Proteomic Analysis Research Articles

Abstract B017: Discovery of cancer-specific small RNAs using a new unbiased analysis of cohort sequence data

Abstract It is well-established that small RNAs such as microRNAs can have important roles as oncogenes or tumor suppressors. The majority of studies of small RNAs in cancer have focused on examining the often subtle deregulation of specific, well-characterized molecules, aiming to understand their role in tumorigenesis. However, these efforts have predominantly concentrated on known, well-annotated RNA sequences, potentially overlooking novel, cancer-specific molecules. In this study, we sought to apply a new computational approach to uncover small RNA molecules that are uniquely associated with cancer and are completely absent from all non- cancerous tissues. To achieve this, we developed an unbiased approach that can detect cancer- specific sequences even if they are lowly abundant, do not overlap with existing genome annotations and even if they do not map to the human reference genome. We applied our framework to hundreds of small RNA-seq samples across a diverse range of cancer types from two large-scale public resources: The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Through this comprehensive analysis, we identified a series of small RNA molecules that are exclusively present in tumor samples and completely absent in adjacent normal tissues across multiple cancer types. Furthermore, these molecules were not detected in a large cohort comprising over 2,500 non-cancerous public samples, underscoring their specificity to cancerous conditions. Some of these molecules are also associated with different patient metadata. For example, one of these candidates exhibited significant correlation with poor patient survival in both Lung Adenocarcinoma and Endometrial Carcinoma within both the TCGA and CPTAC datasets. The discovery of such cancer-specific small RNAs holds immense potential for clinical applications. These molecules could serve as highly specific diagnostic and prognostic biomarkers, aiding in the early detection and stratification of cancers. Moreover, their unique presence in cancer cells, positions them as promising targets for the development of novel therapeutic interventions. In summary, our findings highlight the importance of exploring the full spectrum of small RNAs in cancer research. By moving beyond the constraints of known annotations, we have uncovered previously unknown molecules that could improve cancer diagnostics, prognostics, and treatment. Citation Format: Panagiotis Kalogeropoulos, Maria Alejandra Ulloa, Marc Friedländer. Discovery of cancer-specific small RNAs using a new unbiased analysis of cohort sequence data [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B017.

Proteomic analysis of human Wharton’s jelly mesenchymal stem/stromal cells and human amniotic epithelial stem cells: a comparison of therapeutic potential

Proteomic analysis of human Wharton’s jelly mesenchymal stem/stromal cells and human amniotic epithelial stem cells: a comparison of therapeutic potential

CD40 agonist on patient-derived xenograft mice for the treatment of B-cell acute lymphoblastic leukemia

Abstract Purpose: Cluster of differentiation 40 (CD40) is expressed on B-cell acute lymphoblastic leukemia (B-ALL) cases. However, the effect of CD40 activation on B-ALL cells has never been tested in vivo. Experimental Design: The aim of our preclinical study was to investigate the therapeutic potential of a CD40 agonist in the treatment of B-ALL using patient-derived xenograft (PDX) mouse models. Results: Intravenous administration of the CD40 agonist significantly impeded B-ALL cell proliferation and growth in vivo, accompanied by rapid activation of the extracellular signal-regulated kinase (ERK) pathway, leading to the induction of apoptosis and disruption of cell cycle progression. Co-treatment with a specific inhibitor of ERK further demonstrated that CD40 stimulation induced the pro-apoptosis of B-ALL cells in an ERK-dependent manner. Proteomic analysis revealed alterations in key signaling pathways associated with B-ALL expansion and maintenance. Moreover, the CD40 agonist markedly reduced the frequency of leukemia-initiating cells and leukemia development in PDX mice. Our study showed that the CD40 agonist can be associated with chemotherapeutic agents such as vincristine and dexamethasone, and this combination showed improved effectiveness. Additionally, the CD40 agonist was more effective on pre-B-ALL (EGIL B-III) that expressed CD40, than on common B-ALL (EGIL B-II) that lacked CD40 expression. Conclusion: These findings suggest that CD40 agonists are promising immunotherapeutic candidates for pediatric B-ALL, warranting further clinical investigations to improve patient outcomes in CD40-expressing B-ALL.

