Distinct Protein Expression Profiles Research Articles

Identification of clonally expanded γδ T-cell populations during CAR-Tcell therapy.

Anti-CD19 Chimeric Antigen Receptor (CAR)-Tcell therapies have shown promise for treating B cell malignancies, but the clinical outcome is influenced by both the CAR-T product and the patient's immune system. The role of γδ Tcells in the context of CAR-T cell therapy remains poorly understood. This study investigates the transcriptional heterogeneity, clonal expansion and dynamics of γδ Tcells in patients undergoing anti-CD19 CAR-T cell therapy. Longitudinal single cell multi-omics analysis was performed on γδ Tcells from four patients receiving anti-CD19 CAR-T cell therapy. Single cell RNA-seq, antibody-based protein profiling (AbSeq) and full-length TCRγδ sequences revealed clonally expanded populations displaying plasticity in Tcell differentiation, and temporal dynamics of large clones, suggesting ongoing expansion and differentiation. Clonally expanded γδ Tcells had heterogeneous gene expression profiles, occupying seven transcriptionally distinct clusters. Analysis of chemokine markers indicated cluster-specific homing tendencies of circulating γδ Tcells to peripheral tissues. We found unexpectedly high frequencies of Vδ1 and Vδ3 cells in the blood with distinct gene and protein expression profiles. This analysis provides insights into the dynamic and heterogeneous nature of γδ Tcells following anti-CD19 CAR-T cell therapy, contributing valuable information for optimizing CAR-T cell therapies in B cell malignancies.

Inflammatory protein signatures in individuals with obesity and metabolic syndrome

There is variability in the metabolic health status among individuals presenting with obesity; some may be metabolically healthy, while others may have developed the metabolic syndrome, a cluster including insulin resistance, hypertension, dyslipidemia, and increased risk of cardiovascular disease and type 2 diabetes. The mechanisms contributing to this metabolic heterogeneity are not fully understood. To address this question, plasma samples from 48 individuals with BMI ≥ 35 kg/m2 were examined (27 with and 21 without metabolic syndrome). Fasting plasma samples were subjected to Olink proteomics analysis for 184 cardiometabolic and inflammation-enriched proteins. Data analysis showed a clear differentiation between the two groups with distinct plasma protein expression profiles. Twenty-four proteins were differentially expressed (DEPs) between the two groups. Pathways related to immune cell migration, leukocyte chemotaxis, chemokine signaling, mucosal inflammatory response, tissue repair and remodeling were enriched in the group with metabolic syndrome. Functional analysis of DEPs revealed upregulation of 15 immunological pathways. The study identifies some of the pathways that are altered and reflect metabolic health in individuals with obesity. This provides valuable insights into some of the underlying mechanisms and can lead to identification of therapeutic targets to improve metabolic health in individuals with obesity.

Ultra High‐Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

AbstractBackgroundThe advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized and redefined the approaches to complex biological questions pertaining to tissue heterogeneity, tumor microenvironments, cellular interactions, cellular diversity, and therapeutic response. Most spatial technologies yield single analyte proteomic or transcriptomic datasets from separate formalin‐fixed paraffin‐embedded (FFPE) tissues sections. Multiple studies have demonstrated a poor correlation between RNA expression and protein abundance owing to transcriptional and translational regulation, target turnover, and post‐translational protein modifications. Therefore, a workflow that accurately measures RNA and protein simultaneously within a single tissue section with distinct spatial context is critical to a more complete biological understanding of cellular interactions and activities. Such multimodal omic datasets of protein and DNA or RNA have been termed “spatial proteogenomics”.MethodHere we present a novel spatial proteogenomic (SPG) assay on the GeoMx® Digital Spatial Profiler platform with NGS readout that enables ultra high‐plex digital quantitation of proteins (147‐plex) and RNA (whole transcriptome,>18,000‐plex) from a single FFPE sample. We demonstrated high concordance, R>0.85, and minor change in sensitivity (<11%) between the SPG assay and the single analyte GeoMx Whole Transcriptome Atlas and GeoMx NGS Protein assays. We used the SPG assay to interrogate 23 different glioblastoma multiforme samples across 4 pathologies.ResultsWe observed clustering of both RNA and protein based on cancer pathology and anatomic location. The in‐depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared to that of glioblastoma multiforme (GBM). Spatial proteogenomics allowed simultaneous interrogation of critical protein post‐translational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods.ConclusionsWithin our dataset, we observed >2‐fold higher protein expression levels of phospho‐GSK3β (Ser9) in gcGBM compared to GBM. Inactivation of GSK3β through phosphorylation has been shown to enhance proliferation of GBM cells. We also observed differential protein expression phosphorylated Tau variants. Phospho‐Thr231 Tau was >2‐fold higher in GBM compared to gcGBM. Associated with neurodegenerative Alzheimer’s disease, changes in Tau expression and phosphorylation have also been observed in glioblastoma. Our study exemplifies the utility of the SPG assay in expanding our understanding of glioblastoma multiforme molecular pathology.

