Comprehensive Proteomic Profiling Research Articles

Abstract 12080: Comprehensive Proteomics Profiling of Human Myocardium Reveals Signaling Pathways Dysregulated in Severe Forms of Hypertrophic Cardiomyopathy

Introduction: Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiovascular disease, affecting 1 in 200-500 people. There is significant heterogeneity in disease severity. The signaling pathways that link gene mutations to severe HCM disease remain unknown. Analysis of the myocardial proteome is a novel approach to understanding severe forms of HCM. Hypothesis: Comprehensive proteomics profiling of myocardium identifies signaling pathways that are differentially regulated in severe forms of HCM. Methods: Proteomics profiling of 7289 proteins from myocardium was performed on patients with HCM. Univariable analysis with the Wilcoxon rank sum test or Spearman’s rank correlation test was used to determine the association between protein concentration and 5 clinical indicators of severe HCM: 1) left ventricular ejection fraction (LVEF), 2) atrial fibrillation (AF), 3) ventricular arrhythmias, 4) maximum septal thickness, and 5) late gadolinium enhancement (LGE) by cardiac magnetic resonance (CMR). Pathway analysis of proteins with significantly different concentrations (i.e., nominal p<0.05) in association with each clinical indicator was executed. Results: There were 106 patients with HCM included in the study. Pathway analysis of proteins associated with each indicator of severe HCM revealed dysregulation of inflammatory pathways and Ras-MAPK-related pathways ( Figure ). Metabolic pathways and adhesion pathways were dysregulated in association with LVEF and AF. Dysregulation of angiogenesis pathways (e.g., HIF-1, VEGF) was associated with LGE (FDR<0.05). Conclusions: Comprehensive proteomics profiling of human HCM myocardium was used to identify dysregulated signaling pathways associated with clinical features of severe HCM. Findings from this study support the role of both known (e.g., inflammation, metabolism, adhesion, and angiogenesis) and novel (e.g., Ras-MAPK) pathways in the development of severe forms of HCM.

Abstract 11317: Comprehensive Plasma Proteomics Profiling Identifies Signaling Pathways Dysregulated in Genotype-Positive versus Genotype-Negative Patients With Hypertrophic Cardiomyopathy

Introduction: Only a subset of patients with hypertrophic cardiomyopathy (HCM) have positive genotype. Although genotype-positive patients with HCM are known to have worse prognosis than genotype-negative patients, the underlying mechanism is unclear. Hypothesis/Aims: To test the hypothesis that plasma proteomics profiling identifies signaling pathways that are dysregulated in genotype-positive patients with HCM compared with those with negative genotype. Methods: In this multi-center study, we conducted plasma proteomics profiling of 4986 proteins in patients with HCM who underwent genetic testing. The outcome measure was positive genotype, defined as having a mutation that is pathogenic or likely pathogenic for HCM. We identified plasma proteins with significant (univariable P<0.05) differences in concentration between patients with positive and negative genotype in HCM using the Mann-Whitney-Wilcoxon test. Using these proteins, we performed pathway analysis to determine dysregulated pathways with false discovery rate <0.05. Results: A total of 340 patients with HCM underwent genotyping and 103 patients (30%) had positive genotype for HCM. Among the 4986 proteins, 844 (17%) had significant differences between patients with positive and negative genotypes - a larger percentage than what is expected by chance. Pathway analysis exhibited that both pathways known to be associated with poor prognosis (e.g., TGF-β, metabolic, and inflammation) and novel pathways (e.g., Ras-MAPK and associated pathways such as Pl3K-Akt and JAK-STAT) were dysregulated in genotype-positive patients with HCM compared to those who were genotype-negative ( Figure ). Conclusions: This study serves as the first to apply comprehensive proteomics profiling to identify signaling pathways that are differentially regulated in patients with positive genotype in the HCM population, elucidating dysregulation of both known (e.g., TGF-β) and novel (e.g., Ras-MAPK) pathways.