Harnessing Tumor Cell‐Derived Exosomes for Immune Rejection Management in Corneal Transplantation

AbstractTransplantation remains the definitive treatment for end‐stage organ failures, but its efficacy is frequently compromised by immune rejection. This study introduces a novel strategy by utilizing tumor‐derived exosomes from B16‐F10 melanoma cells (B16‐Exo), diverging from the conventional use of immune cell‐derived exosomes, to alleviate post‐transplantation immune rejection. Utilizing murine corneal transplantation as a model, it is demonstrated that B16‐Exo significantly reduces immune rejection, evidenced by decreased corneal opacity, neovascularization, and immune dysregulation, while enhancing postoperative survival. Proteomic analyses reveal differential expression of pivotal proteins in B16‐Exo, notably the JAK2 protein within the JAK‐STAT signaling pathway, which has been mechanistically demonstrated to amplify the activity of myeloid‐derived suppressor cells (MDSCs) and inhibit T cell proliferation. These findings demonstrate the significant immunomodulatory effect of B16‐Exo in transplant immunology, supporting the continued exploration of tumor‐derived exosomes as a platform to uncover novel immunosuppressive mechanisms in transplantation.

REGγ is essential to maintain bone homeostasis by degrading TRAF6, preventing osteoporosis

Primary osteoporosis, manifesting as decreased bone mass and increased bone fragility, is a “silent disease” that is often ignored until a bone breaks. Accordingly, it is urgent to develop reliable biomarkers and novel therapeutic strategies for osteoporosis treatment. Here, we identified REGγ as a potential biomarker of osteoporotic populations through proteomics analysis. Next, we demonstrated that REGγ deficiency increased osteoclast activity and triggered bone mass loss in REGγ knockout (KO) and bone marrow-derive macrophage (BMM)-conditional REGγ KO mice. However, the osteoclast activity decreased in BMM-conditional REGγ overexpression mice. Mechanistically, we defined that REGγ-20S proteasome directly degraded TRAF6 to inhibit bone absorption in a ubiquitin-independent pathway. More importantly, BMM-conditional Traf6 KO with REGγ KO mice could “rescue” the osteoporosis phenotypes. Based on NIP30 (a REGγ “inhibitor”) dephosphorylation by CKII inhibition activated the ubiquitin-independent degradation of TRAF6, we selected TTP22, an inhibitor of CKII, and defined that TTP22 could alleviate osteoporosis in vitro and in vivo. Overall, our study reveals a unique function of NIP30/REGγ/TRAF6 axis in osteoporosis and provides a potential therapeutic drug TTP22 for osteoporosis.

Abstract B017: MicroRNA and proteomic analyses of plasma extracellular vesicles detect diffuse large B-cell lymphoma

Abstract Background: Liquid biopsy offers a non-invasive method for detection of non-Hodgkin lymphoma (NHL). Tissue biopsy, the standard method of NHL detection, causes patient discomfort and increases risk of infection. Extracellular vesicles (EVs) are secreted by cells as particles with cargos of nucleic acids and proteins enclosed in a lipid bilayer. The most common NHL subtype is diffuse large B-cell lymphoma (DLBCL). We analyzed plasma-derived EVs from DLBCL patients and matching healthy controls for microRNA (miRNA) and protein to identify potential liquid biopsy biomarkers. Approach: Plasma samples (1 mL) from DLBCL patients and healthy controls were eluted through Izon size-exclusion chromatography (SEC) to obtain EVs. The size distribution of EVs was characterized with nanoparticle tracking analysis. For miRNA analysis, SEC EVs from three DLBCL patients and three matching healthy controls underwent further selection by immunocapture and release according to NHL antigens CD19, CD20, CD22, and C37, with an EV microfluidic affinity purification (EV-MAP) chip. Western blot confirmed the presence of these NHL antigens in NHL cell lysate and NHL cell culture SEC EVs, with flow cytometry verifying expression on NHL cells. MiRNA from these immunocaptured EVs were then isolated and sequenced with Qiagen kits. MiRNA levels were assessed for fold change (FC) expression between cases and controls. Upregulated miRNAs from DLBCL patients were compiled with the miRNA Enrichment Analysis and Annotation Tool (miEAA). For proteomic analysis, SEC EVs from ten DLBCL patients and ten matching healthy controls were measured with label-free mass spectrometry and a custom peptide library. Protein levels were assessed for FC expression and compiled with the Mann-Whitney U test. Results: The size of EVs ranged from 50–300 nm. Exclusively different upregulated miRNAs (FC>2, p<0.05, FDR p<0.05) were found by selection with different antigens: None unique with CD19, one with CD20, eight with CD22, and one with CD37. MiR-320b was upregulated with CD20 (FC=52, p=0.0002, FDR p=0.02), and miR-3168 with CD37 (FC=906, p=0.0003, FDR p=0.02). With CD22, miR-190b-5p, let-7c-5p, miR-1-3p, miR-125b-5p, miR-133a-3p, miR-153-3p, miR- 184, and miR-206 were upregulated in DLBCL patients (FC>17, p<0.003, FDR p<0.05). The miEAA recognized all the upregulated CD22 miRNAs as overrepresented in B-cell lymphoma, except for miR-190b-5p. Proteomic analysis of EVs found 42 different exo-proteins with AUC>0.90 (p<0.05) and 12 different exo-proteins with AUC>0.95 (p<0.009) upregulated in DLBCL patients. Two upregulated exo-proteins (FC>2.81, p<0.0002, adjusted p<0.004), ADAM metallopeptidase with thrombospondin type 1 motif 13 (ADAMTS13) and von Willebrand Factor (vWF), achieved a perfect AUC=1 (p=0.00001) for all DLBCL patients and healthy controls. Conclusions: These results support the hypothesis that liquid biopsy of plasma EVs detect DLBCL. Upregulated miRNA and proteomic signatures via EVs indicate the presence of DLBCL for non-invasive NHL detection. Citation Format: Arthur A. Lee, Sagar Rayamajhi, Mengjia Hu, Harsh Pathak, Rajni V. Puri, Kamilla Isakova, Mei Han, Claire S. Berquist, Samuel G. Mackintosh, Stephanie D. Byrum, Dennis W. Province, Mohammod M. Rahman, Foyez Ahmmed, Leonidas E. Bantis, Malgorzata A. Witek, Steven A. Soper, Andrew K. Godwin, Haitham Abdelhakim. MicroRNA and proteomic analyses of plasma extracellular vesicles detect diffuse large B-cell lymphoma [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B017.