Defining the proteomic landscape of cultured macrophages and their polarization continuum.

Macrophages have previously been characterized based on phenotypical and functional differences into suggested simplified subtypes of MØ, M1, M2a and M2c. These macrophage subtypes can be generated in a well-established primary monocyte culture model that produces cells expressing accepted subtype surface markers. To determine how these subtypes retain functional similarities and better understand their formation, we generated all four subtypes from the same donors. Comparative whole-cell proteomics confirmed that four distinct macrophage subtypes could be induced from the same donor material, with > 50% of 5435 identified proteins being significantly altered in abundance between subtypes. Functional assessment highlighted that these distinct protein expression profiles are primed to enable specific cell functions, indicating that this shifting proteome is predictive of meaningful changes in cell characteristics. Importantly, the 2552 proteins remained consistent in abundance across all macrophage subtypes examined, demonstrating maintenance of a stable core proteome that likely enables swift polarity changes. We next explored the cross-polarization capabilities of preactivated M1 macrophages treated with dexamethasone. Importantly, these treated cells undergo a partial repolarization toward the M2c surface markers but still retain the M1 functional phenotype. Our investigation of polarized macrophage subtypes therefore provides evidence of a sliding scale of macrophage functionality, with these data sets providing a valuable benchmark resource for further studies of macrophage polarity, with relevance for cell therapy development and drug discovery.

Abstract 108: Rejuvenation Potential Of Extracellular Vesicles From Renal Distal Tubular Cells - A Promising Strategy To Prevent Aging-associated Hypertension And Renal Function Impairment

Ageing is characterized by progressive multi-organ functional decline and disrupted homeostasis adaptation. Hypertension and kidney damage become increasingly prevalent as individuals age. Given its high metabolic activity and constant exposure to reactive oxygen species, the kidney is particularly susceptible to age-related deterioration. In our study, aged mice exhibited a notable decline in glomerular filtration rate (GFR) and urinary excretion of sodium, potassium, and calcium, alongside elevated urinary creatinine levels, indicating impaired renal function associated with ageing. Histologically, aged kidneys showed glomerular collapse, thickening of the glomerular basement membrane, and increased glomerular sclerosis. Cellular senescence plays a critical role in renal ageing. Senescent cells display an array of changes in gene and protein expression and thus also altered the contents packaged into extracellular vesicles (EVs), secreted into the extracellular milieu. The protein and RNA composition of EVs varied depending on the age and pathological status of the originating parent cells. Our data showed an increased expression of EV biogenesis protein HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in aged DCT cells (aDCTs). Consistently, with an increase in EV secretion in aDCTs. Administration of young DCT (yDCT)-derived EVs into aged kidneys resulted in a significant improvement of GFR and urinary ion excretion, accompanied by a reduction in age-associated elevation of systolic blood pressure (SBP). Conversely, when administering aDCT-derived EVs to young mice, we saw a significant decrease in GFR and an increase in SBP, indicating a detrimental effect of aDCT-EVs. Proteomic analysis revealed distinct protein expression profiles between yDCT-EVs and aDCT-EVs. These differentially expressed proteins are highly enriched in ageing regulatory pathways, underscoring the crucial role of DCT-EVs in kidney rejuvenation. Intriguingly, we identified a subset of proteins exclusively present in either yDCT-EVs or aDCT-EVs. Our future research will focus on identifying the key components of DCT-EVs responsible for driving kidney rejuvenation.

Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles.

We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.

