Bartemes, Kathleen R.

Abstract Background: Analyzing interactions and the microanatomical distribution of the tumor immune microenvironment (TIME) is essential for a comprehensive understanding of tumor progression. Imaging Mass Cytometry (IMC) is a high-dimensional tissue imaging system that enables the deeper and multiparametric in situ exploration of tumor microenvironments at a single-cell level. This study describes a pipeline for analyzing 39-plex IMC images of human HPV(+) oropharyngeal squamous cell carcinoma (OPSCC) tumor sections, elucidating immune cells' nature, functions, and interactions with tumor cells. The IMC data analysis provides valuable information for clinical studies that could be used for the identification of prognostic biomarkers and mechanisms of resistance to current immunotherapies. Methods: A retrospective study was conducted on (N=20) patients (10 progressors and 10 non-progressors) with HPV(+) OPSCC. The dataset comprises paired hematoxylin and eosin (H&E) images with IMC data from multiple Regions of Interest (ROIs) (N=82), enabling the in-situ profiling of 39 proteins in primary tumor tissue. Cell segmentation was followed by employing original images and their segmentation masks for cell phenotype identification using a probabilistic neural network method to spatially profile cancer cells, macrophages, NK-M cells, B-cells, and distinct T-cell populations. We identified protein expression at single-cell resolution and investigated the impact of multicellular spatial organization on the disease progression. The spatial neighborhood interaction score of tumor cells with various other cells was computed for all the ROIs across the two groups. Results: The markers showed varying expression levels of intensity distribution, likely due to differences in tissue sample composition. Specifically, CD3, CD4, CD8, CD19, CD20, and CD68 showed significantly higher intensity in non-progressors. Interestingly, FoxP3 also had a significantly higher intensity level in non-progressors. Cell phenotyping emphasized that non-progressors generally have increased levels of NK-M cell markers. Spatial analysis revealed a significant increase in interaction between CD3 cells and tumor cells in non-progressors (p-value=0.07, Mann-Whitney U test). Furthermore, a significant rise in the interaction between B-cells and FoxP3+ cells was observed in non-progressors (p-value<0.05, Mann-Whitney U test) suggesting a coordinated suppression of tumor growth. Conclusion: We developed a deep learning-based pipeline to analyze spatial relationships in the TIME of IMC data, demonstrating its clinical relevance in predicting disease progression. Our findings emphasize the importance of spatial relationships in the TME for response and suggest that proximity between either CD3+ T-cells to cancer cells or B-cells to FoxP3+ cells are candidate biomarkers. Citation Format: Sumanth Reddy Nakkireddy, Routman David, Kathleen Bartemes, Daniel Ma, Tae Hyun Hwang, Kathryn Van Abel, Chadi Nimeh Abdel-Halim. AI-enhanced spatial proteomics reveals B-cells & FoxP3+ cells interactions in HPV(+) oropharyngeal squamous cell carcinoma Progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5488.

Abstract Although the majority of HPV (+) oropharyngeal squamous cell carcinoma (OPSCC) patients exhibit a favorable prognosis, approximately 20% face recurrent or metastatic disease, posing management challenges. Therefore, the identification of robust prognostic markers for risk stratification is essential. Our study focused on the comprehensive characterization of intratumor heterogeneity within the tumor immune microenvironment (TME) in both primary tumors and metastatic lymph nodes. Utilizing computational approaches, we integrated hematoxylin and eosin (H&E) and 11 adjacent immunohistochemistry (IHC)-stained slides to investigate the cellular composition and functional characteristics across different regions within the TME. Based on these detailed immune characteristics, we classified patients into specific immune subtypes. Our integrative TME analysis indicated that patients with high tumor-infiltrating lymphocytes (TIL), increased CD8 + levels, and reduced CD163 + cell counts within their primary tumors were likely to have a more favorable progression-free survival outcome. The integration of H&E and IHC data enhances the functional characterization of immune phenotypes of the TME with biological interpretability and improves patient stratification in HPV(+) OPSCC.

