demonstrate significant differences in V gene usage. Kaplan-Meier curve and log-rank analysis did not identify a statistical difference in progression-free survival (PFS) (P=0.900) or overall survival (OS) (P=0.200) between high and low on-treatment TCR diversity groups, although the high diversity group exhibited a trend toward increased OS.

Conclusions

We report the second study investigating peripheral TCR repertoire diversity in SCLC. With a limited sample size, no statistically significant associations between peripheral TCR diversity and clinical outcomes were observed, though further study is warranted.

T cell dynamism and immune-related adverse events

Immune-related adverse events (irAEs) are a major complication of immune checkpoint inhibitors (ICIs) and occur in an unpredictable fashion. In a Med article, Nunez et al. profile peripheral blood markers in patients treated with ICIs, identifying that dynamic changes in proliferating T cells and cytokine upregulation are associated with irAEs.

Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis

The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome and low-pass whole-genome sequencing and global DNA methylation microarrays. Expression subtype changes were observed in ~30% of samples and were coincident with DNA clonality shifts, especially involving HER2. Downregulation of estrogen receptor (ER)-mediated cell-cell adhesion genes through DNA methylation mechanisms was observed in metastases. Microenvironment differences varied according to tumor subtype; the ER+/luminal subtype had lower fibroblast and endothelial content, while triple-negative breast cancer/basal metastases showed a decrease in B and T cells. In 17% of metastases, DNA hypermethylation and/or focal deletions were identified near HLA-A and were associated with reduced expression and lower immune cell infiltrates, especially in brain and liver metastases. These findings could have implications for treating individuals with metastatic breast cancer with immune- and HER2-targeting therapies.

Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs

MOTIVATION

Making sense of networked multivariate association patterns is vitally important to many areas of high-dimensional analysis. Unfortunately, as the data-space dimensions grow, the number of association pairs increases in O(n2); this means that traditional visualizations such as heatmaps quickly become too complicated to parse effectively.

RESULTS

Here, we present associationSubgraphs: a new interactive visualization method to quickly and intuitively explore high-dimensional association datasets using network percolation and clustering. The goal is to provide an efficient investigation of association subgraphs, each containing a subset of variables with stronger and more frequent associations among themselves than the remaining variables outside the subset, by showing the entire clustering dynamics and providing subgraphs under all possible cutoff values at once. Particularly, we apply associationSubgraphs to a phenome-wide multimorbidity association matrix generated from an electronic health record and provide an online, interactive demonstration for exploring multimorbidity subgraphs.

AVAILABILITY AND IMPLEMENTATION

An R package implementing both the algorithm and visualization components of associationSubgraphs is available at https://github.com/tbilab/associationsubgraphs. Online documentation is available at https://prod.tbilab.org/associationsubgraphs_info/. A demo using a multimorbidity association matrix is available at https://prod.tbilab.org/associationsubgraphs-example/.

Rare immune-related adverse events in patients with melanoma: incidence, spectrum, and clinical presentations

Immune-related adverse events (irAEs) are side effects of immune checkpoint inhibitor therapy (ICI). While common irAEs have been well characterized, there are more limited data on rare immune related adverse events (RirAEs) due to low incidence. Lack of characterization of these entities has led to difficulties in accurate diagnosis and management. Here, we conducted a multi-institution analysis of all patients with stage III/IV melanoma who developed RirAEs after being treated with ICIs (anti-PD-1/L1, anti-CTLA-4, and combination PD-1/CTLA-4 blockade) at three institutions (Vanderbilt University Medical Center, Massachusetts General Hospital, and Melanoma Institute of Australia). RirAEs were defined as those occurring in approximately <1% of patients treated with anti-PD-1 or <2% with combination. Of 2834 patients who received ICIs, 82 developed RirAEs and were more common with combination PD-1/CTLA-4 blockade (4.6%) vs. anti-PD-1/L1 agents (2.8%). Overall median time from ICI start to RirAE was 86 days (interquartile range 42-235 days) with significantly earlier onset in combination therapy (p < 0.001). The spectrum of RirAEs spanned across several organ systems. Most RirAEs were grade 2 (57 [41.3%]) and grade 3 (40 [29.0%]) with relatively few grade 4 (11 [8.0%]) or 5 (5 [3.6%]) events. Steroid re-escalation (21.4%) or additional immunosuppression (13.8%) were commonly required. RirAE recurrence occurred in 22.6% with ICI rechallenge; 37.1% had new irAEs with rechallenge. In conclusion, RirAEs associated with ICIs in melanoma patients occurred, in aggregate, in 2-5% of patients treated with anti-PD-1-based therapy. Steroid re-escalation and alternative immunosuppression use were frequently required but fatal irAEs were fairly uncommon.

T cells specific for α-myosin drive immunotherapy-related myocarditis

Immune-related adverse events, particularly severe toxicities such as myocarditis, are major challenges to the utility of immune checkpoint inhibitors (ICIs) in anticancer therapy1. The pathogenesis of ICI-associated myocarditis (ICI-MC) is poorly understood. Pdcd1-/-Ctla4+/- mice recapitulate clinicopathological features of ICI-MC, including myocardial T cell infiltration2. Here, using single-cell RNA and T cell receptor (TCR) sequencing of cardiac immune infiltrates from Pdcd1-/-Ctla4+/- mice, we identify clonal effector CD8+ T cells as the dominant cell population. Treatment with anti-CD8-depleting, but not anti-CD4-depleting, antibodies improved the survival of Pdcd1-/-Ctla4+/- mice. Adoptive transfer of immune cells from mice with myocarditis induced fatal myocarditis in recipients, which required CD8+ T cells. The cardiac-specific protein α-myosin, which is absent from the thymus3,4, was identified as the cognate antigen source for three major histocompatibility complex class I-restricted TCRs derived from mice with fulminant myocarditis. Peripheral blood T cells from three patients with ICI-MC were expanded by α-myosin peptides. Moreover, these α-myosin-expanded T cells shared TCR clonotypes with diseased heart and skeletal muscle, which indicates that α-myosin may be a clinically important autoantigen in ICI-MC. These studies underscore the crucial role for cytotoxic CD8+ T cells, identify a candidate autoantigen in ICI-MC and yield new insights into the pathogenesis of ICI toxicity.

Adjuvant palbociclib for ER+ breast cancer (PALLAS Trial (ABCSG-42/AFT-05/PrE0109/BIG-14-13): A preplanned analysis of the stage IIA cohort

390216

Background: CDK4/6 inhibitors have become standard of care for advanced hormone receptor positive, HER2-negative (HR+/HER2-) breast cancer in combination with endocrine therapy (ET), with one approved for high-risk patients (pts) in the adjuvant setting. The PALLAS Trial investigated the addition of palbociclib to adjuvant ET in pts with stage II-III breast cancer. Stage IIA patients were specifically enrolled to evaluate the potential benefit of using palbociclib with adjuvant ET pts diagnosed at lower risk who may have more indolent disease. Methods: In the prospective, randomized, phase III PALLAS trial, pts with HR+/HER2- early breast cancer were randomly assigned to receive adjuvant ET for at least 5 years with or without 2 years of palbociclib (125 mg orally once daily, days 1-21 of a 28-day cycle). ET was of provider’s choice. Stage IIA enrollment was capped at 1,000 patients. While the primary end point of the overall study was invasive disease-free survival (iDFS) for the entire cohort, there was a preplanned analysis of recurrence and survival endpoints in the stage IIA cohort. Outcomes were compared between arms using stratified log-rank tests and Cox models (stratification factors: chemotherapy and age ≤ 50). Results: Among 5,796 pts enrolled at 406 centers in 21 countries worldwide between 9/1/2015 and 11/30/2018, a total of 1,010 stage IIA pts were enrolled. The protocol-defined number of events occurred at a median follow-up of 50 months for this subgroup (43.1 months for the overall study). Median age within this subgroup was 54 (range 29-85 yrs), and 410 (40.6%) were pre/perimenopausal, 506 (50.1%) T2/N0 (vs T0-1/N1), 272 (26.9%) grade 3 (vs. grade1/2), and 561 (55.5%) received chemotherapy. iDFS events occurred in 31 of 503 (6.2%) pts who received palbociclib plus ET and in 45 of 507 (8.9%) pts who received ET alone, resulting in a statistically nonsignificant difference in iDFS at 4 years (92.9% vs. 92.1%; hazard ratio, 0.75; CI, 0.48 to 1.19; P = .23). Nonsignificant differences were also observed for invasive breast cancer-free, distant recurrence-free, and locoregional cancer-free survival. No significant differences in iDFS were observed in subgroups including age group, receipt of chemotherapy, tumor grade, and clinical risk (T1/N1 vs. T2/N0).Conclusions: In this preplanned analysis of the stage IIA cohort of the PALLAS trial, the addition of adjuvant palbociclib to standard ET did not improve outcomes over ET alone, suggesting no benefit from the agent in reducing the incidence of early relapse in pts with lower-stage HR+/HER2- breast cancer. Future analyses will incorporate genomic risk and other molecular patterns from the extensive transPALLAS correlative program. Additional follow-up (10-year minimum) is also underway to assess the impact of palbociclib exposure on late recurrence in HR+ disease. Clinical trial information: NCT02513394.

