Surface Protein Markers Research Articles

Abstract P004: Mapping the tumor-sentinel node immune migratome demonstrates a key role for CCR7+ dendritic cells in the successful response to immunoradiotherapy

Abstract Immune checkpoint inhibition has demonstrated no benefit when combined with chemoradiotherapy for locally advanced HNSCC, raising the possibility that standard therapies compromise the response to immunotherapy. To address this hypothesis, we previously demonstrated that ablating tumor draining lymphatics abolishes the response to immune-oncology therapy. Specifically, we defined that the response to immunotherapy is coordinated by interferon type-I signaling through the cDC1 population in tumor-draining lymph nodes. These findings support the premise that successful tumor responses to immuno-oncology therapies is predicated upon intact and functional, locoregional anatomy. Accordingly, we hypothesize that lymphatic-preserving, tumor-directed immune oncology therapy will promote antitumor immunity by enhancing surveillance along the tumor-immune-lymphatic axis. To explore this, we employ a novel mouse reporter model that allows precise spatiotemporal labeling of immune effector cells. Combined with sentinel lymph node mapping, our reporter model enables selective labeling of immune effectors within the tumor microenvironment and subsequent tracking and characterization of these cells as they migrate to the sentinel lymph node. This approach led us to define the “cancer immune migratome” - the repertoire of immune cells actively migrating from tumors to lymph nodes during an antitumor response. For precise cellular identification, we employed CITE-sequencing, which integrates single-cell RNA expression with surface protein markers, allowing us to comprehensively define the characteristics of migrating immune cells. This work represents the first characterization of immune cell populations migrating from the tumor to the sentinel lymph node, revealing the diversity and dynamics of these populations in antitumor immunity. We then develop a tumor-directed, lymphatic-sparing radiotherapy model to modulate the tumor immune microenvironment without inducing tumor regression. Sequential administration of tumor-directed radiotherapy followed by PD-1 checkpoint inhibition achieves complete and durable responses. Analysis of the cancer immune migratome during immunoradiotherapy revealed a crucial role for an activated population of CCR7+ dendritic cells. These migratory dendritic cells are reprogrammed, via rational sequencing of radiation and immunotherapy, from their canonical role in immune tolerance to actively drive antitumor immunity. This reprogramming enhances T cell priming, clonotypic expansion, and, ultimately, the successful tumor response to immunoradiotherapy. Disruption of sentinel lymphatic channels or selective blockade of CCR7+ DC entry into the SLN abrogates the response to immunoradiotherapy. Overall, this work supports rationally sequencing immune-sensitizing, lymphatic-preserving, tumor-directed radiotherapy followed by immune checkpoint inhibition to optimize tumor response. Our findings support a therapeutic strategy that enhances host response to immunotherapy by directing activated dendritic cells to sentinel lymph nodes. Citation Format: Robert Saddawi-Konefka, Riyam Al Msari, Shiqi Tang, Lauren M. Clubb, Santiago Fassardi, Riley Jones, Farhoud Faraji, Shiruyeh Schokrpur, Bryan S. Yung, Michael M. Allevato, Shawn M. Jensen, Bernard A. Fox, Richard Bell, J. Silvio Gutkind, Andrew Sharabi, Joseph A. Califano. Mapping the tumor-sentinel node immune migratome demonstrates a key role for CCR7+ dendritic cells in the successful response to immunoradiotherapy. [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr P004

Effect of adipose mesenchymal stem cell-derived exosomes on allergic rhinitis in mice.

At present, the treatment for allergic rhinitis (AR) is only limited to symptom relief, and AR is not able be cured. It is important to find new therapeutic regimens for AR. To explore the effect of adipose mesenchymal stem cell-derived exosomes (AMSC-exos) on AR in mice. Primary human AMSCs were cultured up to fourth or fifth passage AMSCs which were used to extract AMSC-exos by ultracentrifugation. The AMSC-exos were identified in size, morphology and surface marker proteins. AR mouse models were made, and then effects of the AMSC-exos on AR mouse models were observed by injection of AMSC-exos into their tail veins. A total of 21 mice were divided into normal mice with injection of phosphate buffered saline (PBS) group (Normal+PBS group, 7 mice), AR mice with injection of AMSC-exos group (AR+AMSC-exos group, 7 mice) and AR mice with injection of PBS (AR+PBS group, 7 mice). After injection of AMSC-exos and PBS, symptoms were observed in mice and inflammatory factors including IL-4, IL-5, IFN- γ and Ig-E were determined. Mice were sacrificed, nasal mucosa was collected for HE staining and qRT-PCR. After injection of AMSC-exos, compared with the AR+PBS group, symptoms were significantly improved, inflammatory factor levels were significantly decreased, disturbed and thickened mucosal layer was relieved, and the numbers of goblet cells and eosinophils were reduced in the AR+AMSC-exos group. AMSC-exos can improve symptoms and inflammatory level in the AR mice.