Abstract Background: Reliable non-invasive biomarkers for human papillomavirus (HPV) associated oropharyngeal squamous cell carcinoma (OPX) are lacking. We performed a discovery and validation study of methylated DNA markers (MDMs) for detection of OPX. In addition, we sought to evaluate the MDM profiles in saliva gargle samples from normal controls (nSAL). Methods: Formalin fixed paraffin embedded OPX and gender-balanced normal oropharyngeal tissue (NOP) were pathologically reviewed and punched for DNA extraction and sequenced using reduced representation bisulfite sequencing (RRBS). A tiling algorithm was used to define candidate MDMs. Highest ranked (e.g., area under the receiver operating characteristic curve (AUC), fold-change, p-value) candidate MDMs were validated by qMSP in independent OPX and NOP samples. nSAL DNA was used to assess MDM background signal. Discrimination between OPX tissue, NOP, and nSAL was assessed using AUC with corresponding 95% confidence intervals. HPV was confirmed with p16 staining or DNA in situ hybridization. Results: RRBS discovery assessed 18 OPX, 18 NOP, and 18 normal WBC samples. 234 MDM candidates from approximately 3 × 106 CpGs at >10X coverage were identified. 36 MDMs were selected for validation in independent patient samples which included 32 OPX, 36 NOP, and 35 nSAL specimens. OPX patients were older (median 51; IQR 45-54 years) than NOP patients (median 29; IQR 24-42). 69 and 61% of OPX and NOP patients were female, respectively. The majority of OPX patients were Stage I (n=27, 84%). We observed excellent discrimination between OPX and NOP in the validation set; the median AUC across 36 MDMs was 0.90 (IQR 0.87-0.95). The 10 highest performing markers (PARP15, EPDR1, SHROOM1, EMBP1.rs, IFFO1, MAX.chr19.118, ZNF763, ITGB4, FAM19A2, and MT1IP) exhibited AUCs ranging from 0.95-0.99. Strong discrimination was also observed between OPX and nSAL (Median AUC=0.97; IQR=0.93-0.99). All 10 of the highest-performing markers in tissue exhibited AUCs of at least 0.97 for discriminating OPX versus nSAL. Median fold change between NOP and nSAL across all MDMs was 1.9 (IQR 1.4-3.8), demonstrating low background signal in nSAL. Conclusions: We found strong discrimination in a panel of 36 MDMs between OPX case and control tissue as well as between OPX case tissue and normal saliva. The low background signal observed in normal saliva makes this media a strong candidate for non-invasive detection of OPX. Further studies are in development to assess the utility of measuring these MDMs in both case and control saliva and blood for detecting OPX non-invasively. Citation Format: Benjamin R. Gochanour, David M. Routman, Kathleen R. Bartemes, William R. Taylor, Douglas W. Mahoney, Rondell P. Graham, Xiaoming Cao, Calise K. Berger, Sara S. Then, Karen A. Doering, Kelli N. Burger, Patrick H. Foote, John B. Kisiel, Kathryn M. Van Abel. Discovery and validation of methylated DNA markers of human papillomavirus associated oropharyngeal squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PO-039.

Abstract Background: Recent studies support that high levels of tumor-infiltrating lymphocytes (TILs) were associated with better prognosis in HPV(+) oropharyngeal squamous cell carcinoma (OPSCC). While these studies provide a potential role for TILs as a prognostic biomarker, the analyses were relied on manual quantification performed by pathologists, resulting in inter-observer variability. Deep Learning (DL)-based whole slide hematoxylin and eosin (H&E) image analyses may overcome these challenges. However, this analysis only provides the presence of cell types without consideration for the functional roles of each cell within the tumor immune microenvironment (TME). In this work, we develop a computational pipeline to integrate paired H&E and immunohistochemistry (IHC) images to functionally characterize TILs and investigate their prognostic utility. Methods: We analyzed 88 patients: 42 stage I, 39 stage II, and 7 stage III. Our data contain both H&E and IHCs examining FoxP3, CD3, PD-L1, CD20, etc. on serial sections of the tissue. In-house DL-based H&E analysis used to identify TILs, tumors, and stroma in each tumor, then performed registration between adjacent H&E and IHC images from the same tissue. The patients were then classified into three basic immune phenotypes: immune inflamed (IN; high TILs in the tumor region), immune excluded (EX; TILs are mostly localized in stroma), and immune desert (ID; few/no TILs) based on TIL enrichment in the TME. To functionally characterize TILs, we quantified protein expression from the adjacent IHCs. For example, we further classified each patient into different subtypes based on enriched protein expression (e.g., FoxP3 high IN, FoxP3 low IN). We used the Kaplan-Meier method and multivariate Cox analysis to evaluate the prognostic value of different subtypes enriched with different proteins to predict disease-free survival (DFS). Results: The IN group with 43 patients was significantly associated with good prognosis. Interestingly, further stratification of the IN subgroup based on Foxp3 quantification on TIL regions (i.e., high FoxP3 IN and low FoxP3 IN) showed that high protein expression of FoxP3 in TILs in the IN subgroup is significantly associated with a better prognosis compared to other immune subgroups (HR, 0.16; p-value, 0.003). Multivariate analysis, including other clinical covariates showed that the immune subtypes associated with high FoxP3 are independently associated with DFS. These results demonstrate that DL-based integrative IHC and H&E image analysis could be used to identify subgroups with distinct clinical outcomes. Furthermore, our results reveal unknown roles for Foxp3 expression in the TILs in HPV(+) OPSCC as a prognostic biomarker, a finding which should be evaluated in a larger cohort. Citation Format: Sumanth Reddy Nakkireddy, Inyeop Jang, Minji Kim, Linda X. Yin, Michael Rivera, Joaquin J. Garcia MD, Kathleen R. Bartemes, David M. Routman, Eric J. Moore, Daniel J. Ma, Kathryn M. Van Abel, Tae Hyun Hwang. Integrative spatial analysis of paired IHC and H&E images identifies Foxp3 enriched tumor-infiltrating lymphocytes associated with disease-free survival in human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma. [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 4638.