High-Throughput Plasma Proteomics to Define the Precursor Multiple Myeloma Proteome and Identify Candidate High-Risk Disease Biomarkers of Progression

Introduction Multiple Myeloma (MM) develops from well-defined precursors Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM), where patients remain stable or may unknowingly rapidly progress. Bone marrow (BM) biopsies are not routine for precursor disease management, and precursor patients are limited to monitoring few proteins within peripheral blood (PB) for signs of progressive disease. Deep proteome profiling of PB circulating proteins may help track disease; however, the dynamic range of the plasma proteome has limited the depth of detection for MS-based proteomics without first depleting abundant proteins and fractionating the samples after digestion to peptides. Technological advancements in multiplex immunoassays with low cross-reactivity and off-target events have enabled plasma profiling for disease stage classification, defining high-risk disease features, and novel therapeutic target discovery. Here, we perform the first comprehensive plasma proteomic profiling study on patients across the MM disease continuum and longitudinal sequential samples from progressive and stable disease. Methods We carried out high-throughput plasma proteomic profiling for approximately 3000 proteins simultaneously using the Olink® Explore 3072 library and Proximity Extension Assay (PEA) technology. Targeted proteins are recognized by multiplexed, matched pairs of antibodies labelled with unique DNA oligonucleotides that upon binding come into proximity, hybridize, and are extended to generate a unique sequence for protein identification with NextGen DNA sequencing. We profiled 423 PB plasma samples from 348 individuals, including MGUS (n=67), SMM (n=179), MM (n=44), and healthy controls (n=58). Sequential samples from patients with progressive disease (n=27) and patients with stable disease with matched clinical follow-up time were also profiled. Precursor defined samples from progressors ranged 1.03-5.88 yrs prior to diagnosis and were untreated in the precursor setting, while MM disease samples were also collected prior to any active disease therapy. Patients had a median clinical follow-up time of 7.05 years. T-tests, ANOVAs, and a linear mixed effect (LME) model were used to identify proteins that change across disease stages, progression status, and time. Results were adjusted for multiple testing using the Benjamini-Hochberg Method. Results We identified 751 significantly dysregulated proteins with the majority upregulated in progressive disease. We captured circulating levels of proteins highly expressed on the surface of plasma cells, including CD38, SDC1, BCMA and SLAMF7, highlighting the utility of PEA technology to monitor clinically-relevant targets for which monoclonal antibodies, antibody-drug conjugates, CAR-T and BiTE therapies are being developed. We identified proteins that significantly distinguished MGUS, SMM, and NDMM from healthy donors (n=222, 423 and 494), where increasing B-cell maturation antigen (BCMA) was a significant classifier and positive control. Consistent with previous findings, baseline BCMA levels were also significantly elevated in SMM-MM progressors vs. SMM non-progressors, further supporting the potential utility of BCMA measurements during routine blood tests of precursor MM patients. Proinflammatory cytokines were also identified, including IL1, IL5, IL6, IL16, and IL18, known to create a BM environment that promotes malignant cell development by suppressing the microenvironment, promoting cellular adhesion, or increasing angiogenesis. Four novel proteins that are vital for calcium homeostasis and integrin-mediated cell adhesion significantly increased from healthy to MM and were also significantly elevated in SMM progressors vs. SMM non-progressors, nominating these proteins as candidate biomarkers of high-risk disease. Conclusion We performed the most comprehensive plasma proteomics study to date, which characterized disease stage proteomes and identified candidate high-risk disease biomarkers in longitudinal progressor samples. Further advancements are underway to validate the accuracy levels of the novel candidates, test the performance of a classification model that recognizes disease stage-specific proteins, and determine how best to integrate proteins into current MM risk stratification models.