Abstract PR013: Highly accurate detection of early-stage colorectal cancer using tumor and immune extracellular vesicles biomarkers

Abstract Introduction: Colorectal cancer (CRC) is one of the most common cancers worldwide, and early detection is critical for successful treatment and improved survival rates. However, precancerous and early-stage CRC present significant diagnostic challenges due to the small size of lesions and the very low expression of tumor-specific biomarkers in the bloodstream. Current genomics-based diagnostic methods struggle to detect these lesions, making it imperative to develop more sensitive and specific approaches. Circulating extracellular vesicles (EVs) are emerging as a promising solution for early-stage CRC detection, since EVs are produced by tumor cells as well as the tumor microenviroment and host immune cells. Thus, EVs may offer the means to detect and monitor small early-stage tumors through both direct detection of tumor- associated biomarkers as well through tumor specific host response and tumor microenvironment biomarkers. Methods: To identify novel early-stage CRC specific biomarkers, we performed proteomics analysis on EVs purified from patient plasma using size exclusion chromatography and a proprietary buffer system that enhances EV and corona protein recovery. TrueDiscovery™ Data-independent acquisition (DIA) mass spectrometry (MS) analysis was conducted on 24 pre- cancer/stage 0 and 25 stage 1 CRC patients and 75 normal patient plasma samples. An in-house developed machine learning pipeline was used to identify differentially expressed proteins and model candidate multiplexes to identify those with extremely high diagnostic accuracy (> 0.99). Results: An average of ∼2,500 proteins were identified per sample and included in bioinformatics analysis. Comparative analysis between control patient EVs and either pre- cancerous/Stage 0, or Stage 1 colon cancer EVs using an in-house Machine Learning pipeline identified 336 and 493 differentially expressed proteins for each group (FDR adjusted p-value < 0.001). Of these, the best 17 pre/stage 0 proteins and 53 stage 1 proteins were trained and tested using Support Vector Machine to assess all potential 3-plexes in order to identify those with mean diagnostic accuracy > 99%. This yielded 5 3-plexes in precancer/stage 0 and 34 3-plexes in stage 1 with near perfect diagnostic accuracy. These plexes are currently being assessed in single analyte and multiplex immunoassays with the goal of translating candidate 3-plexes to the clinical. Conclusions: Key biomarkers from CRC patient EVs indicate the potential to detect and diagnose early-stage and low tumor burden cancers using our methods. Interestingly, the most accurate 3-plexes consist of proteins from immune, inflammatory and metabolic processes, suggesting that for the detection of early stage cancer it may be critical to include both tumor and host specific biomarkers. Citation Format: Poorva Mudgal, Cheryl Bandoski, Zachary Opheim, Martin Mehnert, Valesca Anschau, Issa Isaac, Alan Ezrin, Todd Hembrough. Highly accurate detection of early-stage colorectal cancer using tumor and immune extracellular vesicles biomarkers [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR013.