Photothermal therapeutic effect by gold nanostars/extracellular vesicles nanocomplex on melanoma cells.

Photothermal therapy (PTT) is a method for treating cancer using the heat generated by light irradiation, often in combination with light-absorbing materials. Efficient PTT requires a drug delivery system to deliver light-absorbing materials to cancerous tissues. Gold nanostars (GNSs) enable efficient PTT through absorbing long-wavelength light. In this study, we established a platform for preparing GNS-loaded extracellular vesicles (EVs), that were expected to provide the combined biological functionality of EVs and photothermal conversion properties. By electrostatically binding cationic polyethylene glycol (PEG)-modified GNSs (PEG-GNSs) to naturally negatively charged EVs, EV/PEG-GNS nanocomplexes (EV-GNSs) were obtained by simply mixing the two components. The prepared EV-GNSs were approximately 200 nm in size and exhibited a negative surface charge. The surface protein marker of EVs, CD63, was detected using western blot, suggesting that the EVs were intact. In vitro evaluation showed that EV-GNSs exhibited better photothermal conversion properties than PEG-GNSs alone. When EV-GNSs were added to the cells, high laser-responsive cytotoxicity was observed following laser irradiation. Thus, EV-GNSs developed in this study may be suitable for PTT using gold-based nanoparticles.

EasyFlow: An open-source, user-friendly cytometry analyzer with graphic user interface (GUI).

Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and fluorescent protein transgenes, and is widely utilized to study developmental biology, systems biology, microbiology, and many other fields. A common file format (FCS format, defined by the International Society for Advancement of Cytometry (ISAC)) has been universally adopted, facilitating data exchange between different machines. A diverse spectrum of software packages has been developed for the analysis of flow cytometry data. However, those are either 1) costly proprietary softwares, 2) open source packages with prerequisite installation of R or Python and sometimes require users to have experience in coding, or 3) online tools that are limiting for analysis of large data sets. Here, we present EasyFlow, an open-source flow cytometry analysis graphic user interface (GUI) based on Matlab or Python, that can be installed and run locally across platforms (Windows, MacOS, and Linux) without requiring previous coding knowledge. The Python version (EasyFlowQ) is also developed on a popular plotting framework (Matplotlib) and modern user interface toolkit (Qt), allowing more advanced users to customize and keep contributing to the software, as well as its tutorials. Overall, EasyFlow serves as a simple-to-use tool for inexperienced users with little coding experience to use locally, as well as a platform for advanced users to further customize for their own needs.

Exploring Extracellular Vesicle Surface Protein Markers Produced by Glioblastoma Tumors: A Characterization Study Using In Vitro 3D Patient-Derived Cultures.

Glioblastoma (GBM) is an aggressive brain cancer with limited treatment options. Extracellular vesicles (EVs) derived from GBM cells contain important biomarkers, such as microRNAs, proteins, and DNA mutations, which are involved in tumor progression, invasion, and resistance to treatment. Identifying surface markers on these EVs is crucial for their isolation and potential use in noninvasive diagnosis. This study aimed to use tumor-derived explants to investigate the surface markers of EVs and explore their role as diagnostic biomarkers for GBM. Tumor explants from nine GBM patients without IDH1/IDH2 mutations or 1p-19q co-deletion were cultured to preserve both tumor viability and cytoarchitecture. EVs were collected from the tumor microenvironment using differential centrifugation, filtration, and membrane affinity binding. Their surface protein composition was analyzed through multiplex protein assays. RNA-Seq data from TCGA and GTEx datasets, along with in silico single-cell RNA-seq data, were used to assess EV surface biomarker expression across large GBM patient cohorts. The in vitro model successfully replicated the tumor microenvironment and produced EVs with distinct surface markers. Biomarker analysis in large datasets revealed specific expression patterns unique to GBM patients compared with healthy controls. These markers demonstrated potential as a GBM-specific signature and were correlated with clinical data. Furthermore, in silico single-cell RNA-seq provided detailed insights into biomarker distribution across different cell types within the tumor. This study underscores the efficacy of the tumor-derived explant model and its potential to advance the understanding of GBM biology and EV production. A key innovation is the isolation of EVs from a model that faithfully mimics the tumor's original cytoarchitecture, offering a deeper understanding of the cells involved in EV release. The identified EV surface markers represent promising targets for enhancing EV isolation and optimizing their use as diagnostic tools. Moreover, further investigation into their molecular cargo may provide crucial insights into tumor characteristics and evolution.