CAR T-Related Toxicities Based on Dynamic Proteomic Profiles Identifies Risk Factors for Cytokine Release Syndrome (CRS) and Immune Effector Cell -Associated Neurotoxicity Syndrome (ICANS)

TK and SM are Co-first authors INTRODUCTION Treatment with chimeric antigen receptor (CAR) T-cells significantly improved outcomes in relapsed/refractory non-Hodgkin lymphoma (NHL) and multiple myeloma (MM). CAR-T activation and anti-tumor cytotoxicity are associated with bystander inflammatory reactions resulting in CRS and/or ICANS. Due to complex cytokine profiles, disease heterogeneity, and variability between commercial CAR-T products, identification of risk factors associated with CRS and/or ICANS has been challenging. In this study, we used plasma proteomic profiling at different timepoints to identify possible inflammatory mediators associated with CRS and ICANS METHODS We prospectively collected plasma samples from patients who received CAR-T cells therapy between 9/2021 to 12/2022 at several time points - before lymphodepletion chemotherapy on day -5 (relative to CAR-T cell infusion), prior to CAR T-cell infusion on day 0, and post CAR T-cell therapy on days 1, 2, 3, and 7. Protein profiling analyses were conducted at Eve Technologies (Calgary, Alberta, Canada) using an assay measuring 71 total cytokines and chemokines. Proteins levels were compared across different time points used Wilcoxon rank test, while features associated with CRS/ICANS were identified using logistic regression. Receiver operating characteristic (ROC) analysis used to identify variables predictive for CRS. Area under the curve (AUC) of at least 0.8 was used and best cutoffs were determined according to Youden index. P-values <0.05 were considered statistically significant. This study was supported in part by The Frederick A. Deluca Foundation. RESULTS Overall, 56 patients with available cytokine assays at all time points were included. The median age was 65 years (IQR: 57-74) and 70% were men. Of all patients, 26 (46%) had diffuse large B-cell lymphoma (DLBCL), 23 (41%) MM, 4 (7%) mantle cell lymphoma, and 3 (6) follicular lymphoma. Ide-cel (39%), liso-cel (36%), and axi-cel (17%) were the most used CAR-T cell products. All patients received lymphodepleting chemotherapy with fludarabine/cyclophosphamide. In total, 35 (63%) patients developed CRS (grade 1, 89%; grade 2, 8%; grade 3, 3%) and 18 (32%) patients developed ICANS (grade 1, 72%; grade 2, 22%; grade 3, 6%). Compared to patients who did not develop CRS, patients with CRS had lower median absolute lymphocyte counts at day -5 (0.02 x10 9/L vs. 0.05, p=0.0146), higher baseline CRP (13 vs. 4 mg/L, p=0.0005), and higher ferritin (914 vs. 442 mg/L, p=0.048). No differences in the type of CAR-T products (p=0.090), percentages of DLBCL or MM (p=0.270) were observed between CRS and no CRS cohorts ( Panel-A). First, we investigated the proteomic profiles at baseline for CRS odds. Hemoglobin (odd ratio [OR]: 0.6, 95%CI: 0.4-0.8) was associated with lower odds for CRS while IL6 (2.0, 1.2-3.3) and stem cell factor (scf 2.2, 1.2-4.2) were associated with higher odds of CRS. We then analyzed the differences in cytokine levels between day 0 and day 3 to select cytokines with significant changes for further analysis ( Panel-B). At day 3, groa (1.9, 1.1-3.3), IL3 (1.6, 1.2-2.1), IL5 (1.5, 1.2-1.9), IL6 (1.7, 1.3-2.3), IL10 (2.0, 1.3-3.0), TNFα (2.0, 1.1-3.6), and mcp2 (2.5, 1.2-5.3) were all associated with higher odds for CRS. Based on ROC analysis at day 3, best cutoff points to estimate CRS (value, sensitivity/specificity) for IL3 (3, 80%/90%), IL5 (197, 74%/85%), IL6 (11, 70%/85%), and IL10 (53, 74%/85%) were identified. Based on that, elevated IL3 (OR:24, 95%CI: 6-105), IL5 (11, 3-40), IL6 (21, 5-95), and IL10 (12, 3-46) were associated with higher odds for CRS. For ICANS, day 3 IL3 (1.5, 1.2-1.9), IL6 (1.2, 1.1-1.5), IL8 (2.1, 1.4-3.3), and IL10 (1.7, 1.3-2.4) were associated with higher odds for ICANS. Best cutoff points to estimate ICANS at day 3 (value, sensitivity/specificity) for IL3 (5, 78%/76%), IL6 (115, 78%/78%), IL10 (130, 81%/80%), and IL8 (21, 83%/81%) were identified. Based on that, elevated IL3 (OR:10, 95%CI: 3-37), IL6 (11, 3-43), IL10 (13, 3-51), and IL8 (19, 4-81) were associated with higher odds for ICANS. CONCLUSIONS In our comprehensive plasma proteomic profiles analysis, we identified cutoffs for IL3, IL6, IL5 and IL10 that may be predictive for CRS and ICANS regardless of CAR-T cell product. Our results are clinically applicable and may be used to recognize patients at risk for CRS and/or ICANS who may be eligible for prophylactic therapies.