Epigenetic Repression of STING by MYC Promotes Immune Evasion and Resistance to Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer

The MYC oncogene is frequently amplified in triple-negative breast cancer (TNBC). Here, we show that MYC suppression induces immune-related hallmark gene set expression and tumor-infiltrating T cells in MYC-hyperactivated TNBCs. Mechanistically, MYC repressed stimulator of interferon genes (STING) expression via direct binding to the STING1 enhancer region, resulting in downregulation of the T-cell chemokines CCL5, CXCL10, and CXCL11. In primary and metastatic TNBC cohorts, tumors with high MYC expression or activity exhibited low STING expression. Using a CRISPR-mediated enhancer perturbation approach, we demonstrated that MYC-driven immune evasion is mediated by STING repression. STING repression induced resistance to PD-L1 blockade in mouse models of TNBC. Finally, a small-molecule inhibitor of MYC combined with PD-L1 blockade elicited a durable response in immune-cold TNBC with high MYC expression, suggesting a strategy to restore PD-L1 inhibitor sensitivity in MYC-overexpressing TNBC.

Abstract LB176: Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network identifies microenvironment features as drivers of metastasis

Background: Metastatic breast cancer (MBC) patients often have short survival, and successful treatment represents one of the most challenging aspects of cancer care. This poor prognosis is likely multifactorial, including increased clonal heterogeneity, drug resistance mechanisms, and alterations of the tumor microenvironment.

Methods: The primary data source was multi-platform data coming from the AURORA US Project that includes RNAseq, DNAseq, and DNA methylation arrays, which assayed 55 MBC patients representing 51 primary cancers and 102 linked metastatic specimens. In addition, RNA sequencing data from two other datasets of primary tumor-metastasis pairs were also used (i.e. UNC Tumor Donation Program/RAP dataset (24 primary and 74 metastasis specimens), and the GEICAM/2009-03 ConvertHER trial dataset (102 primaries and 102 metastatic pairs)). In total, this combined RNAseq dataset contained 177 primary tumors and 278 metastases, including 28 liver, 18 lung, 12 brain, and 24 lymph node metastases. We used these data to address two pressing questions, namely: 1) do gene expression features vary in primary tumors vs metastases according to PAM50 expression subtype, and 2) do gene expression features vary according to site of metastasis.

Results: Using the AURORA multi-platform data, we determined that 17% of metastatic tumors (mainly TNBC/Basal-like) showed reduced expression of HLA-A that was associated with DNA methylation and/or focal DNA deletions near the HLA-A locus; these methylated tumors also showed concomitant lower immune cell infiltrates. Reduced expression of HLA-A gene and immune cell infiltrates were also validated at the RNA level in RAP dataset. Next, RNA expression differences were examined using the combined data set and varied according to tumor subtype. ER+/Luminal metastases had lower fibroblast and endothelial cell content, while triple negative (TNBC)/Basal-like metastases showed a dramatic decrease in T cell and B cell signatures/features. Comparative analyses between primary and site-specific metastasis (i.e., primary vs liver metastasis) or between sites of metastases (i.e., liver vs lung metastasis) revealed that both liver and brain, on average, had low immune cell features regardless of the primary tumor phenotype. Even within the same patient, we detected low immune cell features in brain and liver metastases compared to lung and lymph node metastases. Lastly, liver metastases showed a gain of Luminal B/HER2E gene expression features and MYC targets, and brain TNBC metastasis showed a gain of cell differentiation/Luminal-related gene signatures.

Conclusions: These findings could have direct implications for the treatment of MBC patients with immune-based therapies and suggest new therapeutic avenues depending upon the tumor metastasis phenotype, and site of metastasis.

Citation Format: Susana Garcia Recio, Toshinori Hinoue, Gregory L. Wheeler, Benjamin J. Kelly, Justin M. Balko, Katherine A. Hoadley, Peter W. Laird, Elaine R. Mardis, Charles M. Perou. Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network identifies microenvironment features as drivers of metastasis [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 LB176.

Abstract 2726: Host myeloid response drives anti-PD-L1 resistance in murine models of triple negative breast cancer

Immune checkpoint inhibitors (ICI) have improved patient overall and progression-free survival in some cancer types with limited success in breast cancer. Clinical trials in triple negative breast cancer (TNBC) patients, who harbor extensive tumor-infiltrating lymphocytes within tumor stroma, have demonstrated increased progression-free survival (IMpassion130) and pathologic complete response (KEYNOTE-522). Thus, combinations of ICI and chemotherapy have been FDA-approved for metastatic TNBC. However, the therapeutic benefit of ICI alone is poorly characterized. We sought to model ICI response in vivo to ascertain the immune repertoire responsible for ICI efficacy in breast cancer and identify the therapeutic benefit of ICI alone or in combination with approved chemotherapeutics.

We used an immunocompetent EMT6 orthotopic mammary tumor model to investigate the efficacy of single-agent ICI (anti-PD-L1) or in combination with standard-of-care chemotherapy (paclitaxel or doxorubicin). Analysis of the primary tumor immune landscape was performed by flow cytometry and single-cell RNA sequencing. Peripheral blood from mice was serially sampled by bulk and T-cell receptor (TCR) sequencing to identify systemic genomic alterations and T-cell expansion, respectively.

Single-agent ICI robustly suppressed primary tumor growth (p =0.0046) and extended survival (p&lt;0.0001) beyond the control group. While chemotherapy demonstrated moderate therapeutic efficacy, it did not enhance ICI benefit. Transcriptomic and phenotypic profiling of the tumor microenvironment (TME) revealed increased T cells, dendritic cells, and NK cells in the combination groups versus chemotherapy alone, but this did not translate into improved benefit. Interestingly, despite using a genetically identical tumor model and murine host, ICI induced heterogeneous responses, ranging from complete response to intrinsic resistance. The longitudinal analysis of peripheral blood from heterogeneously responding mice uncovered enriched myeloid signatures and clonal T cell expansion corresponding to ICI resistance and response, respectively.

In conclusion, we identify a heterogeneously ICI-responsive in vivo model that emulates TNBC patient response to combinatorial ICI approaches. We report the efficacy of single-agent ICI in upregulating cytotoxic immune cell infiltration and expansion within the primary tumor, thereby diminishing tumor growth and enhancing survival. We describe host-specific signatures, specifically myeloid cells, that correlate with differential responses to immunotherapy, which models heterogeneous patient response to ICI. Ongoing characterization of matched peripheral blood and TME samples may identify systemic biomarkers and tumor antigen-specific T cell clones to accurately predict ICI response in patients and uncover mechanisms for sensitizing tumors refractory to ICI.