AbstractObjectiveWe aim to explore the prognostic value of tumor‐infiltrating lymphocytes (TILs) in the primary tumor and metastatic lymph nodes of patients with HPV(+)OPSCC. We hypothesize that TILS density at both sites is associated with disease‐free survival in HPV(+)OPSCC.Study DesignMatched case‐control study among HPV(+)OPSCC patients who underwent intent‐to‐cure surgery. Cases developed locoregional or distant recurrence. Controls were matched based on age, sex, pathologic T, N, and overall stage, year of surgery, type of adjuvant treatment received, and the Adult Comorbidity Evaluation‐27 (ACE‐27) score.SettingSingle tertiary care center, May 2007 to December 2016.MethodsTumoral TILs (tTILs) density was defined as % TILs; stromal TILs (sTILs) density was defined as absent/sparse or moderate/dense crowding. Associations between TILs and time to disease progression were assessed using Cox regression models.ResultsForty‐four case‐control pairs (N = 88) were included: 42 (48%) AJCC pStage I, 39 (44%) pStage II, and 7 (8%) pStage III. tTILs density ≥10% (hazard ratio [HR] 0.41, 95% confidence interval [CI] 0.17‐0.99, p = .048) and a moderate/dense sTILs density (HR 0.21, 95% CI 0.06‐0.75, p = .016) in the primary tumor were significantly associated with decreased risk of progression. TILs density in the lymph node was associated with decreased risk of progression but did not reach statistical significance. The tTILs and sTILs density correlated strongly between the primary tumor and lymph node. Concordance between the pathologists' was moderate (60%‐70%).ConclusionsIn HPV(+)OPSCC, a higher density of tumoral and stromal TILs in the primary tumor and possibly the lymph node may predict a lower risk of disease progression.

Abstract Innate lymphoid cells (ILCs) are emerging as important effector cells in innate immunity and tissue homeostasis. Group 2 ILCs (ILC2s) have been identified in organs and tissues, such as adipose tissue, small intestine, lungs and skin, where they are involved in helminth immunity, type 2 immune responses, and tissue pathology and recovery. Using flow cytometry, we identified ILC2s in mouse uteri and confirmed IL-5, but not IL-13, production in response to IL-33 both in vivo and in vitro. Furthermore, intraperitoneal administration of IL-33 induced recruitment of activated ILC2s to uteri as well as to lungs. To investigate the possibility that uterine ILC2s might play a role in maintaining a healthy pregnancy, we mated ST2-/- females (on a Balb/c background) with ST2-/-, MHC-matched Balb/c and MHC-mismatched C57B6 males (ST2 is the IL-33 receptor). Balb/c, C57B6 and Balb/c x C57B6 pairs were used as controls. Litter sizes were not significantly different among the pairings. We defined viable pups as those still alive 24 hours after parturition. Total numbers of non-viable pups, percent of litters with at least one non-viable pup and percent of non-viable pups per litter were significantly increased in ST2-/- x C57B6 pairs when compared to control pairs. Thus, IL-33-responsive ILC2s are present in murine uterine tissue and may play roles in successful reproduction.

Abstract Human eosinophils have been reported to express both the mRNA and protein for the high affinity IgE receptor (FcεRI); it is speculated that this receptor plays a role in eosinophil mediator release in allergic diseases. However, questions still remain. How much of the FcεRI protein is actually expressed on the cell surface of the eosinophil? If they are present, are these IgE receptors associated with effector functions of eosinophils? To address these issues, we studied blood eosinophils from patients with ragweed hay fever. A high level of low affinity IgG receptor (FcγRII, CD32), but no expression of FcεRI, was detectable on the eosinophil surface by standard FACS analysis. However, after in vitro sensitization with biotinylated chimeric IgE (cIgE), cell-bound cIgE was detected by PE-conjugated streptavidin. This cIgE binding was partially inhibited by anti-FcεRI mAb, suggesting that eosinophils do express minimal amounts of FcεRI detectable only by a sensitive method. Indeed, FACS analysis of whole blood showed that eosinophils express ∼0.5% of the FcεRI that basophils express. When stimulated with human IgE or anti-human IgE, these eosinophils did not exert effector functions; there was neither production of leukotriene C4 or superoxide anion nor any detectable degranulation response. In contrast, eosinophils possessed membrane-bound human IgG and showed functional responses when stimulated with human IgG or anti-human IgG. Thus, IgG and/or cytokines, such as IL-5, appear to be more important for eosinophil activation in allergic diseases than IgE.