Comparative transcriptomic and proteomic analyses of two salt-tolerant alfalfa (Medicago sativa L.) genotypes: investigation of the mechanisms underlying tolerance to salt

Abiotic stressors such as salt stress restrict plant development and output, which lowers agricultural profitability. In this study, alfalfa (Medicago sativa L.) varieties with different levels of salt tolerance were examined using high-throughput RNA sequencing (RNA-Seq) and Tandem Mass Tags (TMT) technologies to study the reactions of the root systems to salt stress, from transcriptomics and proteomics perspectives. The varieties Atlantic (AT) and Zhongmu-1 (ZM-1) were selected and evaluated after 2 h and 6 h of treatment with 150 mM NaCl. The results showed that under salt stress for 2 h, 1810 differentially expressed genes (DEGs) and 160 differentially expressed proteins (DEPs) in AT were screened, while 9341 DEGs and 193 DEPs were screened in ZM-1. Under salt stress for 6 h, 7536 DEGs and 118 DEPs were screened in AT, while 11,754 DEGs and 190 DEPs were screened in ZM-1. Functional annotation and pathway enrichment analyses indicated that the DEGS and DEPs were mainly involved in the glutathione metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, and photosynthesis pathways. A series of genes related to salt tolerance were also identified, including GSTL3 and GSTU3 of the GST gene family, PER5 and PER10, of the PER gene family, and proteins such as APR and COMT, which are involved in biosynthesis of secondary metabolites. This study provides insights into salt resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for alfalfa breeding in the future.

Proteomic analysis of the combined effects of cannabigerol and 3-O-ethyl ascorbic acid on kinase-dependent signalling in UVB-irradiated human keratinocytes

Proteomic analysis of the combined effects of cannabigerol and 3-O-ethyl ascorbic acid on kinase-dependent signalling in UVB-irradiated human keratinocytes

Proteomic Profiling of COVID-19 Patients Sera: Differential Expression with Varying Disease Stage and Potential Biomarkers

Background/Objectives: SARS-CoV-2 is one of the viruses that caused worldwide health issues. This effect is mainly due to the wide range of disease prognoses it can cause. The aim of this study is to determine protein profiles that can be used as potential biomarkers for patients’ stratification, as well as potential targets for drug development. Methods: Eighty peripheral blood samples were collected from heathy as well as SARS-CoV-2 patients admitted at a major tertiary care center in Riyadh, Saudi Arabia. A label-free quantitative mass spectrometry-based proteomic analysis was conducted on the extracted sera. Protein–protein interactions and functional annotations of identified proteins were performed using the STRING. Results: In total, two-hundred-eighty-eight proteins were dysregulated among all four categories. Dysregulated proteins were mainly involved in the network map of SARS-CoV-2, immune responses, complement activation, and lipid transport. Compared to healthy subjects, the most common upregulated protein in all three categories were CRP, LGALS3BP, SAA2, as well as others involved in SARS-CoV-2 pathways such as ZAP70 and IGLL1. Notably, we found fifteen proteins that significantly discriminate between healthy/recovered subjects and moderate/under medication patients, among which are the SERPINA7, HSPD1 and TTC41P proteins. These proteins were also significantly downregulated in under medication versus moderate patients. Conclusions: Our results emphasize the possible association of specific proteins with the SARS-CoV-2 pathogenesis and their potential use as disease biomarkers and drug targets. Our study also gave insights about specific proteins that are likely increased upon infection but are likely restored post recovery.

Large‐scale deep proteomic analysis in Alzheimer's disease brain regions across race and ethnicity

AbstractINTRODUCTIONAlzheimer's disease (AD) is the most prevalent neurodegenerative disease, yet our comprehension predominantly relies on studies within non‐Hispanic White (NHW) populations. Here we provide an extensive survey of the proteomic landscape of AD across diverse racial/ethnic groups.METHODSTwo cortical regions, from multiple centers, were harmonized by uniform neuropathological diagnosis. Among 998 unique donors, 273 donors self‐identified as African American, 229 as Latino American, and 434 as NHW.RESULTSWhile amyloid precursor protein and the microtubule‐associated protein tau demonstrated higher abundance in AD brains, no significant race‐related differences were observed. Further proteome‐wide and focused analyses (specific amyloid beta [Aβ] species and the tau domains) supported the absence of racial differences in these AD pathologies within the brain proteome.DISCUSSIONOur findings indicate that the racial differences in AD risk and clinical presentation are not underpinned by dramatically divergent patterns in the brain proteome, suggesting that other determinants account for these clinical disparities.Highlights We present a large‐scale proteome (∼10,000 proteins) of DLPFC (998) and STG (244) across AD cases. About 50% of samples were from racially and ethnically diverse brain donors. Key AD proteins (amyloid and tau) correlated with CERAD and Braak stages. No significant race‐related differences in amyloid and tau protein levels were observed in AD brains. AD‐associated protein changes showed a strong correlation between the brain proteomes of African American and White individuals. This dataset advances understanding of ethnoracial‐specific AD pathways and potential therapies.