Citation Format: Ann Hanna, Xiaopeng Sun, Paula I. Gonzalez-Ericsson, Violeta Sanchez, Justin M. Balko. Host myeloid response drives anti-PD-L1 resistance in murine models of triple negative breast cancer [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 2726.

Abstract 1351: Lauryn Werner

Clinical studies have linked usage of progestins (synthetic progesterone) to breast cancer risk. However, little is understood regarding the role of native progesterone (P4), signaling through the progesterone receptor (PR), in breast tumor formation. Recently, we reported a link between PR and immune signaling pathways, showing that P4/PR can repress type I interferon signaling pathways. Given these findings, we sought to investigate whether P4/PR drive immunomodulation in the mammary gland and promote tumor formation. To determine the effect of P4 on immune cell populations in the murine mammary gland, mice were treated with P4 or placebo pellets for 21 days. We found that mice treated with P4 exhibited changes in the mammary gland indicative of an inhibited immune response compared to placebo-treated mice. To assess the effect of PR overexpression on mammary gland tumor development as well as immune cell populations in the mammary gland, a transgenic mouse model was used in which PR is overexpressed throughout the entire mouse. Immune cell populations were assessed in the mammary glands by flow cytometry, which revealed decreased numbers of various immune cell populations. Transgenic mice were also monitored for mammary gland tumor development over a 2-year timespan. Following development of mammary gland tumors, immune cell populations in the tumors and spleens of transgenic and control mice were analyzed by flow cytometry. Upon long-term monitoring, we determined that multi-parous PR overexpressing mice developed significantly more mammary gland tumors than control mice. Additionally, tumors from PR overexpressing mice contained fewer infiltrating immune cells, and RNA sequencing analysis of tumor samples revealed that immune-related gene signatures were lower in tumors from PR overexpressing mice as compared to control mice. Finally, we utilized syngeneic mammary gland tumor models to evaluate the effect of P4 on the growth of PR+ mammary gland tumors in vivo, which revealed that P4 promoted tumor growth and decreased immune cell infiltration of PR+ mammary gland tumors. Together, these findings offer a novel mechanism of P4-driven mammary gland tumor development and provide rationale in investigating the usage of anti-progestin therapies to promote immune-mediated elimination of mammary gland tumors.

Citation Format: Lauryn Rose Werner, Katelin A. Gibson, Merit L. Goodman, Dominika E. Helm, Katherine R. Walter, Sean M. Holloran, Gloria M. Trinca, Richard C. Hastings, Howard H. Yang, Ying Hu, Junping Wei, Gangjun Lei, Xiao-Yi Yang, Rashna Madan, Alfredo A. Molinolo, Mary A. Markiewicz, Prabhakar Chalise, Margaret L. Axelrod, Justin M. Balko, Kent W. Hunter, Zachary C. Hartman, Carol A. Lange, Christy R. Hagan. Lauryn Werner [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 1351.

Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer

Biomarkers of response are needed in breast cancer to stratify patients to appropriate therapies and avoid unnecessary toxicity. We used peripheral blood gene expression and cell type abundance to identify biomarkers of response and recurrence in neoadjuvant chemotherapy treated breast cancer patients. We identified a signature of interferon and complement response that was higher in the blood of patients with pathologic complete response. This signature was preferentially expressed by monocytes in single cell RNA sequencing. Monocytes are routinely measured clinically, enabling examination of clinically measured monocytes in multiple independent cohorts. We found that peripheral monocytes were higher in patients with good outcomes in four cohorts of breast cancer patients. Blood gene expression and cell type abundance biomarkers may be useful for prognostication in breast cancer.

Significance

Biomarkers are needed in breast cancer to identify patients at risk for recurrence. Blood is an attractive site for biomarker identification due to the relative ease of longitudinal sampling. Our study suggests that blood-based gene expression and cell type abundance biomarkers may have clinical utility in breast cancer.

Immune-checkpoint inhibitors: long-term implications of toxicity

The development of immune-checkpoint inhibitors (ICIs) has heralded a new era in cancer treatment, enabling the possibility of long-term survival in patients with metastatic disease, and providing new therapeutic indications in earlier-stage settings. As such, characterizing the long-term implications of receiving ICIs has grown in importance. An abundance of evidence exists describing the acute clinical toxicities of these agents, although chronic effects have not been as well catalogued. Nonetheless, emerging evidence indicates that persistent toxicities might be more common than initially suggested. While generally low-grade, these chronic sequelae can affect the endocrine, rheumatological, pulmonary, neurological and other organ systems. Fatal toxicities also comprise a diverse set of clinical manifestations and can occur in 0.4-1.2% of patients. This risk is a particularly relevant consideration in light of the possibility of long-term survival. Finally, the effects of immune-checkpoint blockade on a diverse range of immune processes, including atherosclerosis, heart failure, neuroinflammation, obesity and hypertension, have not been characterized but remain an important area of research with potential relevance to cancer survivors. In this Review, we describe the current evidence for chronic immune toxicities and the long-term implications of these effects for patients receiving ICIs.

Mechanisms of MHC-I Downregulation and Role in Immunotherapy Response

Immunotherapy has become a key therapeutic strategy in the treatment of many cancers. As a result, research efforts have been aimed at understanding mechanisms of resistance to immunotherapy and how anti-tumor immune response can be therapeutically enhanced. It has been shown that tumor cell recognition by the immune system plays a key role in effective response to T cell targeting therapies in patients. One mechanism by which tumor cells can avoid immunosurveillance is through the downregulation of Major Histocompatibility Complex I (MHC-I). Downregulation of MHC-I has been described as a mechanism of intrinsic and acquired resistance to immunotherapy in patients with cancer. Depending on the mechanism, the downregulation of MHC-I can sometimes be therapeutically restored to aid in anti-tumor immunity. In this article, we will review current research in MHC-I downregulation and its impact on immunotherapy response in patients, as well as possible strategies for therapeutic upregulation of MHC-I.

Abstract P1-04-03: Host myeloid response to tumor and immunotherapy is associated with heterogeneity in outcomes to anti-PDL1

Background: Immune checkpoint inhibitors (ICI) have improved patient overall and progression-free survival in some cancer types but yielded limited success in breast cancer. Phase-III clinical trials in triple negative breast cancer (TNBC) patients, who harbor extensive tumor-infiltrating lymphocytes within tumor stroma, have demonstrated increased progression-free survival (IMpassion130) and pathologic complete response (KEYNOTE-522). Consequently, combinations of ICI and chemotherapy have been FDA-approved for metastatic TNBC patients, and potentially in the early breast cancer setting. Despite FDA-approval, the therapeutic benefit of ICI alone and the most efficacious chemotherapy combinations are poorly characterized. Objective: We sought to model ICI response in vivo to elucidate the mechanisms responsible for immunotherapy efficacy in breast cancer and ascertain the therapeutic benefits of different chemotherapeutic combinations with ICI. Methods: In this study, we used an immunocompetent EMT6 orthotopic mammary tumor model to investigate the efficacy of single-agent immunotherapy and in combination with standard-of-care chemotherapy (paclitaxel [PAC] or doxorubicin [DOX]). We used single-cell RNA sequencing to analyze the cellular landscape of the primary tumor in response to combinatorial therapeutic strategies. Additionally, we serially sampled and analyzed peripheral blood from mice with differential responses by bulk and T-cell receptor (TCR) sequencing to identify systemic genetic alterations and T-cell expansion. Results: Single-agent anti-PD-L1 robustly suppressed primary tumor growth (p =0.0046) and extended survival (p&lt;0.0001) beyond the isotype control group. While either PAC or DOX demonstrated moderate therapeutic efficacy, neither agent potentiated single-agent anti-PD-L1 benefit. Interestingly, despite using a genetically identical tumor model and murine host, anti-PD-L1 induced heterogeneous responses, ranging from complete response to complete intrinsic resistance. The longitudinal analysis of peripheral blood from heterogeneously responding mice uncovered signatures of myeloid cell recruitment corresponding to transient responses ultimately converting to resistance. We also identified specific clonal T cell expansion present only in responders. Single-cell transcriptomic profiling of the tumor microenvironment revealed an increase of T cells and natural killer cells and reduction of regulatory T cells in the combination groups versus chemotherapy alone, although this did not translate into improved benefit. Finally, we performed gene-set enrichment analysis on infiltrating T cells and identified a robust signature of cytotoxic T cell activation characterized by a significant enrichment in inflammatory pathways in both single-agent anti-PD-L1 and in combination with chemotherapy. Conclusions: This study identifies a heterogeneously ICI-responsive in vivo model that emulates TNBC patient response to combinatorial ICI approaches. We describe the efficacy of single-agent ICI in upregulating cytotoxic immune cell infiltration and expansion within the primary tumor, thereby diminishing tumor growth and enhancing survival. Moreover, this study describes differential responses in a genetically similar host, which reflects heterogeneous patient response to ICI. Further characterization may identify systemic biomarkers and tumor antigen-specific T cell clones to accurately predict immunotherapy response in patients and uncover mechanisms for sensitizing tumors refractory to ICI. This study also has potentially significant clinical implications for re-evaluating the benefits of chemotherapy in combination with ICI in TNBC patients.