Abstract 4310: Ultra high-plex spatial proteogenomic investigation of giant cell glioblastoma multiforme immune infiltrates reveals distinct protein and RNA expression profiles

Abstract The advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized and redefined the approaches to complex biological questions pertaining to tissue heterogeneity, tumor microenvironments, cellular interactions, cellular diversity, and therapeutic response. Most spatial technologies yield single analyte proteomic or transcriptomic datasets from separate formalin-fixed paraffin-embedded (FFPE) tissues sections. Multiple studies have demonstrated a poor correlation between RNA expression and protein abundance owing to transcriptional and translational regulation, target turnover, and post-translational protein modifications. Therefore, a workflow that accurately measures RNA and protein simultaneously within a single tissue section with distinct spatial context is critical to a more complete biological understanding of cellular interactions and activities. Such multimodal omic datasets of protein and DNA or RNA have been termed “spatial proteogenomics”. Here we present a novel spatial proteogenomic (SPG) assay on the GeoMx® Digital Spatial Profiler platform with NGS readout that enables ultra high-plex digital quantitation of proteins (147-plex) and RNA (whole transcriptome, > 18,000-plex) from a single FFPE sample. We demonstrated high concordance, R > 0.85, and minor change in sensitivity (<11%) between the SPG assay and the single analyte GeoMx Whole Transcriptome Atlas and GeoMx NGS Protein assays. We used the SPG assay to interrogate 23 different glioblastoma multiforme samples across 4 pathologies. We observed clustering of both RNA and protein based on cancer pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared to that of glioblastoma multiforme (GBM). Spatial proteogenomics allowed simultaneous interrogation of critical protein post-translational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods. Within our dataset, we observed >2-fold higher protein expression levels of phospho-GSK3β (Ser9) in gcGBM compared to GBM. Inactivation of GSK3β through phosphorylation has been shown to enhance proliferation of GBM cells. We also observed differential protein expression phosphorylated Tau variants. Phospho-Thr231 Tau was >2-fold higher in GBM compared to gcGBM. Associated with neurodegenerative Alzheimer’s disease, changes in Tau expression and phosphorylation have also been observed in glioblastoma. Our study exemplifies the utility of the SPG assay in expanding our understanding of glioblastoma multiforme molecular pathology. Citation Format: Shilah Bonnett, Alyssa Rosenbloom, Giang Ong, Mark Conner, Daniel Newhouse, Felicia New, Hiromi Sato, Chi Pha, Saskia Ilcisin, John Lyssand, Gary Geiss, Joseph M. Beechem. Ultra high-plex spatial proteogenomic investigation of giant cell glioblastoma multiforme immune infiltrates reveals distinct protein and RNA expression profiles. [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 4310.

Integrative Genomic and Proteomic Profiling for Personalized Oncological Treatments: Enhancing Therapeutic Efficacy and Reducing Adverse Effects in Breast Cancer Patients

Breast cancer is still one of the most common and difficult tumors to cure that impact women globally. Conventional treatment methods frequently result in inconsistent patient outcomes and serious side effects. By using integrative genomic and proteomic profiling to produce individualized oncological medicines, this study tackles the serious issue of the one-size-fits-all treatment paradigm. The study aimed to ascertain distinct genetic mutations and protein expression profiles in tumors pertaining to breast cancer, establish a connection between these molecular discoveries and clinical results, and customize treatments to optimize therapeutic effectiveness while reducing adverse effects. The most important contribution of this study is the comprehensive identification of both common and unique genetic mutations such as TP53, PIK3CA, BRCA1 and BRCA2 and the elucidation of their corresponding protein expression profiles. This molecular knowledge has helped develop individualized treatment protocols that have been shown to significantly improve treatment outcomes. Specifically, patients who received personalized treatment based on their molecular profiles experienced an average 60% reduction in tumor size compared to 35% with standard treatment. In addition, individualized treatments resulted in a lower mean adverse event score of 3 compared to conventional treatments of 7, highlighting a significant reduction in treatment-related adverse events. The results of this study highlight the potential of personalized medicine to optimize breast cancer treatment by matching treatment strategies to the unique molecular characteristics of each patient's tumor. These findings pave the way for future research aimed at improving individualized treatments, improving the availability and affordability of molecular profiling techniques, and expanding the application of these techniques to wider and more diverse patient populations. With continued innovation and clinical validation, integrated genomic and proteomic profiling promises to set new standards for personalized oncology care, ultimately improving patient outcomes and quality of life.