Abstract 4129523: MicroRNA-1282 Rescues Diabetic Limb Ischemia Via a SERF2-Protein Aggregation Pathway

Introduction: Patients with diabetes are at higher risk of chronic limb-threatening ischemia (CLTI), a severe form of peripheral artery disease (PAD) causing restricted blood flow to the lower limbs due, in part, to impaired angiogenesis. However, the role of microRNAs (miRNAs) in diabetic CLTI remains poorly understood. By integrating plasma miRNA sequencing data from PAD patients with diabetes with a diabetic CLTI mouse model, we have recently identified the conserved miRNA miR-1282 that is in cis-antisense orientation to SERF2, a gene associated with amyloid aggregation. Therefore, we hypothesize that miR-1282 orchestrates endothelial angiogenesis and proteostasis during diabetic CLTI. Methods: Using miR-1282 overexpression or SERF2 knockdown studies, we characterized mouse orthologs of human miR-1282 and SERF2 for angiogenesis, apoptosis, protein aggregation, and oxidative stress in diabetic mouse skeletal muscle endothelial cells (ECs). In vivo, miR-1282 mimics were delivered intramuscularly to assess their impact on blood flow recovery, angiogenesis, and protein aggregation. Mechanistic insights in ECs were gained via RNA-seq, predictive algorithms, and proteomic analyses. Results: miR-1282 inhibited the expression of its cis-antisense target SERF2 by 98%. miR-1282 is a hypoxia-induced endothelial-enriched miRNA, and its expression was inversely correlated with SERF2 expression. miR-1282 levels were markedly reduced after femoral artery ligation (FAL) in diabetic db/db mice. Overexpression of miR-1282 or SERF2 knockdown enhanced angiogenesis and reduced protein aggregation, apoptosis, and oxidative stress in both normal and hypoxic conditions in vitro. Delivery of miR-1282 mimics in db/db mice improved blood flow recovery by 108% and angiogenesis by 98%, and reduced protein aggregation by 48% and tissue necrosis. Coupling RNA-seq profiling and prediction algorithms of ECs upon miR-1282 overexpression or SERF2 knockdown revealed EREG, BAG5, CASP3, ARG1, and HSP90AA1 as potential downstream regulators. Pathway enrichment analysis implicated inhibition of endothelial apoptosis, ER stress, and protein stability among the most dysregulated processes. Conclusion: A novel mouse ortholog of human miR-1282 augments endothelial functions and diminishes protein aggregation in diabetic CLTI via suppression of its cis-antisense target SERF2. These findings uncover new potential therapeutic targets in treating diabetic CLTI.

Abstract 4119195: Proteomic Analysis of Primary Angioplasty in Acute Myocardial Infarction: Implications for Left Ventricular Remodelling and Recovery of Function

Introduction: Acute myocardial infarction (AMI) is a leading global cause of mortality. Following primary percutaneous coronary intervention (PCI), 25% require hospitalisation for symptomatic heart failure. Further understanding of the molecular pathogenesis and the temporal relationship of the protein profile associated with ischaemic insult and subsequent cardiac remodelling is required to improve risk stratification following AMI. Methods: 20 patients with AMI presenting to Royal Free Hospital in London were recruited for proteomic analysis (O link Proximity Extension Immunoassay) at presentation and at 24 and 72 hours following primary PCI. All underwent initial CMR on admission and at 6 month follow up to assess for myocardial oedema, left ventricular volumes and function and assessment of scar. Results: Proteomic biomarkers that increased on discharge following AMI were: IGFBP2 (8% increase, p=0.001), MMP-10 (5% increase, p=0.001), TIMP4 (14.4% increase, p<0.001), CSF-1 (3.4% increase, p<0.001), CHI3L1 (15% increase, p<0.001), ST2 (19% increase, p=0.001), TGF-alpha (17% increase, p=0.001), IL6 (38% increase, p<0.001), and NT-proBNP (93% increase, p<0.001). The only biomarker that significantly decreased was IGFBP-1 (24% decrease, p=0.003). Notably, increased post-PCI biomarkers correlated with reduced infarct size at follow-up, including CCL23 (R=-0.6, p=0.016), IL6 (R=-0.051, p=0.04), NT-proBNP (R=-0.72, p=0.002). High biomarkers at initial presentation associated with reduced left ventricular end diastolic volume (LVEDV) were CSF-1 (R=-0.64, p=0.03) and CCL23 (R=-0.76, p=0.006). Discussion: Following AMI, we observed increase in proteins implicated in inflammation, angiogenesis and tissue repair. IGFBP1 as a stress hormone significantly decreased after PCI. Markers that showed linear association with reduced cardiac preload measured by LVEDV were linked with angiogenesis promotion and resolution of inflammation.