Citation Format: Ann Hanna, Xiaopeng Sun, Paula I. Gonzalez-Ericsson, Violeta M. Sanchez, Melinda E. Sanders, Justin M. Balko. Host myeloid response to tumor and immunotherapy is associated with heterogeneity in outcomes to anti-PDL1 [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-04-03.

Abstract P4-04-07: Progesterone promotes immunomodulation and tumor development in the murine mammary gland

Clinical studies have linked usage of progestins (synthetic progesterone) to breast cancer risk. However, little is understood regarding the role of native progesterone (P4), signaling through the progesterone receptor (PR), in breast tumor formation. Recently, we reported a link between PR and immune signaling pathways, showing that P4/PR can repress type I interferon signaling pathways. Given these findings, we sought to investigate whether P4/PR drive immunomodulation in the mammary gland and promote tumor formation. To determine the effect of P4 on immune cell populations in the murine mammary gland, mice were treated with P4 or placebo pellets for 21 days. We found that mice treated with P4 exhibited changes in the mammary gland indicative of an inhibited immune response compared to placebo-treated mice. To assess the effect of PR overexpression on mammary gland tumor development as well as immune cell populations in the mammary gland, a transgenic mouse model was used in which PR is overexpressed throughout the entire mouse. Immune cell populations were assessed in the mammary glands by flow cytometry, which revealed decreased numbers of various immune cell populations. Transgenic mice were also monitored for mammary gland tumor development over a 2-year timespan. Following development of mammary gland tumors, immune cell populations in the tumors and spleens of transgenic and control mice were analyzed by flow cytometry. Upon long-term monitoring, we determined that multi-parous PR overexpressing mice developed significantly more mammary gland tumors than control mice. Additionally, tumors from PR overexpressing mice contained fewer infiltrating immune cells, and RNA sequencing analysis of tumor samples revealed that immune-related gene signatures were lower in tumors from PR overexpressing mice as compared to control mice. Finally, we utilized syngeneic mammary gland tumor models to evaluate the effect of P4 on the growth of PR+ mammary gland tumors in vivo, which revealed that P4 promoted tumor growth and decreased immune cell infiltration of PR+ mammary gland tumors. Together, these findings offer a novel mechanism of P4-driven mammary gland tumor development and provide rationale in investigating the usage of anti-progestin therapies to promote immune-mediated elimination of mammary gland tumors.

Citation Format: Lauryn R Werner, Katelin A Gibson, Merit L Goodman, Dominika E Helm, Katherine R Walter, Sean M Holloran, Gloria M Trinca, Richard C Hastings, Howard H Yang, Ying Hu, Junping Wei, Gangjun Lei, Xiao-Yi Yang, Rashna Madan, Alfred A Molinolo, Mary A Markiewicz, Prabhakar Chalise, Margaret L Axelrod, Justin M Balko, Kent W Hunter, Zachary C Hartman, Carol A Lange, Christy R Hagan. Progesterone promotes immunomodulation and tumor development in the murine mammary gland [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-04-07.

Pharmacological Activation of cGAS for Cancer Immunotherapy

When compartmentally mislocalized within cells, nucleic acids can be exceptionally immunostimulatory and can even trigger the immune-mediated elimination of cancer. Specifically, the accumulation of double-stranded DNA in the cytosol can efficiently promote antitumor immunity by activating the cGAMP synthase (cGAS) / stimulator of interferon genes (STING) cellular signaling pathway. Targeting this cytosolic DNA sensing pathway with interferon stimulatory DNA (ISD) is therefore an attractive immunotherapeutic strategy for the treatment of cancer. However, the therapeutic activity of ISD is limited by several drug delivery barriers, including susceptibility to deoxyribonuclease degradation, poor cellular uptake, and inefficient cytosolic delivery. Here, we describe the development of a nucleic acid immunotherapeutic, NanoISD, which overcomes critical delivery barriers that limit the activity of ISD and thereby promotes antitumor immunity through the pharmacological activation of cGAS at the forefront of the STING pathway. NanoISD is a nanoparticle formulation that has been engineered to confer deoxyribonuclease resistance, enhance cellular uptake, and promote endosomal escape of ISD into the cytosol, resulting in potent activation of the STING pathway via cGAS. NanoISD mediates the local production of proinflammatory cytokines via STING signaling. Accordingly, the intratumoral administration of NanoISD induces the infiltration of natural killer cells and T lymphocytes into murine tumors. The therapeutic efficacy of NanoISD is demonstrated in preclinical tumor models by attenuated tumor growth, prolonged survival, and an improved response to immune checkpoint blockade therapy.

Framework for Implementing and Tracking a Molecular Tumor Board at a National Cancer Institute-Designated Comprehensive Cancer Center

BACKGROUND

Over the past few years, tumor next-generation sequencing (NGS) panels have evolved in complexity and have changed from selected gene panels with a handful of genes to larger panels with hundreds of genes, sometimes in combination with paired germline filtering and/or testing. With this move toward increasingly large NGS panels, we have rapidly outgrown the available literature supporting the utility of treatments targeting many reported gene alterations, making it challenging for oncology providers to interpret NGS results and make a therapy recommendation for their patients.

METHODS

To support the oncologists at Vanderbilt-Ingram Cancer Center (VICC) in interpreting NGS reports for patient care, we initiated two molecular tumor boards (MTBs)-a VICC-specific institutional board for our patients and a global community MTB open to the larger oncology patient population. Core attendees include oncologists, hematologist, molecular pathologists, cancer geneticists, and cancer genetic counselors. Recommendations generated from MTB were documented in a formal report that was uploaded to our electronic health record system.

RESULTS

As of December 2020, we have discussed over 170 patient cases from 77 unique oncology providers from VICC and its affiliate sites, and a total of 58 international patient cases by 25 unique providers from six different countries across the globe. Breast cancer and lung cancer were the most presented diagnoses.

CONCLUSION

In this article, we share our learning from the MTB experience and document best practices at our institution. We aim to lay a framework that allows other institutions to recreate MTBs.

IMPLICATIONS FOR PRACTICE

With the rapid pace of molecularly driven therapies entering the oncology care spectrum, there is a need to create resources that support timely and accurate interpretation of next-generation sequencing reports to guide treatment decision for patients. Molecular tumor boards (MTB) have been created as a response to this knowledge gap. This report shares implementation strategies and best practices from the Vanderbilt experience of creating an institutional MTB and a virtual global MTB for the larger oncology community. This report describe a reproducible framework that can be adopted to initiate MTBs at other institutions.