Distinct characteristics of microglia from neurogenic and non-neurogenic regions of the human brain in patients with Mesial Temporal Lobe Epilepsy.

The study of microglia isolated from adult human brain tissue provides unique insight into the physiology of these brain immune cells and their role in adult human brain disorders. Reports of microglia in post-mortem adult human brain tissue show regional differences in microglial populations, however, these differences have not been fully explored in living microglia. In this study biopsy tissue was obtained from epileptic patients undergoing surgery and consisted of both cortical areas and neurogenic ventricular and hippocampal (Hp) areas. Microglia were concurrently isolated from both regions and compared by immunochemistry. Our initial observation was that a greater number of microglia resulted from isolation and culture of ventricular/Hp tissue than cortical tissue. This was found to be due to a greater proliferative capacity of microglia from ventricular/Hp regions compared to the cortex. Additionally, ventricular/Hp microglia had a greater proliferative response to the microglial mitogen Macrophage Colony-Stimulating Factor (M-CSF). This enhanced response was found to be associated with higher M-CSF receptor expression and higher expression of proteins involved in M-CSF signalling DAP12 and C/EBPβ. Microglia from the ventricular/Hp region also displayed higher expression of the receptor for Insulin-like Growth Factor-1, a molecule with some functional similarity to M-CSF. Compared to microglia isolated from the cortex, ventricular/Hp microglia showed increased HLA-DP, DQ, DR antigen presentation protein expression and a rounded morphology. These findings show that microglia from adult human brain neurogenic regions are more proliferative than cortical microglia and have a distinct protein expression profile. The data present a case for differential microglial phenotype and function in different regions of the adult human brain and suggest that microglia in adult neurogenic regions are "primed" to an activated state by their unique tissue environment.

Collagen Modulates the Biological Characteristics of WJ-MSCs in Basal and Osteoinduced Conditions.

Transcriptomic analysis revealed mesenchymal stem/stromal cells (MSCs) from various origins exhibited distinct gene and protein expression profiles dictating their biological properties. Although collagen type 1 (COL) has been widely studied in bone marrow MSCs, its role in regulating cell fate of Wharton jelly- (WJ-) MSCs is not well understood. In this study, we investigated the effects of collagen on the characteristics of WJ-MSCs associated with proliferation, surface markers, adhesion, migration, self-renewal, and differentiation capabilities through gene expression studies. The isolated WJ-MSCs expressed positive surface markers but not negative markers. Gene expression profiles showed that COL not only maintained the pluripotency, self-renewal, and immunophenotype of WJ-MSCs but also primed cells toward lineage differentiations by upregulating BMP2 and TGFB1 genes. Upon osteoinduction, WJ-MSC-COL underwent osteogenesis by switching on the transcription of BMP6/7 and TGFB3 followed by activation of downstream target genes such as INS, IGF1, RUNX2, and VEGFR2 through p38 signalling. This molecular event was also accompanied by hypomethylation at the OCT4 promoter and increase of H3K9 acetylation. In conclusion, COL provides a conducive cellular environment in priming WJ-MSCs that undergo a lineage specification upon receiving an appropriate signal from extrinsic factor. These findings would contribute to better control of fate determination of MSCs for therapeutic applications related to bone disease.

Potential antihypertensive mechanism of egg white-derived peptide QIGLF revealed by proteomic analysis

Previous work has shown that egg white-derived peptide QIGLF has significant in vivo antihypertensive activity. This study aimed to clarify the antihypertensive mechanisms of QIGLF on spontaneously hypertensive rats (SHRs) by a serum proteomic approach. Here, the tandem mass tag (TMT) quantitative proteomic was performed to discover serum protein changes in SHRs with QIGLF. As a result, SHRs with 4 weeks of QIGLF treatment have distinct serum protein expression profiles by principal component and Pearson's correlation coefficient analysis. Based on Gene Ontology (GO) annotation, oxygen transport and organelle fusion were found to be a regulated major biological process. Besides, aldosterone regulated sodium reabsorption, mitophagy, gap junction, and tight junction were significantly regulated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. QIGLF might exert antihypertensive effects in the SHRs by inhibiting Na+ reabsorption and oxidative stress, restoring gap junction and tight junction.