Abstract We used an established model of asthma that involves intranasal administration of the fungal extract of Alternaria. Upon lung exposure to Alternaria, IL-33 was released by epithelial cells within one hour, followed by increased production of IL-5 in the lungs. We also found elevated serum levels of IL-5 in response to Alternaria exposure, which reached a peak at 6 hours post Alternaria administration. After prolonged exposure to Alternaria over 6 days, a significant increase in mature eosinophils was observed in bone marrow. In addition, the serum from mice challenged with Alternaria was able to stimulate bone marrow cells to undergo eosinophil maturation in vitro. Intraperitoneal administration of IL-5-blocking antibody in vivo decreased eosinophil maturation in bone marrow in response to intranasal Alternaria below intranasal PBS baseline levels. We have shown the source of IL-5 is by type 2 innate lymphoid cells directly through IL-5 reporter mice, and indirectly through IL-5 serum levels in CD127 knockout mice. Taken together, this study illustrates that the type 2 innate immune responses in the lungs leads to enhanced production of eosinophils in the bone marrow through the increase in lung and blood levels of IL-5. Thus, distant organs communicate during allergic inflammation by using cytokines as mediators. This concept will aid in the identification of novel therapeutic strategies to alleviate symptoms of asthma and allergic diseases.

Abstract Interleukin (IL)-1 family member cytokines are likely pivotal as interfaces between innate and adaptive immune responses. IL-33, an IL-1 family member, is implicated in airway Th2-type responses, including eosinophilia, increased mucus production and hyperresponsiveness. Our goal was to elucidate the immunological mechanisms involved in IL-33-mediated Th2-type responses in the lungs. Airway exposure of naïve BALB/c mice to IL-33 resulted in bronchoalveolar lavage (BAL) eosinophilia and increased lung levels of IL-5 and IL-13, but not IL-4 or IFNγ. Naïve Rag1-/- mice showed similar airway eosinophilia and cytokine responses as wild-type mice, suggesting a role for innate immune cells. By FACS analysis, IL-5-producing lung cells lacked CD3, B220 and other lineage markers (i.e. Lin-), but they expressed CD44 and CD25; markers for NK cells, mast cells, basophils and eosinophils were undetectable. FACS-sorted Lin-CD25+CD44+ lung cells expressed GATA-3 and the IL-33 receptor, T1/ST2, and responded to IL-33 by producing IL-5 and IL-13; morphologically, these lung cells resembled lymphocytes. In vitro blockade of CD25+ cells with anti-CD25 mAb (PC61) abrogated IL-33-induced Th2 cytokine production. Thus, mouse lungs contain a novel subset of innate immune cells that respond to IL-33. These airway cells may initiate early Th2-type immune responses and induce asthma and other allergic diseases.

Abstract Eosinophil activation and subsequent release of inflammatory mediators are implicated in the pathophysiology of allergic diseases. Eosinophils are activated by various classes of secretagogues, such as cytokines (e.g., IL-5), lipid mediators (e.g., platelet-activating factor (PAF)), and Ig (e.g., immobilized IgG). However, do these agonists act directly on eosinophils or indirectly through the generation of intermediate active metabolites? We now report that endogenous PAF produced by activated eosinophils plays a critical role in eosinophil functions. Human eosinophils produced superoxide when stimulated with immobilized IgG, soluble IL-5, or PAF. Pretreating eosinophils with pertussis toxin abolished their responses to these stimuli, suggesting involvement of a metabolite(s) that acts on G proteins. Indeed, PAF was detected in supernatants from eosinophils stimulated with IgG or IL-5. Furthermore, structurally distinct PAF antagonists, including CV6209, hexanolamine PAF, and Y-24180 (israpafant), inhibited IgG- or IL-5-induced superoxide production and degranulation. Previous reports indicated that exogenous PAF stimulates eosinophil eicosanoid production through formation of lipid bodies. We found in this study that IgG or IL-5 also induces lipid body formation and subsequent leukotriene C4 production mediated by endogenous PAF. Finally, inhibition of cytosolic phospholipase A2, one of the key enzymes involved in PAF synthesis, attenuated both PAF production and effector functions of eosinophils. These findings suggest that endogenous PAF plays important roles in eosinophil functional responses to various exogenous stimuli, such as cytokines and Igs. Therefore, inhibition of PAF synthesis or action may be beneficial for the treatment of eosinophilic inflammation.