Snorkel-tag based affinity chromatography for recombinant extracellular vesicle purification.

Extracellular vesicles (EVs) are lipid nanoparticles and play an important role in cell-cell communications, making them potential therapeutic agents and allowing to engineer for targeted drug delivery. The expanding applications of EVs in next generation medicine is still limited by existing tools for scaling standardized EV production, single EV tracing and analytics, and thus provide only a snapshot of tissue-specific EV cargo information. Here, we present the Snorkel-tag, for which we have genetically fused the EV surface marker protein CD81, to a series of tags with an additional transmembrane domain to be displayed on the EV surface, resembling a snorkel. This system enables the affinity purification of EVs from complex matrices in a non-destructive form while maintaining EV characteristics in terms of surface protein profiles, associated miRNA patterns and uptake into a model cell line. Therefore, we consider the Snorkel-tag to be a widely applicable tool in EV research, allowing for efficient preparation of EV standards and reference materials, or dissecting EVs with different surface markers when fusing to other tetraspanins in vitro or in vivo.

Surface protein analysis of breast cancer exosomes using visualized strategy on centrifugal disk chip

Breast cancer, the most common cancer among women worldwide, lacks specific tumor markers for accurate diagnosis. Recent advances have highlighted tumor-derived exosomes as a promising non-invasive biomarker for cancer detection. Continuous monitoring of surface protein markers on exosomes in the blood could offer valuable insights for breast cancer diagnosis. However, integrating the isolation and detection of exosomes from whole blood is bulky, time-consuming, and requires professional operations. To address this difficulty, we developed a method of integrated centrifugal disk chip (CD chip) exosome enrichment directly from whole blood followed by a colorimetric visualization strategy for multiplex analysis. The disc consists of multi-chambers and multi-microchannels with immediate smartphone-enabled processing of colorimetric results. The combination of CEA + CA125 + EGFR on-chip detection could significantly differentiate the different stages of cancer in tumor-bearing mice and successfully distinguish between breast cancer patients and healthy individuals. Crucially, small volumes (100 μL) of blood samples were adequate. In addition, the chip was simple and fast, with results within 10 min, which provides immediate exosomal information through consecutive blood sampling, which could potentially result in a more timely and well-informed clinical breast cancer diagnosis.

Research on the biophysical properties of circulating tumor cells

This article reviews the biophysical properties of circulating tumor cells (CTCs) and their significance in tumor metastasis and liquid biopsy. CTCs are tumor cells that have shed from solid tumors or metastatic foci and entered the bloodstream, possessing various biological markers. They may be cleared by the immune system, enter a dormant state, or form clusters to facilitate metastasis. The physical properties of CTCs, including cell size, density, rigidity, and dielectric properties, differ from normal blood cells, providing a theoretical basis for separation and detection. The biological characteristics of CTCs include epithelial cell properties, expression of specific surface marker proteins, and the characteristics of epithelial-mesenchymal transition, which are crucial for the aggressiveness and metastatic potential of tumors. The development of CTC detection technologies, such as the Cell Search system, has been clinically applied, but the heterogeneity of tumor cells remains a major challenge in research. The development of composite separation technologies that combine various properties of CTCs is expected to improve the sensitivity, specificity, and efficiency of CTC detection, thereby playing an important role in the personalized treatment and prognostic assessment of tumors.