Protein Profiling of Malaria-Derived Extracellular Vesicles Reveals Distinct Subtypes

Malaria is caused by obligate intracellular parasites belonging to the genus Plasmodium. Red blood cells (RBCs) infected with different stages of Plasmodium spp. release extracellular vesicles (EVs). Extensive studies have recently shown that these EVs are involved in key aspects of the parasite’s biology and disease pathogenesis. However, they are yet to be fully characterized. The blood stages of Plasmodium spp., namely the rings, trophozoites and schizonts, are phenotypically distinct, hence, may induce the release of characteristically different EVs from infected RBCs. To gain insights into the biology and biogenesis of malaria EVs, it is important to characterize their biophysical and biochemical properties. By differential centrifugation, we isolated EVs from in vitro cultures of RBCs infected with different stages of Plasmodium falciparum. We performed a preliminary characterization of these EVs and observed that important EV markers were differentially expressed in EVs with different sedimentation properties as well as across EVs released from ring-, trophozoite- or schizont-infected RBCs. Our findings show that RBCs infected with different stages of malaria parasites release EVs with distinct protein expression profiles.

MED12 Regulates Human Adipose-Derived Stem Cell Adipogenesis and Mediator Kinase Subunit Expression in Murine Adipose Depots.

The mediator kinase module plays a critical role in the regulation of transcription during metabolic processes. Here we demonstrate that in human adipose-derived stem cells (hASCs), kinase module subunits have distinct mRNA and protein expression profiles during different stages of adipogenesis. In addition, siRNA-mediated loss of MED12 results in decreased adipogenesis as evident through decreased lipid accumulation and decreased expression of PPARγ, a master regulator of adipogenesis. Moreover, the decrease in adipogenesis and reduced PPARγ expression are observed only during the early stages of MED12 knockdown. At later stages, knockdown of MED12 did not have any significant effects on adipogenesis or PPARγ expression. We also observed that MED12 was present in a protein complex with PPARγ and C/EBPα during all stages of adipogenesis in hASCs. In 3T3-L1 preadipocytes and adipocytes, MED12 is present in protein complexes with PPARγ1, C/EBPα, and STAT5A. CDK8, another member of the kinase module, was only found to interact with C/EBPα. We found that the expression of all kinase module subunits decreased in inguinal, gonadal, and retroperitoneal white adipose tissue (WAT) depots in the fed state after an overnight fast, whereas the expression of kinase module subunits remained consistent in mesenteric WAT (mWAT) and brown adipose tissue. These data demonstrate that the kinase module undergoes physiologic regulation during fasting and feeding in specific mouse adipose tissue depots, and that MED12 likely plays a specific role in initiating and maintaining adipogenesis.

Deep Proteomic Analysis on Biobanked Paraffine-Archived Melanoma with Prognostic/Predictive Biomarker Read-Out.

Simple SummaryMalignant melanoma is one of the most aggressive cancer types among the solid tumors; therefore, more clinically applicable protein biomarkers predicting survival and therapy response have mandatory importance, impacting patient treatment. The aim of the study was to discover new proteins in biobanked FFPE samples that relate to progression-free survival and response to targeted- and immuno-therapies in patients with melanoma. Protein expressions were detected and quantified by high-resolution mass spectrometry and were integrated with the clinical data and in-depth histopathology characterization. Sample groups with distinct protein expression profiles were connected to longer and shorter survival as well as other clinicopathologic features. In addition, key regulating proteins were assigned, as predictive of progression-free survival in immuno- and/or targeted therapy. Some of the proteins exhibited functionally important correlations to progression and therapy response, which ultimately contributes to a better understanding of melanoma pathology.The discovery of novel protein biomarkers in melanoma is crucial. Our introduction of formalin-fixed paraffin-embedded (FFPE) tumor protocol provides new opportunities to understand the progression of melanoma and open the possibility to screen thousands of FFPE samples deposited in tumor biobanks and available at hospital pathology departments. In our retrospective biobank pilot study, 90 FFPE samples from 77 patients were processed. Protein quantitation was performed by high-resolution mass spectrometry and validated by histopathologic analysis. The global protein expression formed six sample clusters. Proteins such as TRAF6 and ARMC10 were upregulated in clusters with enrichment for shorter survival, and proteins such as AIFI1 were upregulated in clusters with enrichment for longer survival. The cohort’s heterogeneity was addressed by comparing primary and metastasis samples, as well comparing clinical stages. Within immunotherapy and targeted therapy subgroups, the upregulation of the VEGFA-VEGFR2 pathway, RNA splicing, increased activity of immune cells, extracellular matrix, and metabolic pathways were positively associated with patient outcome. To summarize, we were able to (i) link global protein expression profiles to survival, and they proved to be an independent prognostic indicator, as well as (ii) identify proteins that are potential predictors of a patient’s response to immunotherapy and targeted therapy, suggesting new opportunities for precision medicine developments.