Single-Cell Multi-Omics Reveals Type-2 Functionality in Maintaining CAR T Cell Longevity Associated with 8-Year Leukemia Remission

Despite a high response rate in chimeric antigen receptor (CAR) T therapy for acute lymphocytic leukemia (ALL), ~50% of patients relapse within the first year, representing an urgent question to address in the next stage of cellular immunotherapy. The pioneering clinical trials conducted at Upenn/CHOP provide a unique opportunity to examine the molecular determinants of ultra-long CAR T persistence. We performed single-cell multi-omics profiling of ~700k pre-infusion CD19-targeted 4-BB CAR T cells from 82 pediatric ALL patients and 6 healthy donors. Patient demographics were collected between Sep-2012 to July-2022. To uncover the hallmarks of CAR T longevity, we correlated the single-cell atlas with the duration of B-cell aplasia (BCA), a widely used pharmacodynamic measurement of CAR T persistence, and classified all the patients into 5 groups (Table 1). Five patients in our cohort have exhibited a median BCA duration of 8.4 years (BCA-L group) and another 11 patients continue to have BCA with a median time of 5.1 years (BCA-O group). To remove potential confounding variables between trial design, 42 patients including the 5 BCA-L were analyzed as the Discovery Cohort, while the other 40 patients including the 11 BCA-O were used as Validation Cohort. Our analysis of CD19-specific stimulated CAR T cells from the Discovery Cohort revealed a prominent role of type-1 function, which was highly represented but had no discernible correlation with long-term persistence. Unexpectedly, we identified that elevated type-2 functionality was significantly associated with BCA-L patients maintaining CAR T persistence of 8.4 years, and this signature was robustly presented in the BCA-O patients in our Validation Cohort. Higher type-2 cytokine level of long-term persistent CAR T cells was independently validated using both flow cytometry and multiplexed secretomic assay. Through ligand-receptor interaction analysis, type-2 cytokines were found to regulate a cluster of Tim-3+terminal effector cells showing over activation of cytotoxicity, impaired immune function, elevated exhaustion signature and diminished proliferative potentiality, and CAR T cells from BCA-L patients showed reduced dysfunctional hallmarks. We next conducted in vitro functional studies to assess the impact of adding type-2 cytokine (IL-4) during CAR-specific activation on CAR T fitness. The addition of 10ng/mL IL-4 significantly boosted the proliferation and mitigated dysfunction of CAR T cells from 6 patients in the BCA2 group that only mediated short-term response (~3 months) and had negligible impact on their type-1 functionality. Remarkably, the functional profile of short-term BCA2 CAR T cells after IL-4 supplementation exhibited a comparable pattern to that of long-term BCA-L CAR T cells, particularly in terms of type-2 pathway, oxidative phosphorylation metabolism, PI3K/AKT signaling, mTOR signaling, and cell cycle regulation. To investigate the response of the host following CAR T infusion, we performed a comprehensive proteomic profiling of post-infusion serum proteins in a total of 41 patients. Baseline measurements (-2 to 0 days before CAR T infusion) showed a significantly higher level of type-2 cytokines in long-term patients. From the rapid expansion period (day 6-8) until 11 days post-infusion, we consistently observed significantly higher levels of circulating type-2 cytokines in 5-year or 8-year relapse-free responders. Conversely, no difference was observed in type-1 cytokines. In a leukemic NSG mouse model, both type-2 high and low CAR T cells were highly effective in reducing tumor burden in the first two weeks. However, type-2 high CAR T had significantly superior expansion, and the absolute CAR+ cell counts in peripheral blood were 10-fold higher than type-2 low CAR T at day 8 and day 12. To mimic tumor cell relapse, a second dose of tumor cells were injected into mice on day 17. Notably, type-2 high CAR T cells demonstrated a potent capability to elicit recall responses upon leukemia rechallenge, significantly prolonging the survival of tumor-bearing mice compared to type-2 low CAR T. The superior performance could be associated with their decreased exhaustion and increased memory phenotype. Our findings provide key insights into the mediators of CAR T longevity and suggest a potential therapeutic strategy to maintain long-term remission by enhancing type-2 functionality in CAR T cells.