MecA in Streptococcus mutans is a multi-functional protein

ABSTRACT Our recent studies have shown that deficiency of MecA in Streptococcus mutans significantly affects cell division, growth, and biofilm formation. In this study, an in vitro mixed-species model, proteomics, and affinity pull-down assays were used to further characterize the MecA-mediated regulation in S. mutans . The results showed that compared with the wild type, UA159, the mecA mutant significantly reduced its production of glucans and weakened its ability to facilitate mixed-species biofilm formation. Relative to the wild type, the mecA mutant also displayed unique characteristics, including colony morphology, growth rate, and biofilm formation that did not fully resemble any of the clpP, clpX, clpE, clpCE, and clpC individual or combinational mutants. Deletion of mecA was shown to result in alteration of >337 proteins, including down expression of GtfBC&D and adhesin P1. More than 277 proteins were differentially expressed in response to clpP deletion, including increased expression of GtfB. By cross-referencing the two proteomes, a distinctive set of proteins was found to be altered in the mecA mutant, indicating a ClpP-independent role of MecA in the regulation of S. mutans . When analyzed using affinity pull-down, ClpC, ClpX, ClpE, and CcpA were among the members identified in the MecA-associated complex. Further analysis using a bacterial two-hybrid system confirmed CcpA, ClpX, and ClpE as members of the MecA interactome. These results further suggest that MecA in S. mutans is more than an adapter of the Clp-proteolytic machinery, although the mechanism that underlies the Clp-independent regulation and its impact on S. mutans pathophysiology await further investigation. IMPORTANCE MecA is known as an adaptor protein that works in concerto with ATPase ClpC and protease ClpP in the regulated proteolysis machinery. The results presented here provide further evidence that MecA in S. mutans , a keystone cariogenic bacterium, plays a significant role in its ability to facilitate mixed-species biofilm formation, a trait critical to its cariogenicity. Proteomics analysis, along with affinity pull-down and bacterial two-hybrid system, further confirm that MecA can also regulate S. mutans physiology and biofilm formation through pathways independent of the Clp proteolytic machinery, although how it functions independently of Clp awaits further investigation.

Abstract 4125992: Eicosapentaenoic Acid (EPA) Increases Expression of Nrf2-mediated Antioxidant Response Element and Heme Oxygenase-1 in Cytokine-Activated Endothelial Cells

Background: Endothelial cell (EC) nuclear factor erythroid 2-related factor (Nrf2) translocates to the nucleus during inflammation to mediate transcription of genes in the antioxidant response elements (ARE). An ARE regulates mRNA encoding HMOX-1, thioredoxin (TXN), and NAD(P)H quinone oxidoreductase-1 (NQO1), among others. Parkinson disease protein 7 (PARK7) and p62 work independently to prevent Keap1-mediated degradation of Nrf2 during oxidative stress. Eicosapentaenoic acid (EPA) administered as icosapent ethyl reduced CV events (REDUCE-IT). We tested the effects of EPA on ARE protein expression in ECs from multiple tissues during cytokine challenge. Methods: Human brain, pulmonary and vascular ECs were treated with IL-6 (12 ng/mL) for 2 hours and then incubated with EPA (40 µM) for 24 h. Global proteomic analysis performed by LC-MS measured relative protein expression. Significant (p<0.05) changes between treatment groups >1-fold were analyzed by differential enrichment analysis of proteomics data (DEP) and included in gene set enrichment analyses (GSEA). Significantly modulated pathways within the Gene Ontology (GO) database were identified as those with an adjusted-p value <0.05. Results: Proteomic analysis revealed that EPA significantly modulated ≥600 proteins in ECs distinct from IL-6 challenge alone. In EC, EPA significantly modulated the “cellular response to oxidative stress” pathway (GO: 0034599) relative to IL-6 alone. Within this GO pathway, EPA increased levels of catalase (1.2-fold, 1.1-fold, 1.1-fold) and mitochondrial glutathione reductase (1.1-fold, 1.1-fold, 1.1-fold) in brain, pulmonary, and vascular ECs, respectively. We also observed a consistent increase in brain, pulmonary, and vascular ECs of p62 (1.3-fold, 1.2-fold, and 1.2-fold, respectively), and ARE members HMOX-1 (1.5-fold, 1.7-fold, and 2.1-fold, respectively), and NQO1 (1.1-fold, 1.2-fold, and 1.3-fold, respectively). TXN was increased in pulmonary and vascular ECs (1.1-fold and 1.2-fold, respectively) with EPA. Mitochondrial TXN (also called TXN2) increased in brain ECs with EPA 1.1-fold. EPA also significantly increased levels of PARK7 1.1-fold. Conclusions: During inflammation, EPA enhanced expression of cytoprotective proteins in the ARE, notably HMOX-1, along with its regulators, in ECs from multiple tissues. Augmented endogenous antioxidant pathways may contribute to EPA’s clinical benefits.