Breast cancer resistance mechanisms: challenges to immunotherapy

PURPOSE

The clinical implementation of immunotherapy has profoundly transformed cancer treatment. Targeting the immune system to mount anti-tumor responses can elicit a systemically durable response. Employing immune checkpoint blockade (ICB) has suppressed tumor growth and vastly improved patient overall and progression-free survival in several cancer types, most notably melanoma and non-small cell lung carcinoma. Despite widescale clinical success, ICB response is heterogeneously efficacious across tumor types. Many cancers, including breast cancer, are frequently refractory to ICB. In this review, we will discuss the challenges facing immunotherapy success and address the underlying mechanisms responsible for primary and acquired breast cancer resistance to immunotherapy.

FINDINGS

Even in initially ICB-responsive tumors, many acquire resistance due to tumor-specific alterations, loss of tumor-specific antigens, and extrinsic mechanisms that reshape the immune landscape within the tumor microenvironment (TME). The tumor immune interaction circumvents the benefits of immunotherapy; tumors rewire the tumor-suppressive functions of activated immune cells within their stroma to propagate tumor growth and progression.

CONCLUSIONS

The breast cancer immune TME is complex and the mechanisms driving resistance to ICB are multifaceted. Continued study in both preclinical models and clinical trials should help elucidate these mechanisms so they can be targeted to benefit more breast cancer patients.

Artificial image objects for classification of breast cancer biomarkers with transcriptome sequencing data and convolutional neural network algorithms

BACKGROUND

Transcriptome sequencing has been broadly available in clinical studies. However, it remains a challenge to utilize these data effectively for clinical applications due to the high dimension of the data and the highly correlated expression between individual genes.

METHODS

We proposed a method to transform RNA sequencing data into artificial image objects (AIOs) and applied convolutional neural network (CNN) algorithms to classify these AIOs. With the AIO technique, we considered each gene as a pixel in an image and its expression level as pixel intensity. Using the GSE96058 (n = 2976), GSE81538 (n = 405), and GSE163882 (n = 222) datasets, we created AIOs for the subjects and designed CNN models to classify biomarker Ki67 and Nottingham histologic grade (NHG).

RESULTS

With fivefold cross-validation, we accomplished a classification accuracy and AUC of 0.821 ± 0.023 and 0.891 ± 0.021 for Ki67 status. For NHG, the weighted average of categorical accuracy was 0.820 ± 0.012, and the weighted average of AUC was 0.931 ± 0.006. With GSE96058 as training data and GSE81538 as testing data, the accuracy and AUC for Ki67 were 0.826 ± 0.037 and 0.883 ± 0.016, and that for NHG were 0.764 ± 0.052 and 0.882 ± 0.012, respectively. These results were 10% better than the results reported in the original studies. For Ki67, the calls generated from our models had a better power for prediction of survival as compared to the calls from trained pathologists in survival analyses.

CONCLUSIONS

We demonstrated that RNA sequencing data could be transformed into AIOs and be used to classify Ki67 status and NHG with CNN algorithms. The AIO method could handle high-dimensional data with highly correlated variables, and there was no need for variable selection. With the AIO technique, a data-driven, consistent, and automation-ready model could be developed to classify biomarkers with RNA sequencing data and provide more efficient care for cancer patients.

Tumor-Specific Major Histocompatibility-II Expression Predicts Benefit to Anti-PD-1/L1 Therapy in Patients With HER2-Negative Primary Breast Cancer

PURPOSE

Immunotherapies targeting PD-1/L1 enhance pathologic complete response (pCR) rates when added to standard neoadjuvant chemotherapy (NAC) regimens in early-stage triple-negative, and possibly high-risk estrogen receptor-positive breast cancer. However, immunotherapy has been associated with significant toxicity, and most patients treated with NAC do not require immunotherapy to achieve pCR. Biomarkers discerning patients benefitting from the addition of immunotherapy from those who would achieve pCR to NAC alone are clearly needed. In this study, we tested the ability of MHC-II expression on tumor cells, to predict immunotherapy-specific benefit in the neoadjuvant breast cancer setting.

PATIENTS AND METHODS

This was a retrospective tissue-based analysis of 3 cohorts of patients with breast cancer: (i) primary nonimmunotherapy-treated breast cancers (n = 381), (ii) triple-negative breast cancers (TNBC) treated with durvalumab and standard NAC (n = 48), and (iii) HER2-negative patients treated with standard NAC (n = 87) or NAC and pembrolizumab (n = 66).

RESULTS

HLA-DR positivity on ≥5% of tumor cells, defined a priori, was observed in 10% and 15% of primary non-immunotherapy-treated hormone receptor-positive and triple-negative breast cancers, respectively. Quantitative assessment of MHC-II on tumor cells was predictive of durvalumab + NAC and pembrolizumab + NAC (ROC AUC, 0.71; P = 0.01 and AUC, 0.73; P = 0.001, respectively), but not NAC alone (AUC, 0.5; P = 0.99).

CONCLUSIONS

Tumor-specific MHC-II has a strong candidacy as a specific biomarker of anti-PD-1/L1 immunotherapy benefit when added to standard NAC in HER2-negative breast cancer. Combined with previous studies in melanoma, MHC-II has the potential to be a pan-cancer biomarker. Validation is warranted in existing and future phase II/III clinical trials in this setting.

Targeting MYCN-expressing triple-negative breast cancer with BET and MEK inhibitors

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer that does not respond to endocrine therapy or human epidermal growth factor receptor 2 (HER2)-targeted therapies. Individuals with TNBC experience higher rates of relapse and shorter overall survival compared to patients with receptor-positive breast cancer subtypes. Preclinical discoveries are needed to identify, develop, and advance new drug targets to improve outcomes for patients with TNBC. Here, we report that MYCN, an oncogene typically overexpressed in tumors of the nervous system or with neuroendocrine features, is heterogeneously expressed within a substantial fraction of primary and recurrent TNBC and is expressed in an even higher fraction of TNBCs that do not display a pathological complete response after neoadjuvant chemotherapy. We performed high-throughput chemical screens on TNBC cell lines with varying amounts of MYCN expression and determined that cells with higher expression of MYCN were more sensitive to bromodomain and extraterminal motif (BET) inhibitors. Combined BET and MEK inhibition resulted in a synergistic decrease in viability, both in vitro and in vivo, using cell lines and patient-derived xenograft (PDX) models. Our preclinical data provide a rationale to advance a combination of BET and MEK inhibitors to clinical investigation for patients with advanced MYCN-expressing TNBC.

Hydroxychloroquine as Pre-exposure Prophylaxis for Coronavirus Disease 2019 (COVID-19) in Healthcare Workers: A Randomized Trial

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly emerging virus causing the ongoing coronavirus disease 2019 (COVID-19) pandemic with no known effective prophylaxis. We investigated whether hydroxychloroquine could prevent SARS-CoV-2 in healthcare workers at high risk of exposure.

Methods

We conducted a randomized, double-blind, placebo-controlled clinical trial of healthcare workers with ongoing exposure to persons with SARS-CoV-2, including those working in emergency departments, intensive care units, COVID-19 hospital wards, and first responders. Participants across the United States and in the Canadian province of Manitoba were randomized to hydroxychloroquine loading dose then 400 mg once or twice weekly for 12 weeks. The primary endpoint was confirmed or probable COVID-19–compatible illness. We measured hydroxychloroquine whole-blood concentrations.

Results

We enrolled 1483 healthcare workers, of whom 79% reported performing aerosol-generating procedures. The incidence of COVID-19 (laboratory-confirmed or symptomatic compatible illness) was 0.27 events/person-year with once-weekly and 0.28 events/person-year with twice-weekly hydroxychloroquine compared with 0.38 events/person-year with placebo. For once-weekly hydroxychloroquine prophylaxis, the hazard ratio was .72 (95% CI, .44–1.16; P = .18) and for twice-weekly was .74 (95% CI, .46–1.19; P = .22) compared with placebo. Median hydroxychloroquine concentrations in whole blood were 98 ng/mL (IQR, 82–120) with once-weekly and 200 ng/mL (IQR, 159–258) with twice-weekly dosing. Hydroxychloroquine concentrations did not differ between participants who developed COVID-19–compatible illness (154 ng/mL) versus participants without COVID-19 (133 ng/mL; P = .08).