Regulatory effect of Diwu Yanggan Decoction on lysoglycerophospholipids in circulating exosomes in a mouse model of nonalcoholic fatty liver disease

To evaluate the regulatory effect of Diwu Yanggan (DWYG) Decoction on lysoglycerophospholipids (Lyso-GPLs) in circulating exosomes in a mouse model of nonalcoholic fatty liver disease (NAFLD). Circulating exosomes isolated from mouse serum by size exclusion chromatography were morphologically characterized using transmission electron microscope and examined for surface markers CD9, CD63 and TSG101 using Western blotting. Twenty-four male Kunming mice were randomized into 3 groups for normal feeding (control, n=8) or high-fat diet feeding for 1 week to induce NAFLD, after which the latter mice were given DWYG decoction (treatment group, n=8) or normal saline (model group, n=8) by gavage for 4 weeks. After the last treatment, blood samples were collected from the mice for testing serum TC, HDL-C, LDL-C, ALT and AST levels and isolating circulating exosomes. Using multivariate statistical analysis based on targeted metabolomics strategy, the potential biomarkers for Lyso-GPLs in the exosomes were screened. The isolated exosomes about 100 nm in size had a typical saucer-like structure with distinct double-layer membranes and a mean particle size of 137.5 nm and expressed the specific surface marker proteins CD9, CD63 and TSG101. The mouse models of NAFLD had significantly increased serum levels of TC, HDL-C, LDL-C and AST and lowered serum ALT level. A total of 43 Lyso-GPLs with significant reduction after DWYG Decoction treatment were identified in NAFLD mice. DWYG Decoction can regulate Lyso-GPLs in circulating exosomes in NAFLD mice, which provides a new clue for studying the therapeutic mechanism of DWYG Decoction for liver disease.

ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets.

CITE-seq enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to oligonucleotide tags. Due to the high copy number of surface protein molecules, sequencing antibody-derived tags (ADTs) allows for robust protein detection, improving cell-type identification. However, variability in antibody staining leads to batch effects in the ADT expression, obscuring biological variation, reducing interpretability, and obstructing cross-study analyses. Here, we present ADTnorm (https://github.com/yezhengSTAT/ADTnorm), a normalization and integration method designed explicitly for ADT abundance. Benchmarking against 14 existing scaling and normalization methods, we show that ADTnorm accurately aligns populations with negative- and positive-expression of surface protein markers across 13 public datasets, effectively removing technical variation across batches and improving cell-type separation. ADTnorm enables efficient integration of public CITE-seq datasets, each with unique experimental designs, paving the way for atlas-level analyses. Beyond normalization, ADTnorm includes built-in utilities to aid in automated threshold-gating as well as assessment of antibody staining quality for titration optimization and antibody panel selection. Applying ADTnorm to a published COVID-19 CITE-seq dataset allowed for identifying previously undetected disease-associated markers, illustrating a broad utility in biological applications.

A Rapid Human Lung Tissue Dissociation Protocol Maximizing Cell Yield and Minimizing Cellular Stress.

The human lung is a complex organ that comprises diverse populations of epithelial, mesenchymal, vascular, and immune cells, which gains even greater complexity during disease states. To effectively study the lung at a single-cell level, a dissociation protocol that achieves the highest yield of viable cells of interest with minimal dissociation-associated protein or transcription changes is key. Here, we detail a rapid collagenase-based dissociation protocol (Col-Short) that provides a high-yield single-cell suspension that is suitable for a variety of downstream applications. Diseased human lung explants were obtained and dissociated through the Col-Short protocol and compared with four other dissociation protocols. Resulting single-cell suspensions were then assessed with flow cytometry, differential staining, and quantitative real-time PCR to identify major hematopoietic and nonhematopoietic cell populations, as well as their activation states. We observed that the Col-Short protocol provides the greatest number of cells per gram of lung tissue, with no reduction in viability when compared with previously described dissociation protocols. Col-Short had no observable surface protein marker cleavage as well as lower expression of protein activation markers and stress-related transcripts compared with four other protocols. The Col-Short dissociation protocol can be used as a rapid strategy to generate single cells for respiratory cell biology research.

O-266 Multi-omics landscape of uterine fluid-derived extracellular vesicles across the menstrual cycle