Abstract 4137735: Chronic Oxidative Stress Induces Hypertension and Abdominal Aortic Aneurysm in Chemogenetic Mice Model

Background: Aortic aneurysms account for ~10,000 deaths annually in the USA. Oxidative stress is implicated in both abdominal (AAA) and thoracic (TAA) aneurysm formation, but the mechanisms are incompletely understood. We used a chemogenetic approach to modulate oxidative stress in the vascular wall by creating a transgenic mouse (DAAO-TG Tie2 ) that expresses yeast D-amino acid oxidase (DAAO) driven by the endothelial Tie2 promoter. DAAO generates the reactive oxygen species hydrogen peroxide from D-amino acids. Vascular tissues contain L-amino acids, so yeast DAAO is quiescent until DAAO-TG Tie2 mice are provided with D-amino acids. Here we characterize the cellular and molecular consequences of vascular oxidative stress in DAAO-TG Tie2 mice. Hypothesis: Chronic oxidative stress in the vascular wall causes arterial dysfunction. Aim: To characterize the phenotype of DAAO-TG Tie2 mice after oxidative stress induction in vascular endothelium. To identify the mechanisms whereby vascular oxidative stress causes arterial dysfunction and hypertension. Methods: Systolic blood pressure and aortic sonography were measured weekly in D-alanine-fed DAAO-TG Tie2 . Proteomic analyses were used to identify mechanistic targets, which were validated using biochemical and immunohistochemical methods. Results: D-alanine-fed DAAO-TG Tie2 mice develop systolic hypertension and abdominal but not thoracic aortic aneurysms; treated mice die in >3 months with burst abdominal aortic aneurysms. Transgene expression is similar in abdominal and thoracic endothelium. Levels of oxidative stress markers (oxidized proteins, lipid, and DNA) were similar in thoracic and abdominal aorta. Proteomic analyses established phenotypic switching in abdominal but not thoracic aorta, and also revealed activation of the oxidant-activated kinase ASK1 and of the MAP kinase cascade in abdominal but not thoracic aorta. Immunoblot analyses showed a marked decrease in JNK1 phosphorylation by phosphatase DUSP3 and an increase in vascular KLF4, leading to phenotypic switching of contractile to synthetic VSMCs. Conclusion: Chronic chemogenetic oxidative stress induces hypertension and abdominal aortic aneurysm formation caused by KLF4-dependent VSMC phenotypic switching.

The Coexistence of Klebsiella pneumoniae and Candida albicans Enhanced Biofilm Thickness but Induced Less Severe Neutrophil Responses and Less Inflammation in Pneumonia Mice Than K. pneumoniae Alone

Due to the possible coexistence of Klebsiella pneumoniae (KP) and Candida albicans (CA), strains of KP and CA with biofilm production properties clinically isolated from patients were tested. The production of biofilms from the combined organisms (KP+CA) was higher than the biofilms from each organism alone, as indicated by crystal violet and z-stack immunofluorescence. In parallel, the bacterial abundance in KP + CA was similar to KP, but the fungal abundance was higher than CA (culture method), implying that CA grows better in the presence of KP. Proteomic analysis was performed to compare KP + CA biofilm to KP biofilm alone. With isolated mouse neutrophils (thioglycolate induction), KP + CA biofilms induced less prominent responses than KP biofilms, as determined by (i) neutrophilic supernatant cytokines (ELISA) and (ii) neutrophil extracellular traps (NETs), using immunofluorescent images (neutrophil elastase, myeloperoxidase, and citrullinated histone 3), peptidyl arginine deiminase 4 (PAD4) expression, and cell-free DNA. Likewise, intratracheal KP + CA in C57BL/6 mice induces less severe pneumonia than KP alone, as indicated by organ injury (serum creatinine and alanine transaminase) (colorimetric assays), cytokines (ELISA), bronchoalveolar lavage fluid parameters (bacterial culture and neutrophil abundances using a hemocytometer), histology score (H&E stains), and NETs (immunofluorescence on the lung tissue). In conclusion, the biofilm biomass of KP + CA was mostly produced from CA with less potent neutrophil activation and less severe pneumonia than KP alone. Hence, fungi in the respiratory tract might benefit the host in some situations, despite the well-known adverse effects of fungi.