Conclusions

Pre-exposure prophylaxis with hydroxychloroquine once or twice weekly did not significantly reduce laboratory-confirmed COVID-19 or COVID-19–compatible illness among healthcare workers.

Clinical Trials Registration

Clinicaltrials.gov NCT04328467.

Genomic evaluation of tumor mutational burden-high (TMB-H) versus TMB-low (TMB-L) metastatic breast cancer to reveal unique mutational features

1091

Background: Tumor mutational burden (TMB) has emerged as an imperfect biomarker of immune checkpoint inhibition (ICI) outcomes in solid tumors. Despite the approval for pembrolizumab in all TMB-high (TMB-H) solid tumors, the optimal clinical approach to TMB-H or hypermutated advanced/metastatic breast cancer (MBC) is unknown with sparse prospective data. We hypothesize that TMB-H MBC will have unique genomic alterations compared to TMB-low (TMB-L) breast cancer that could inform novel therapeutic approaches. Methods: Tumor samples (N = 5621) obtained from patients with MBC were analyzed by next-generation sequencing (NGS) of DNA (592-gene panel or whole exome sequencing) and RNA (whole transcriptome sequencing) at Caris Life Sciences (Phoenix, AZ). TMB was calculated based on recommendations from the Friends of Cancer Research TMB Harmonization Project (Merino et al., 2020), with the TMB-H threshold set to ≥ 10 muts/Mb. IHC was performed for PD-L1 (Ventana SP142 ≥1% immune cells). Deficient mismatch repair (dMMR)/high microsatellite instability (MSI-H) was tested by IHC and NGS, respectively. Results: TMB-H was identified in 8.2% (n = 461) of MBC samples, with similar frequencies observed across molecular subtypes (7.8-8.6%, p = 0.85): HR+/HER2- (n = 3087) 7.8%, HR+/HER2+ (n = 266) 8.3%, HR-/HER2+ (n = 179) 7.8%, TNBC (n = 1476) 8.6%. The frequency of TMB-H was significantly increased in lobular (16%) versus ductal (5%) MBC (p < 0.01). TMB-H samples were enriched in genitourinary (42%), soft tissue (20%), and gastrointestinal non-liver (16%) biopsy specimens. Compared to TMB-L tumors, TMB-H tumors exhibited significantly higher mutation rates for TP53 (60 v 52%), PIK3CA (55 vs 31%), ARID1A (34 vs 11%), CDH1 (27 vs 11%), NF1 (22 vs 9%), RB1 (14 vs 5%), KMT2C (12 vs 7%), PTEN (12 vs 7%), ERBB2 (7 vs 2.9%), and PALB2 (3.3 vs 1%) genes (p < 0.05 each). Copy number alteration and fusion rates did not differ between TMB-H and TMB-L breast cancers. PI3K/AKT/MTOR, TP53, Histone/Chromatin remodeling, DNA damage repair (DDR), RAS, and cell cycle pathway alterations were detected in > 25% TMB-H MBCs (p < 0.05 each). dMMR/MSI-High (7.2 vs 0.3%, p < 0.01) and PD-L1 positivity (36 vs 28%, p < 0.05) frequencies were significantly increased in TMB-H tumors. DNA signature analyses including APOBEC and homologous recombination repair deficiency, as well as gene expression profiling to assess immune-related signatures and tumor microenvironment are underway. Conclusions: TMB-H breast cancers contain a unique genomic profile enriched with targetable mutations such as PIK3CA, ARID1A, NF1, PTEN, ERBB2, and PALB2. Concurrent predictive biomarkers of response to immune checkpoint inhibition such as MSI-H and PDL-1 positivity are also more prevalent in TMB-H MBC. These findings suggest novel combination strategies within TMB-H MBC could be explored.

Progesterone promotes immunomodulation and tumor development in the murine mammary gland

BACKGROUND

Clinical studies have linked usage of progestins (synthetic progesterone [P4]) to breast cancer risk. However, little is understood regarding the role of native P4, signaling through the progesterone receptor (PR), in breast tumor formation. Recently, we reported a link between PR and immune signaling pathways, showing that P4/PR can repress type I interferon signaling pathways. Given these findings, we sought to investigate whether P4/PR drive immunomodulation in the mammary gland and promote tumor formation.

METHODS

To determine the effect of P4 on immune cell populations in the murine mammary gland, mice were treated with P4 or placebo pellets for 21 days. Immune cell populations in the mammary gland, spleen, and inguinal lymph nodes were subsequently analyzed by flow cytometry. To assess the effect of PR overexpression on mammary gland tumor development as well as immune cell populations in the mammary gland, a transgenic mouse model was used in which PR was overexpressed throughout the entire mouse. Immune cell populations were assessed in the mammary glands, spleens, and inguinal lymph nodes of 6-month-old transgenic and control mice by flow cytometry. Transgenic mice were also monitored for mammary gland tumor development over a 2-year time span. Following development of mammary gland tumors, immune cell populations in the tumors and spleens of transgenic and control mice were analyzed by flow cytometry.

RESULTS

We found that mice treated with P4 exhibited changes in the mammary gland indicative of an inhibited immune response compared with placebo-treated mice. Furthermore, transgenic mice with PR overexpression demonstrated decreased numbers of immune cell populations in their mammary glands, lymph nodes, and spleens. On long-term monitoring, we determined that multiparous PR-overexpressing mice developed significantly more mammary gland tumors than control mice. Additionally, tumors from PR-overexpressing mice contained fewer infiltrating immune cells. Finally, RNA sequencing analysis of tumor samples revealed that immune-related gene signatures were lower in tumors from PR-overexpressing mice as compared with control mice.

CONCLUSION

Together, these findings offer a novel mechanism of P4-driven mammary gland tumor development and provide rationale in investigating the usage of antiprogestin therapies to promote immune-mediated elimination of mammary gland tumors.

Automated Dissection Protocol for Tumor Enrichment in Low Tumor Content Tissues

Tumor enrichment in low tumor content tissues, those below 20% tumor content depending on the method, is required to generate quality data reproducibly with many downstream assays such as next generation sequencing. Automated tissue dissection is a new methodology that automates and improves tumor enrichment in these common, low tumor content tissues by decreasing the user-dependent imprecision of traditional macro-dissection and time, cost, and expertise limitations of laser capture microdissection by using digital image annotation overlay onto unstained slides. Here, digital hematoxylin and eosin (H&E) annotations are used to target small tumor areas using a blade that is 250 µm² in diameter in unstained formalin fixed paraffin embedded (FFPE) or fresh frozen sections up to 20 µm in thickness for automated tumor enrichment prior to nucleic acid extraction and whole exome sequencing (WES). Automated dissection can harvest annotated regions in low tumor content tissues from single or multiple sections for nucleic acid extraction. It also allows for capture of extensive pre- and post-harvest collection metrics while improving accuracy, reproducibility, and increasing throughput with utilization of fewer slides. The described protocol enables digital annotation with automated dissection on animal and/or human FFPE or fresh frozen tissues with low tumor content and could also be used for any region of interest enrichment to boost adequacy for downstream sequencing applications in clinical or research workflows.

A Genetic Mouse Model Recapitulates Immune Checkpoint Inhibitor-Associated Myocarditis and Supports a Mechanism-Based Therapeutic Intervention

Immune checkpoint inhibitors (ICI) targeting CTLA4 or PD-1/PD-L1 have transformed cancer therapy but are associated with immune-related adverse events, including myocarditis. Here, we report a robust preclinical mouse model of ICI-associated myocarditis in which monoallelic loss of Ctla4 in the context of complete genetic absence of Pdcd1 leads to premature death in approximately half of mice. Premature death results from myocardial infiltration by T cells and macrophages and severe ECG abnormalities, closely recapitulating the clinical and pathologic hallmarks of ICI-associated myocarditis observed in patients. Using this model, we show that Ctla4 and Pdcd1 functionally interact in a gene dosage-dependent manner, providing a mechanism by which myocarditis arises with increased frequency in the setting of combination ICI therapy. We demonstrate that intervention with CTLA4-Ig (abatacept) is sufficient to ameliorate disease progression and additionally provide a case series of patients in which abatacept mitigates the fulminant course of ICI myocarditis. SIGNIFICANCE: We provide a preclinical model of ICI-associated myocarditis which recapitulates this clinical syndrome. Using this model, we demonstrate that CTLA4 and PD-1 (ICI targets) functionally interact for myocarditis development and that intervention with CTLA4-Ig (abatacept) attenuates myocarditis, providing mechanistic rationale and preclinical support for therapeutic clinical studies.See related commentary by Young and Bluestone, p. 537.This article is highlighted in the In This Issue feature, p. 521.