Abstract Study question Do extracellular vesicles (EVs) mirror the cyclic physiological changes in endometrial tissue, reflecting the endometrial maturation along the entire menstrual cycle? Summary answer Multi-omics data highlights the importance of EVs during the mid-secretory phase and EVs cargo reflects the state of the tissue throughout the menstrual cycle. What is known already Extracellular vesicles isolated from uterine fluid (UF) during the mid-secretory phase have been characterized for their pivotal role in embryo-maternal communication, particularly in the context of microRNAs (miRNAs) and mRNA. EVs have been posited as potential biomarkers in a minimally invasive liquid biopsy approach for assessing endometrial receptivity, hopefully replacing the endometrial tissue biopsy-based testing. However, the dynamics of EVs and their cargo throughout the distinct phases of the menstrual cycle remain unknown. This is the first study to elucidate UF-EV content throughout the maturation of the endometrium. Study design, size, duration Whole-exome RNA and small-RNA sequencing was performed on 15 paired samples, comprising UF and endometrial biopsy (EB), obtained from healthy female subjects across the menstrual cycle. This initial dataset was expanded with 35 additional UF samples. Cumulatively, the analysis encompassed samples (EB and UF) across the menstrual cycle’s four distinct phases: proliferative (n = 10), early-secretory (ES) (n = 17), mid-secretory (MS) (n = 20), and late-secretory (LS) (n = 18). Additionally, 20 UF-EV samples were used for flow cytometry surface proteome analysis. Participants/materials, setting, methods Participants were excluded when infertility-associated conditions were found and included when they had at least one child born, with no hormonal medications used for three months before the sampling. EVs were extracted from UF with size-exclusion chromatography (SEC) and subsequently with glycosaminoglycan-based precipitation. The EVs were characterized with nanoparticle tracking analysis, western blot, transmission electron microscopy and flow-cytometry surface proteome analysis (MACSPlex) for 37 surface markers. Single-end RNA and small-RNA sequencing were performed on NextSeq1000. Main results and the role of chance The transcriptome, miRNome, and protein surface markers of UF-EVs were characterized throughout the menstrual cycle. Transcriptome profiling was performed in comparison to the preceding phase. During the ES phase, 5,507 differentially expressed genes (DEGs) were observed, most of them being downregulated and associated with G-coupled-protein signaling, while in the MS phase, 867 DEGs were identified associated with nucleosome assembly and cell differentiation. Interestingly in the LS phase, the histone genes associated with nucleosome assembly were upregulated compared to MS, highlighting that histone dynamics change corresponding to the menstrual cycle. The exploration of gene ontology revealed consistent enrichment of genes related to extracellular vesicles in UF-EV and EBs across the menstrual cycle. The miRNA analysis of UF-EVs and EB showed significant overlap in miRNA expression level especially in the MS phase. Furthermore, we found 16 unique miRNAs in the mid-secretory phase whose targets were associated with embryo morphogenesis and cell adhesion. MACSPlex analysis revealed that CD9 and CD63, canonical EV markers, were significantly abundant during the MS phase, indicative of an enriched secretion of EVs during the preparation of the endometrium for embryo implantation. These insights underscore that the cargo of UF-EVs reflects the dynamic changes in the endometrial tissue. Limitations, reasons for caution The research on UF-EVs faced notable challenges due to the irregular and non-standardized collection methods of UF in gynecological practice. This variability in UF collection introduces potential confounding factors. The study also operated with a limited sample size, underscoring the need for further validation. Wider implications of the findings Our study indicates that the UF-EVs reflect the menstrual cycle-related molecular changes and UF-EV analysis could be potentially used to follow the menstrual cycle-related molecular processes in the uterine environment. Trial registration number not applicable

High-dimensional single-cell analysis of human natural killer cell heterogeneity

Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to microbes and tumors. Historically, their classification hinged on a limited array of surface protein markers. Here, we used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to dissect the heterogeneity of NK cells. We identified three prominent NK cell subsets in healthy human blood: NK1, NK2 and NK3, further differentiated into six distinct subgroups. Our findings delineate the molecular characteristics, key transcription factors, biological functions, metabolic traits and cytokine responses of each subgroup. These data also suggest two separate ontogenetic origins for NK cells, leading to divergent transcriptional trajectories. Furthermore, we analyzed the distribution of NK cell subsets in the lung, tonsils and intraepithelial lymphocytes isolated from healthy individuals and in 22 tumor types. This standardized terminology aims at fostering clarity and consistency in future research, thereby improving cross-study comparisons.