Phosphoproteomic Characterization of Primary AML Samples and Relevance for Response Toward FLT3-inhibitors.

Phosphoproteomic Characterization of Primary AML Samples and Relevance for Response Toward FLT3-inhibitors.

Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes.

Male and female gametocytes are sexual precursor cells essential for mosquito transmission of malaria parasite. Differentiation of gametocytes into fertile gametes (known as gametogenesis) relies on the gender‐specific transcription program. How the parasites establish distinct repertoires of transcription in the male and female gametocytes remains largely unknown. Here, we report that an Apetala2 family transcription factor AP2‐O3 operates as a transcription repressor in the female gametocytes. AP2‐O3 is specifically expressed in the female gametocytes. AP2‐O3‐deficient parasites produce apparently normal female gametocytes. Nevertheless, these gametocytes fail to differentiate into fully fertile female gametes, leading to developmental arrest in fertilization and early development post‐fertilization. AP2‐O3 disruption causes massive upregulation of transcriptionally dormant male genes and simultaneously downregulation of highly transcribed female genes in the female gametocytes. AP2‐O3 targets a substantial proportion of the male genes by recognizing an 8‐base DNA motif. In addition, the maternal AP2‐O3 is removed after fertilization, which is required for the zygote to ookinete development. Therefore, the global transcriptional repression of the male genes in the female gametocytes is required for safeguarding female‐specific transcriptome and essential for the mosquito transmission of Plasmodium.

Abstract PO-045: Single cell proteomic analysis of lung adenocarcinoma identifies high HLA-DR expression to be associated with indolent tumor behavior

Abstract Lung adenocarcinoma (ADC) is a heterogeneous group of tumors associated with dramatically different survival rates, even when detected at an early stage. We hypothesized that a single cell proteomic approach would allow the dissection of cellular determinants of early lung ADC behavior. We developed a mass cytometry panel of 34 antibodies and validated their performance in four ADC cell lines (A459, H23, PC9 and H3211) and immune cells. We tested our panel in a set of 10 early stage lung ADCs, classified into long- (LPS) (n=4) and short-predicted survival (SPS) (n=6) based on radiomics features. Tumors were disaggregated and cryopreserved until mass cytometry analysis. We identified cellular subpopulations by clustering and analyzed differences in their distribution both within the tumor microenvironment and the epithelial compartment. To validate our results a tissue micro array was generated from lung tissue blocks from patients with LPS and SPS lung adenocarcinoma. Fluorescent staining was performed for PanCK, CD45, CD3, HLA-DR, DAPI. Cell nuclei were segmented using deep learning algorithm and were further processed in KNIME analytical platform where cell segmentation, feature extraction and cell classification were performed. The antibody panel captured the phenotypical differences in ADCs cell lines and PBMCs. When tumors were analyzed long-predicted survival tumors had a higher proportion of immune cells, whereas some short-predicted survival tumors had a higher proportion of fibroblasts/mesenchymal cells. Additionally, tumors show high degree of heterogeneity with distinct protein expression profiles among epithelial subpopulations, and some subsets with high HLA-DR expression were positively correlated with CD4+ and CD8+ T cells with LPS samples being enriched for such subsets. These results were further validated by Fluorescent staining on TMA slides. We found a positive correlation between HLA-DR expression on tumor cells and T cell number (r = 0.25, p = 2.2e-05). For this, in neighborhoods of 100 um diameter for each tumor cell, HLA-DR median signal intensity on neighboring tumor cells and number of T cells were calculated in Python and used as inputs for correlative analysis. Spatial analysis was performed in KNIME by calculation of distances from each T cell to nearest 1st and 2nd tumor cell, for which LPS tumors showed smaller distances for both 1st and 2nd tumor cell compared to SPS tumors (p = 0.039, p = 0.21). Our results demonstrate a distinct cellular profile of epithelial and stromal cells among indolent vs aggressive ADCs with higher HLA-DR expression in indolent tumors, which is associated with greater T cell infiltration. Our results illustrate the heterogeneity of T cell responses and HLA DR expression in lung adenocarcinoma and should further our understanding of mechanisms related to tumorigenesis. This work deserves further validation at the cellular and molecular level to gain further insights into tumor behavior. The work was supported by CA196405 to PPM. Citation Format: Maria-Fernanda Senosain, Tatiana Novitskaya, Georgii Vasiukov, Yong Zou, Aneri Balar, Deon B. Doxie, Jonathan M. Lehman, Rosana Eisenberg, Fabien Maldonado, Andries Zijlstra, Sergey V. Novitskiy, Jonathan M. Irish, Pierre P. Massion. Single cell proteomic analysis of lung adenocarcinoma identifies high HLA-DR expression to be associated with indolent tumor behavior [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-045.