TRIM28 regulates the coagulation cascade inhibited by p72 of African swine fever virus

AbstractIn 2018, African swine fever virus (ASFV) emerged in China, causing extremely serious economic losses to the domestic pig industry. Infection with ASFV can cause disseminated coagulation, leading to the consumption of platelets and coagulation factors and severe bleeding. However, the mechanism of virus-induced coagulation has yet to be established. In our study, ASFV downregulated the coagulation process, as detected by D-dimer (D2D) and Factor X (F10) expression in pigs challenged with ASFV HLJ/18. In vitro, ASFV infection increased Factor IX (F9) and Factor XII (F12) expression while downregulating F10 expression in porcine alveolar macrophages (PAMs). African swine fever virus induced both intrinsic and extrinsic coagulation cascades. In addition, several encoded proteins affect the expression of the crucial coagulation protein F10, and among the encoded proteins, p72 inhibits the activity and expression of F10. Proteomic analysis also revealed that p72 is involved in the coagulation cascade. p72 can interact with F10, and its inhibitory functional domains include amino acids 423–432 and amino acids 443–452. Finally, we found that F10 and p72 interact with tripartite motif-containing protein 28 (TRIM28). TRIM28 knockdown resulted in a decrease in F10 expression. Importantly, TRIM28 contributes to the reduction in F10 protein expression regulated by p72. Our findings revealed an inhibitory effect of the viral protein p72 on the ASFV infection-induced coagulation cascade and revealed a role of TRIM28 in reducing F10 expression, revealing a molecular mechanism of ASFV-associated coagulation.

High‐Yield Bioproduction of Extracellular Vesicles from Stem Cell Spheroids via Millifluidic Vortex Transport

AbstractExtracellular vesicles (EVs) are emerging as novel therapeutics, particularly in cancer and degenerative diseases. Nevertheless, from both market and clinical viewpoints, high‐yield production methods using minimal cell materials are still needed. Herein, a millifluidic cross‐slot chip is proposed to induce high‐yield release of biologically active EVs from less than three million cells. Depending on the flow rate, a single vortex forms in the outlet channels, exposing transported cellular material to high viscous stresses. Importantly, the chip accommodates producer cells within their physiological environment, such as human mesenchymal stem cells (hMSCs) spheroids, while facilitating their visualization and individual tracking within the vortex. This precise control of viscous stresses at the spheroid level allows for the release of up to 30000 EVs per cell at a Reynolds number of ≈400, without compromising cellular integrity. Additionally, it reveals a threshold initiating EV production, providing evidence for a stress‐dependent mechanism governing vesicle secretion. EVs mass‐produced at high Reynolds displayed pro‐angiogenic and wound healing capabilities, as confirmed by proteomic and cytometric analysis of their cargo. These distinct molecular signatures of these EVs, compared to those derived from monolayers, underscore the critical roles of the production method and the 3D cellular environment in EV generation.

Abstract 4119210: Differential Proteomic Expression of IGFßP-1 and IGFßP-2 in Primary Angioplasty for Acute Myocardial Infarction

Introduction: Insulin growth factor (IGF) binding protein-1 and 2 (IGFBP-1 and 2) are implicated in acute myocardial infarction (AMI) and have been suggested as predictors of mortality and development of heart failure. The IGF axis has been shown to play roles in cell proliferation and apoptosis. We analysed the serum IGFBP-1 and 2 levels in AMI before and after percutaneous coronary intervention (PCI) and correlated this with cardiac magnetic resonance (CMR) imaging to better establish their significance as biomarkers in AMI. Methods: Patients with AMI who presented to Royal Free Hospital, London, were recruited for proteomic analysis (O link Proximity Extension Immunoassay) at presentation, 24h and 72h following primary PCI. All underwent both admission and follow-up CMR at 6 months to assess for myocardial oedema, left ventricular volumes and function, and assessment of scar. Results: Proteomic evaluation in 20 AMI patients (male 95%; median age 59) revealed significant reduction in the average IGFBP-1 values at discharge compared with presentation, from 5.93 to 4.52 (24% reduction, p=0.003). Conversely, the average IGFBP-2 values at discharge significantly increased from 7.66 to 8.29 (8% increase, p=0.001). Higher discharge IGFBP-2 value was also correlated with increased indexed left ventricle end diastolic volume (LVEDV) at 6-month follow-up (R=0.54, p=0.032). Discussion: IGFBP-1 and 2 showed significant change following intervention for AMI. IGFBP-1 is a stress hormone, which is directly and indirectly activated by cytokines, dysglycaemia and vasopressin activation. Its subsequent reduction following PCI in AMI indicates relative resolution of inflammation, but this was not correlated with changes in infarct size or LV function at follow-up. IGFBP-2 showed significant upregulation, and higher values at discharge were significantly correlated with increased LDEDV at follow-up, suggesting adverse clinical outcomes within this setting. This data suggests differential roles of IGFBP-1 and 2 in the pathogenesis of AMI.