Pre-treatment peripheral blood immunophenotyping and response to neoadjuvant chemotherapy in operable breast cancer

BackgroundTumor immune infiltration and peripheral blood immune signatures have prognostic and predictive value in breast cancer. Whether distinct peripheral blood immune phenotypes are associated with response to neoadjuvant chemotherapy (NAC) remains understudied.MethodsPeripheral blood mononuclear cells from 126 breast cancer patients enrolled in a prospective clinical trial (NCT02022202) were analyzed using Cytometry by time-of-flight with a panel of 29 immune cell surface protein markers. Kruskal–Wallis tests or Wilcoxon rank-sum tests were used to evaluate differences in immune cell subpopulations according to breast cancer subtype and response to NAC.ResultsThere were 122 evaluable samples: 47 (38.5%) from patients with hormone receptor-positive, 39 (32%) triple-negative (TNBC), and 36 (29.5%) HER2-positive breast cancer. The relative abundances of pre-treatment peripheral blood T, B, myeloid, NK, and unclassified cells did not differ according to breast cancer subtype. In TNBC, higher pre-treatment myeloid cells were associated with lower pathologic complete response (pCR) rates. In hormone receptor-positive breast cancer, lower pre-treatment CD8 + naïve and CD4 + effector memory cells re-expressing CD45RA (TEMRA) T cells were associated with more extensive residual disease after NAC. In HER2 + breast cancer, the peripheral blood immune phenotype did not differ according to NAC response.ConclusionsPre-treatment peripheral blood immune cell populations (myeloid in TNBC; CD8 + naïve T cells and CD4 + TEMRA cells in luminal breast cancer) were associated with response to NAC in early-stage TNBC and hormone receptor-positive breast cancers, but not in HER2 + breast cancer.Trial registrationNCT02022202. Registered 20 December 2013.

Buoyant Metal-Organic Framework Corona-Driven Fast Isolation and Ultrasensitive Profiling of Circulating Extracellular Vesicles.

Accurately assaying tumor-derived circulating extracellular vesicles (EVs) is fundamental in noninvasive cancer diagnosis and therapeutic monitoring but limited by challenges in efficient EV isolation and profiling. Here, we report a bioinspired buoyancy-driven metal-organic framework (MOF) corona that leverages on-bubble coordination and dual-encoded surface-enhanced Raman scattering (SERS) nanotags to streamline rapid isolation and ultrasensitive profiling of plasma EVs in a single assay for cancer diagnostics. This integrated bubble-MOF-SERS EV assay (IBMsv) allows barnacle-like high-density adhesion of MOFs on a self-floating bubble surface to enable fast isolation (2 min, near 90% capture efficiency) of tumor EVs via enhanced EV-MOF binding. Also, IBMsv harnesses four-plexed SERS nanotags to profile the captured EV surface protein markers at a single-particle level. Such a sensitive assay allows multiplexed profiling of EVs across five cancer types, revealing heterogeneous EV surface expression patterns. Furthermore, the IBMsv assay enables cancer diagnosis in a pilot clinical cohort (n = 55) with accuracies >95%, improves discrimination between cancer and noncancer patients via an algorithm, and monitors the surgical treatment response from hepatocellular carcinoma patients. This assay provides a fast, sensitive, streamlined, multiplexed, and portable blood test tool to enable cancer diagnosis and response monitoring in clinical settings.

Identification of T cell subpopulations exhibiting a high-degree of TCR-independent, IL-15-induced activation in pateints with acute hepatitis A

Abstract During acute hepatitis A, pre-existing memory CD8+ T cells specific to hepatitis A virus-unrelated antigens are activated by IL-15 in a T-cell receptor (TCR)-independent manner, which is termed bystander activation, and these T cells contribute to liver injury (Immunity 2018, 48:161). However, it has been remained to be elucidated if other types of T cells are also activated by IL-15 without TCR engagement during acute hepatitis A. Here, we performed CITE-seq analysis in combination with single-cell RNA sequencing (scRNA-seq) using peripheral blood mononuclear cells (PBMCs) from patients with acute hepatitis A at acute and convalescent phases and healthy controls. In the scRNA-seq analysis, we used a gene set that was previously known to be upregulated by IL-15 in the absence of TCR stimulation to identify T-cell clusters that undergo TCR-independent, IL-15-induced activation. Among CD8+ T and γδ T cells, subclusters expressing CD45RO, CD57, and KLRG1 exhibited the highest module score of TCR-independent, IL-15-induced activation. Among MAIT cells, subclusters expressing CD8 and CD226 showed the highest module score of TCR-independent, IL-15-induced activation. Notably, these subclusters with the highest module score were exclusively found at the acute stage compared to the convalescent phase. In summary, T cell subpopulations exhibiting a high-degree of TCR-independent, IL-15-induced activation express distinct cell surface protein markers in patients with acute hepatitis A.