A75 ON THE TRAIL OF ALTERNATIVE LIGANDS AND SIGNALING PATHWAYS FOR LGR5

Abstract Background Leucine-rich G protein coupled receptor-5 (LGR5) is a GPCR originally identified as a marker for intestinal stem cells but is now associated to stemness in numerous other tissues. R-spondins (RSPO) are the only reported ligands of LGR5, which upon receptor binding, potentiates the canonical Wnt/b-catenin pathway. Surprisingly, despite the presence of classical GPCR features such as conserved DRY and NPXXY motifs RSPO binding to LGR5 does not induce classical GPCR behaviors such as coupling to heterotrimeric G-proteins or engagement of b-arrestins. For this reason, LGR5 is still considered to be an orphan receptor. Aims Aberrant expression of LGR5 is a common feature of many cancers, including gastrointestinal cancers, but it is still unclear why LGR5 is pro-tumorigenic in some cancers, while anti-tumorigenic in others. One potential explanation is that LGR5 does not only signals through the Wnt/b-catenin pathway, but also to alternative pathways. Thus, the goals of this study were 1), to elucidate LGR5 signaling networks and 2), to identify new LGR5 ligands and activity modulators. We suggested that the intestinal lumen content could be a source of bioactive molecules that could act as alternative LGR5 ligands Methods All experiments were performed on HEK293 cells expressing recombinant LGR5 (HEK293/LGR5) and compared to control cells expressing empty vector. Characterization of LGR5 signaling network was initiated with LC MS/MS spectrometric analyses using cells stimulated with Wnt3a and RSPO1. To identify new LGR5 modulators, commercially available bacteria-derived metabolites (BDM) were tested on HEK293/LGR5 cells stimulated with Wnt3a and RSPO1 and assessed using the TOP-Flash luciferase system. Finally, a mouse intestinal lumen extract (ILE) was investigated in whole-cell impedance assay to detect if it contained native BDM or potential host-derived LGR5 ligands. Results Mass spectrometric analyses revealed distinct protein expression and phosphorylation profiles in HEK293/LGR5 cells stimulated with Wnt3a and RSPO1. The TOP/Flash luciferase assays showed that the flavonoid derivative 3,4-dihydroxyphenylacetic acid (DOPAC) and lipopolysaccharide (LPS) acted as negative regulators of LGR5, while butyrate had no effect. Interestingly, stimulation of HEK293/LGR5 with ILE induced a Gαq-like response in the impedance assay, while control cells did not respond. Conclusions Stimulation of LGR5 with Wnt and RSPO triggered a complex signaling network. In agreement with our hypothesis, some BDM such as DOPAC and LPS were indeed activity modulators of LGR5. Moreover, a still unidentified compound present in the ILE triggered a selective GPCR-like response in HEK293/LGR5 cells. Future works aim at identifying this putative LGR5 ligand(s) and establish the LGR5 interactome using proximity labeling and mass spectrometry. Funding Agencies NSERC, Université de Sherbrooke, FRQS

Unique Pro-Inflammatory Response of Macrophages during Apoptotic Cancer Cell Clearance.