Abstract PS17-14: Evaluating the efficacy of immunotherapy in triple negative breast cancer

The breast cancer microenvironment comprises a complex stroma including tumor-infiltrating lymphocytes (TILs), which can either stimulate tumor progression or promote anti-tumor immunity in response to tumor-derived cues. In general, of all clinical subtypes, triple-negative breast cancer (TNBC) is characterized by the most extensive infiltration of TILs within tumor stroma, which is consistent with the observation that TNBC seems to clinically respond to immunotherapies at the highest rates. Immune checkpoint blockade (ICB), an immunotherapy that promotes prolonged activation of cytotoxic immune cells to mount robust anti-tumorigenic responses, has yielded limited success in treating breast cancer. IMpassion130 was the first clinical trial to indicate that combining anti-PD-L1 with standard-of-care chemotherapy (nab-paclitaxel) to treat TNBC increases progression-free survival in patients exclusively those with PD-L1 positive tumors. Furthermore, the KEYSTONE-522 trial showed that administering anti-PD-1 in addition to various neoadjuvant chemotherapies increased the pathologic complete response in early stage TNBC patients. Despite promising evidence for immunotherapy success, both clinical trials lacked an experimental ICB-only group, and thus cannot address the therapeutic benefit of ICB alone, or which chemotherapy combination would maximize this benefit. Finally, mechanisms of resistance to ICB in breast cancer remain unexplored. We sought to model ICB response in vivo to elucidate the mechanisms responsible for immunotherapy efficacy in breast cancer, explore the synergistic effects of ICB with chemotherapies, and model ICB resistance.In this study, we investigated the efficacy of anti-PD-L1 as single-agent or in combination with paclitaxel or doxorubicin in the EMT6 (Balb/c) orthotopic mammary tumor model. In this model, single-agent immunotherapy was efficacious in reducing primary tumor growth compared to combination treatment, with a small proportion of complete responses, whereas modest benefit was observed with either chemotherapy alone. Following two rounds of treatment, we analyzed the tumor-immune microenvironment by flow cytometry and gene expression analysis. Anti-PD-L1 alone or in combination with either chemotherapy enhanced infiltration of cytotoxic and effector T cell as well as natural killer cells into the tumor microenvironment. Using gene expression analysis, we observed elevated expression of myeloid recruitment and activation markers in combination-treated tumors, supporting a known role of chemotherapy-induced cell death in myeloid recruitment; however as chemotherapy did not add benefit to tumor response or survival, it is unclear if this effect is detrimental or supportive. Interestingly, completely responsive anti-PD-L1 treated tumors that eventually recurred retained resistance to ICB upon re-implantation in naïve recipient mice, suggesting that tumor-intrinsic factors may contribute to resistance.Herein, we explore an in vivo model that corroborates clinical response to combinatorial immunotherapy approaches in breast cancer patients. We report the immunogenic efficacy of single-agent ICB that upregulates tumoricidal immune cell infiltration into the primary tumor, thereby controlling tumor growth, albeit without achieving complete response in all mice. Additionally, post-therapy recurrent tumors retain resistance upon transplantation, indicating tumor-specific adaptive resistance. This study has potentially significant clinical implications for re-evaluating the contributions of chemotherapy in combination with ICB in TNBC patients.

Citation Format: Ann Hanna, Paula I. Gonzalez-Ericsson, Violeta Sanchez, Melinda E. Sanders, Justin M. Balko. Evaluating the efficacy of immunotherapy in triple negative breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-14.

Abstract PS4-19: Evaluation of tumor-specific MHC-II expression as a biomarker

Recently MHC-II protein expression levels in breast cancer tumor cells were shown to predict response to the PD-1 inhibitor pembrolizumab on a neoadjuvant clinical trial for ER+ and TNBC (ISPY-2). To better understand this biomarker and avoid post-market issues, we aimed to investigate possible pitfalls of MHC-II/HLA-DR quantification, prevalence of HLA-DR expression in breast cancer (BC) cells and its association with clinical data in a cohort of 372 BC patents. We assessed tumor and non-tumor HLA-DR expression by multiplex fluorescence immunohistochemistry on 8 TMAs containing 372 surgical BC samples, comprised of 239 ER+ and 123 TNBCs. Patient characteristics are shown in table 1. PanCK was used to define the tumor area and HLA-DR quantification was performed by training an object classifier on QuPath. Upon visual examination, 23 samples showed patchy panCK expression. We excluded normal breast epithelium and in situ components, which showed varying degrees of HLA-DR. 44.4% of breast cancers expressed HLA-DR, with 8.3% showing high tumor expression (HLA-DRHI; ≥20% of tumor cells). TNBC showed higher prevalence of HLA-DRHI cases (35% HLADR+, 14.6% HLA-DRHI, mean tumor HLA-DR expression (% of tumor cells) 10.3%, range 0-84%) than ER+ BC (51% HLADR+, 5.4% HLA-DRHI, mean 7.4%, range 0-66.5%). In some cases, HLA-DR and panCK expression were mutually exclusive. In other cases the lack of panCK expression highlighted the presence of stromal cells within the tumor area that were not evident on H&E. Tumoral MHC-II expression correlated with the presence of TILs for ER+ BC (r=0.18, p=0.0158) and TNBC (r=0.20, p= 0.0450), specifically CD3 (r=0.49 p&lt;0.0001) and CD4 (r=0.48 p&lt;0.0001), and to a lesser extent CD8 (r=0.28, p= 0.013) in a subset of TNBCs on which these stains where performed (n=81). We found no correlation between tumoral MHC-II expression and clinical characteristics (ER and PR within ER+ BC, age, presence of lymph node metastasis, stage, neoadjuvant treatment) in ER+ or TNBC. High tumor HLA-DR expression correlated with poorer recurrence-free survival (RFS) in ER+ BC (p=0.038) but showed no correlation in TNBC. Cox proportional hazard model including clinical data determined that only stage was an independent predictor of survival in ER+. Non-tumoral HLA-DR expression was associated with better RFS (p=0.007) and overall survival (p=0.01) in TNBC; however, only stage was an independent predictor in multivariant analyses. Tumor MHC-II expression in BC has been reported to range from 22% to 48.5% in TNBC or unselected BC, and high tumoral MHC-II expression was reported to be 6.9% in unselected BC and 36.3% in TNBC. Specific rates of HLA-DR expression in ER+ breast cancer have not been extensively investigated. Here we report a similar overall prevalence, but lower number of tumors presenting high HLA-DR expression and an association with poorer survival in ER+ BC. HLA-DR IHC is a robust assay that can be easily used to identify MCH-II high expressing tumors and scoring percentage of tumoral cells should be more reproducible than PD-L1 scoring on immune cells when assessed by a trained pathologist.

Table 1: Patient characteristicsTNBCER+Total number of cases239123Median age48,563Treatmenttreatment naïve26%45%neoadjuvant chemotherapy74%4%pre-surgical letrozole-51%Positive lymph node58%14%StageI27%82%II20%27%III67%8%IV0%1%

Citation Format: Paula Ines Gonzalez Ericsson, Justin M Balko, Violeta Sanchez, Melinda Sanders. Evaluation of tumor-specific MHC-II expression as a biomarker [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-19.