Bimodal single cell RNA sequencing reveals changes in CD4+ T cell transcriptomes with age

Abstract Aging affects the human immune system, resulting in modified autoimmunity, responses to infection and cancer. Here, we studied changes in CD4 T cells in subjects with and without coronary artery disease (CAD). PBMCs of 61 men and women who underwent cardiac catheterization were interrogated by single cell RNA sequencing combined with 49 protein surface markers via CITE-Seq. After quality, we identified 139,343 PBMCs from these patients, 40,816 were CD4 T cells, identified as CD19- CD3+ CD4+ CD8-. Linear regression was used to assess the impact of age on gene expression in these cells, adjusted for disease severity, sex, statin status, diabetes, and smoking status. As expected, the surface markers CD25 and CD45RO were positively and CD45RA negatively correlated with age. Across all subjects, 24 genes: GLUL, F5, CXCL10, CTSA, IL32, IFITM1, LAT2, TNFRSF8, RPN2, HLA.A, RGS1, TRAT1, TIGIT, STAT1, BAX, MKI67, CLC, LGALS1, F13A1, SPON2, CD163, IL3RA, VSIG4, CD200 were significantly correlated with age. Other genes were correlated in cases, but not controls: IL2RA, THBS1, VPREB3, PIK3AP1, TNFSF8, PAX5, IL2, LIF, CLEC4E, MMRN1, KLRC4, ADGRG3, PTPRC, ZNF683, IL22, TNFRSF25, CAVIN2, SYNE2, CD72, CD300A. Significant transcriptomic changes with age were observed in naïve, Th1, Tregs and exTregs CD4+ T cells. We conclude that age significantly changes the proportions and transcriptomes in CD4 + T cells. Also, sex, diabetes and use of statin confound these changes with age.

Enhancing insulin sensitivity in type 2 diabetes mellitus using apelin-loaded small extracellular vesicles from Wharton’s jelly-derived mesenchymal stem cells: a novel therapeutic approach

BackgroundType 2 diabetes mellitus (T2DM), characterized by β-cell dysfunction and insulin resistance (IR), presents considerable treatment challenges. Apelin is an adipocyte-derived factor that shows promise in improving IR; however, it is limited by poor targeting and a short half-life. In the present study, engineered small extracellular vesicles (sEVs) derived from Wharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) loaded with apelin were used to address the limitations of the therapeutic application of apelin.MethodsWJ-MSCs were transduced to obtain engineered sEVs loaded with overexpressed apelin (apelin-MSC-sEVs) and the control sEVs (MSC-sEVs). T2DM mice were injected with apelin-MSC-sEVs and MSC-sEVs, and blood glucose monitoring, glucose and insulin tolerance tests, confocal microscopy, and immunocytochemical analysis were performed. IR models of 3T3-L1 adipocytes were employed to detect GLUT4 expression in each group using western blotting; the affected pathways were determined by measuring the changes in Akt and AMPK signaling and phosphorylation.ResultsUpon successful engineering, WJ-MSCs demonstrated significant overexpression of apelin. The genetic modification did not adversely impact the characteristics of sEVs, ranging from surface protein markers, morphology, to particle size, but generated apelin-overexpressed sEVs. Apelin-MSC-sEVs treatment resulted in notable enhancement of Akt and AMPK pathway activities within 3T3-L1 adipocytes and adipose tissues of T2DM mice. Furthermore, the apelin-loaded sEVs significantly reduced plasma glucose levels, increased pancreatic β-cell proliferation, improved insulin and glucose tolerance, and modulated pro-inflammatory cytokine profiles, compared to mice treated with the control sEVs.ConclusionOur study developed novel genetically engineered apelin-loaded sEVs derived from WJ-MSCs, and demonstrated their potent role in augmenting insulin sensitivity and regulating inflammatory responses, highlighting their therapeutic promise in T2DM management. The findings open new avenues for the development of clinically viable treatments for T2DM in humans using the apelin-loaded sEVs.

CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny

BackgroundThe rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield new insights not revealed with a single modality. For example, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) simultaneously profiles the RNA transcriptome and the surface protein expression. The surface protein markers in CITE-Seq can be used to identify cell populations similar to the iterative filtration process in flow cytometry, also called “gating”, and is an essential step for downstream analyses and data interpretation. While several packages allow users to interactively gate cells, they often do not process multi-omic sequencing datasets and may require writing redundant code to specify gate boundaries. To streamline the gating process, we developed CITEViz which allows users to interactively gate cells in Seurat-processed CITE-Seq data. CITEViz can also visualize basic quality control (QC) metrics allowing for a rapid and holistic evaluation of CITE-Seq data.ResultsWe applied CITEViz to a peripheral blood mononuclear cell CITE-Seq dataset and gated for several major blood cell populations (CD14 monocytes, CD4 T cells, CD8 T cells, NK cells, B cells, and platelets) using canonical surface protein markers. The visualization features of CITEViz were used to investigate cellular heterogeneity in CD14 and CD16-expressing monocytes and to detect differential numbers of detected antibodies per patient donor. These results highlight the utility of CITEViz to enable the robust classification of single cell populations.ConclusionsCITEViz is an R-Shiny app that standardizes the gating workflow in CITE-Seq data for efficient classification of cell populations. Its secondary function is to generate basic feature plots and QC figures specific to multi-omic data. The user interface and internal workflow of CITEViz uniquely work together to produce an organized workflow and sensible data structures for easy data retrieval. This package leverages the strengths of biologists and computational scientists to assess and analyze multi-omic single-cell datasets. In conclusion, CITEViz streamlines the flow cytometry gating workflow in CITE-Seq data to help facilitate novel hypothesis generation.

Abstract 7235: Exosome-mediated delivery of siRNA against NRF2 for treatment of lung cancer

Abstract Nuclear factor erythroid 2-related factor 2 (NRF2) activation is the third most common genetic event in lung adenocarcinomas (25%), primarily induced by loss of function mutations in its master regulator, KEAP1. NRF2 is a key modulator of tumor growth and metabolic reprogramming, resulting in resistance to traditional chemotherapeutics. Due to its role in modulating oxidative stress, sustained NRF2 overexpression promotes disease progression, particularly in lung cancer. This study demonstrates the effective knockdown of NRF2 expression by small interfering RNA (siRNA) delivered via a nanoplatform based on bovine colostrum exosomes to lung cancer cells, both in vitro and in vivo, resulting in inhibition of proliferation and disease progression. Bovine colostrum is an abundant source of exosomes. Here we present a novel exosome-polyethyleneimine matrix (EPM) to deliver therapeutic siRNA targeting NRF2 expression (siNRF2). Specific delivery of the EPM to tumors was further enhanced via folic acid (FA) functionalization, targeting folate receptors highly expressed on lung tumor cells. Exosomes were isolated from standardized colostrum powder through rehydration and differential centrifugation, and characterized by size, polydispersity index (pdi) and surface charge by Zetasizer, and the presence of surface protein markers by Western blot. siNRF2 was loaded onto the EPM, and the resultant EPM-siNRF2 complex was harvested by PEG precipitation. Entrapment efficiency was determined using 5’-32P-labeled siRNA as a tracer. The gene knockdown efficiency of EPM-siNRF2 was assessed in lung cancer (A549) cells by Western blot and the therapeutic effect of target knockdown in vitro was confirmed by analyzing the corresponding modulation in downstream targets of NRF2. The anti-tumor effect was then evaluated using both subcutaneous and orthotropic lung tumor models in immunocompromised mice. The EPM exhibited high entrapment efficiency (>90%) of siNRF2 (up to 20 μg) and protected entrapped siRNA from enzymatic degradation upon exposure to RNases. EPM-siNRF2 dose dependently decreased NRF2 expression in A549 lung cancer cells. When formulated with FA-functionalized exosomes, EPM-siNRF2 inhibited subcutaneous and orthotropic lung tumors in mice by over 57% (p<0.01) and 84% (p<0.001), respectively. Mice treated with FA-EPM-siNRF2 showed decreased levels of NRF2 in tumor tissue, but not in the adjacent lung, indicating FA-mediated targeted delivery. This bovine colostrum exosome based EPM technology showcases high efficiency in gene knockdown and lung tumor inhibition, providing a promising nanoplatform for delivering nucleic acid therapeutics to the tumor site. Funding: Supported from the NIH grant R44 CA-221487, 3P Biotechnology Contract and, in part, Agnes Brown Duggan Endowment. Keywords: Bovine colostrum, Exosomes, NRF2, siRNA, Lung cancer. Citation Format: Raghuram Kandimalla, Margaret Wallen, Jeyaprakash Jeyabalan, Disha N. Moholkar, Wendy Spencer, Ramesh C. Gupta, Farrukh Aqil. Exosome-mediated delivery of siRNA against NRF2 for treatment of lung cancer [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 7235.