The clearance of apoptotic cells by macrophages (efferocytosis) is crucial to maintain normal tissue homeostasis; however, efferocytosis of cancer cells frequently results in inflammation and immunosuppression. Recently, we demonstrated that efferocytosis of apoptotic prostate cancer cells by bone marrow-derived macrophages induced a pro-inflammatory response that accelerated metastatic tumor growth in bone. To evaluate the microenvironmental impact of macrophages and their efferocytic function, we compared peritoneal macrophages (P-MΦ) versus bone marrow-derived macrophages (BM-MΦs) using an efferocytosis in vitro model. The capability to engulf apoptotic prostate cells was similar in BM-MΦs and P-MΦs. Ex vivo analysis of BM-MΦs showed an M2-like phenotype compared with a predominantly M1-like phenotype in P-MΦs. A distinct gene and protein expression profile of pro-inflammatory cytokines was found in BM-MΦs as compared with P-MΦs engulfing apoptotic prostate cancer cells. Importantly, the reprogramming of BM-MΦs toward an M1-like phenotype mitigated their inflammatory cytokine expression profile. In conclusion, BM-MΦs and P-MΦs are both capable of efferocytosing apoptotic prostate cancer cells; however, BM-MΦs exert increased inflammatory cytokine expression that is dependent upon the M2 polarization stage of macrophages. These findings suggest that bone marrow macrophage efferocytosis of apoptotic cancer cells maintains a unique pro-inflammatory microenvironment that may support a fertile niche for cancer growth. Finally, bone marrow macrophage reprogramming towards M1-type by interferon-γ (IFN-γ) induced a significant reduction in the efferocytosis-mediated pro-inflammatory signature.

Abstract 4701: Single cell mass cytometry analysis distinguishes indolent from aggressive lung adenocarcinomas

Abstract Lung adenocarcinoma (ADC) is a heterogeneous group of tumors associated with dramatically different survival rates, even when detected at an early stage. The overarching goal of our research is to identify the cellular and molecular predictors of indolent and aggressive behavior of early lung ADCs. In the work presented here, we hypothesized that mass cytometry, a single cell proteomic approach, would allow the discovery of cellular determinants of early lung ADC behavior. To test this hypothesis, we prepared a mass cytometry panel of 34 labeled antibodies and validated their performance in four lung ADC cell lines (A459, H23, PC9 and H3211), and in peripheral blood mononuclear cells (PBMCs). We then tested our panel in a set of 11 early stage lung ADCs. Based on radiomics features, four of these ADCs were predicted to have long (LS), one intermediate and 6 short survival (SS) establishing the rationale for the comparisons. Tumors were disaggregated into a single cell suspension within one hour after resection and cryopreserved before mass cytometry analysis. We used unsupervised clustering algorithm FlowSOM to identify cellular subpopulations and analyze differences in their distribution both within the tumor microenvironment (TME) and the epithelial compartment. We found that predicted LS tumors had a higher proportion of leukocytes (p-value = 0.027), moderately enriched in CD8+ T cells (p-value = 0.5671), whereas predicted SS tumors had a higher proportion of fibroblasts/mesenchymal cells (p-value = 0.138). Additionally, tumors show high degree of heterogeneity with distinct protein expression profiles among epithelial subpopulations. Epithelial subsets with high vimentin and low HLA-DR, and other subsets expressing p-ERK and p-S6 were mainly present in predicted SS tumors, whereas subsets with a high HLA-DR and low vimentin were mainly present in predicted LS tumors. Also, similarities on the subsets distribution in some samples suggest the presence of ADC molecular subtypes. It remains to elucidate if the observed heterogeneity of the epithelial compartment in combination with a specific composition of the TME could lead to a stronger association with predicted survival. Our preliminary results of mass cytometry in early lung ADCs confirm a distinct cellular profile of epithelial and stromal cells among indolent vs aggressive ADCs. This work deserves further validation at the cellular and molecular level to gain further insights into tumor behavior. [Supported by UO1CA196405 to PPM.] Citation Format: Maria-Fernanda Senosain, Yong Zou, Deon B. Doxie, Aneri Balar, Rosana Eisenberg, Jonathan M. Lehman, Jonathan M. Irish, Pierre P. Massion. Single cell mass cytometry analysis distinguishes indolent from aggressive lung adenocarcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4701.