Abstract PD9-06: Peripheral blood gene signatures predict response to neoadjuvant chemotherapy in breast cancer patients

Purpose: Neoadjuvant chemotherapy (NAC), the standard of care for a subset of breast cancer patients, is known to have immunologic effects. With emerging data showing improved response rates with anti-PD-1/PD-L1 immunotherapy in combination with chemotherapy, the effects of NAC on systemic and local anti-tumor immunity require further study. Biomarkers of anti-tumor immunity are needed to identify which patients are most likely to respond to immunotherapy. Our previous work has shown that changes in the peripheral blood can be observed over the course of NAC for breast cancer. Peripheral blood biomarkers are attractive because of the relative ease of sampling compared to site of disease. Residual cancer burden (RCB) is a useful surrogate marker of long-term prognosis, as patients who experience a pathologic complete response (pCR) have better outcomes than those with residual disease (RD). Methods: We previously identified an 8 gene signature of cytotoxicity, derived from single cell RNA sequencing of PD-1Hi CD8+ T cells, which are enriched for tumor-reactive T cells. Using a custom NanoString panel, we tested expression of this gene signature in whole blood collected prior to definitive surgery in 88 breast cancer patients (TNBC, n=21; HER2+, n=17; ER+, n= 54; PR+, n=53) across two cohorts (VUMC, n=58; DFCI, n=30), 64 of whom had received NAC (pCR, n=11; RD, n=53). We further investigated peripheral blood gene expression using RNA sequencing (n=58; 34 post-NAC, 24 untreated). Results: In two cohorts of breast cancer patients, expression of the 8 gene signature (FGFBP2 + GNLY + GZMB + GZMH + NKG7 + LAG3 + PDCD1 - HLA-G) was highest in patients with RD who experienced a recurrence within three years compared to those with pCR (p&lt;0.01) or those with the highest RCB (RCB III) compared to those with RCB 0/I/II who did not have a recurrence with three years (p&lt;0.05). RNA sequencing showed higher expression of interferon alpha, interferon gamma, and complement gene sets in patients experiencing a pCR compared to those with RD by gene set enrichment analysis (FDR-corrected q-values &lt; 0.05). Conclusions: Expression of immune-related genes in the peripheral blood may predict response to NAC in breast cancer patients and be a useful biomarker for those who would benefit from additional therapies. These results will be further tested in a large cohort of longitudinal samples from breast cancer patients receiving NAC alone or in combination with pembrolizumab from the I-SPY-2 trial, to determine whether peripheral blood gene signatures can predict response to immunotherapy in breast cancer.

Citation Format: Margaret L Axelrod, Paula I Gonzalez-Ericsson, Xiaopeng Sun, Riley E Bergman, Joshua Donaldson, Sara M Tolaney, Ian E Krop, Ana C Garrido-Castro, Melinda E. Sanders, Ingrid A Mayer, Justin M Balko. Peripheral blood gene signatures predict response to neoadjuvant chemotherapy in breast cancer patients [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-06.

Nanoparticle delivery improves the pharmacokinetic properties of cyclic dinucleotide STING agonists to open a therapeutic window for intravenous administration

The stimulator of interferon genes (STING) pathway plays an important role in the immune surveillance of cancer and, accordingly, agonists of STING signaling have recently emerged as promising therapeutics for remodeling of the immunosuppressive tumor microenvironment (TME) and enhancing response rates to immune checkpoint inhibitors. 2'3'-cyclic guanosine monophosphate-adenosine monophosphate (2'3'-cGAMP) is the endogenous ligand for STING, but is rapidly metabolized and poorly membrane permeable, restricting its use to intratumoral administration. Nanoencapsulation has been shown to allow for systemic administration of cGAMP and other cyclic dinucleotides (CDN), but little is known about how nanocarriers affect important pharmacological properties that impact the efficacy and safety of CDNs. Using STING-activating nanoparticles (STING-NPs) - a polymersome platform designed to enhance cGAMP delivery - we investigate the pharmacokinetic (PK)-pharmacodynamic (PD) relationships that underlie the ability of intravenously (i.v.) administered STING-NPs to induce STING activation and inhibit tumor growth. First, we demonstrate that nanoencapsulation improves the half-life of encapsulated cGAMP by 40-fold, allowing for sufficient accumulation of cGAMP in tumors and activation of the STING pathway in the TME as assessed by western blot analysis and gene expression profiling. Nanoparticle delivery also changes the biodistribution profile, resulting in increased cGAMP accumulation and STING activation in the liver and spleen, which we identify as dose limiting organs. As a consequence of STING activation in tumors, i.v. administered STING-NPs reprogram the TME towards a more immunogenic antitumor milieu, characterized by an influx of >20-fold more CD4+ and CD8+ T-cells. Consequently, STING-NPs increased response rates to αPD-L1 antibodies, resulting in significant improvements in median survival time in a B16-F10 melanoma model. Additionally, we confirmed STING-NP monotherapy in an additional melanoma (YUMM1.7) and breast adenocarcinoma (E0771) models leading to >50% and 80% reduction in tumor burden, respectively, and significant increases in median survival time. Collectively, this work provides an examination of the PK-PD relationship governing STING activation upon systemic delivery using STING-NPs, providing insight for future optimization for nanoparticle-based STING agonists and other immunomodulating nanomedicines.

Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: a randomized trial

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly emerging virus causing the ongoing Covid-19 pandemic with no known effective prophylaxis. We investigated whether hydroxychloroquine could prevent SARS CoV-2 in healthcare workers at high-risk of exposure.

METHODS

We conducted a randomized, double-blind, placebo-controlled clinical trial of healthcare workers with ongoing exposure to persons with Covid-19, including those working in emergency departments, intensive care units, Covid-19 hospital wards, and first responders. Participants across the United States and in the Canadian province of Manitoba were randomized to hydroxychloroquine 400mg once weekly or twice weekly for 12 weeks. The primary endpoint was confirmed or probable Covid-19-compatible illness. We measured hydroxychloroquine whole blood concentrations.

RESULTS

We enrolled 1483 healthcare workers, of which 79% reported performing aerosol-generating procedures. The incidence of Covid-19 (laboratory-confirmed or symptomatic compatible illness) was 0.27 events per person-year with once-weekly and 0.28 events per person-year with twice-weekly hydroxychloroquine compared with 0.38 events per person-year with placebo. For once weekly hydroxychloroquine prophylaxis, the hazard ratio was 0.72 (95%CI 0.44 to 1.16; P=0.18) and for twice weekly was 0.74 (95%CI 0.46 to 1.19; P=0.22) as compared with placebo. Median hydroxychloroquine concentrations in whole blood were 98 ng/mL (IQR, 82-120) with once-weekly and 200 ng/mL (IQR, 159-258) with twice-weekly dosing. Hydroxychloroquine concentrations did not differ between participants who developed Covid-19 (154 ng/mL) versus participants without Covid-19 (133 ng/mL; P=0.08).

CONCLUSIONS

Pre-exposure prophylaxis with hydroxychloroquine once or twice weekly did not significantly reduce laboratory-confirmed Covid-19 or Covid-19-compatible illness among healthcare workers.

Evolving insights into the mechanisms of toxicity associated with immune checkpoint inhibitor therapy

Immune checkpoint inhibitors have emerged as a revolutionary treatment option for patients with various types of malignancy. Although these agents afford a significant improvement in outcomes for melanoma and other previously untreatable malignancies, their novel mechanism of action may predispose patients to immune-related adverse effects (irAEs). In the tumour neoantigen environment, these irAEs are due to the activation of the immune system by the blockade of suppressive checkpoints, leading to increases in T-cell activation and proliferation. IrAEs have been reported in almost any organ and at any point in time, even months to years after discontinuation of therapy. Certain populations with distinct physiological changes, genetic risk factors, and specific antigen exposures may be more highly predisposed to develop irAEs. This review discusses the incidence and mechanisms of irAEs and the relationship between host factors and irAE occurrence.