Biological and therapeutic implications of RKIP in Gastrointestinal Stromal Tumor (GIST): an integrated transcriptomic and proteomic analysis

BackgroundGastrointestinal stromal tumors (GIST) represent a significant clinical challenge due to their metastatic potential and limited treatment options. Raf kinase inhibitor protein (RKIP), a suppressor of the MAPK signaling pathway, is downregulated in various cancers and acts as a metastasis suppressor. Our previous studies demonstrated low RKIP expression in GIST and its association with poor outcomes. This study aimed to expand on the previous findings and investigate the biological and therapeutic implications of RKIP loss on GIST.MethodsTo validate the RKIP prognostic significance, its expression was evaluated by immunohistochemistry in 142 bona fide GIST cases. The functional role of RKIP was evaluated in vitro, using the GIST-T1 cell line, which was knocked out for RKIP. The biological and therapeutic implications of RKIP were evaluated by invasion, migration, apoptosis, and 2D / 3D viability assays. Additionally, the transcriptome and proteome of RKIP knockout cells were determined by NanoString and mass spectrometry, respectively.ResultsImmunohistochemical analysis revealed the absence of RKIP in 25.3% of GIST cases, correlating with a tendency toward poor prognosis. Functional assays demonstrated that RKIP knockout increased GIST cells’ invasion and migration potential by nearly 60%. Moreover, we found that RKIP knockout cells exhibited reduced responsiveness to Imatinib treatment and higher cellular viability in 2D and 3D in vitro models, as assessed by apoptosis-related protein expression. Through comprehensive genetic and proteomic profiling of RKIP knockout cells, we identified several putative RKIP-regulated proteins in GIST, such as COL3A1.ConclusionsUsing a multidimensional integrative analysis, we identified, for the first time in GIST, molecules and pathways modulated by RKIP that may potentially drive metastasis and, consequently, poor prognosis in this disease.

Nanoarray Enabled Size-Dependent Isolation and Proteomics Profiling of Small Extracellular Vesicle Subpopulations toward Accurate Cancer Diagnosis and Prognosis.

Small extracellular vesicles (sEVs) have emerged as noninvasive biomarkers in liquid biopsy due to their significant function in pathology and physiology. However, the phenotypic heterogeneity of sEVs presents a significant challenge to their study and has significant implications for their applications in liquid biopsies. In this study, anodic aluminum oxide films with different pore sizes (AAO nanoarray) were introduced to enable size-based isolation and downstream proteomics profiling of sEV subpopulations. The adjustable pore size and abundant Al3+ on the framework of AAOs allowed size-dependent isolation of sEV subpopulations through nanoconfined effects and Lewis acid-base interaction between AAOs and sEVs. Benefiting from the strong concerted effect, the simple AAO nanoarray enabled specific isolation of three sEV subpopulations, termed "50", "90", and "150 nm" groups, from 10 μL of complex biological samples within 10 min with high capture efficiencies and purities. Moreover, the nanopores of AAOs also acted as nanoreactors for comprehensive proteomic profiling of the captured sEV subpopulations to reveal their heterogeneity. The AAO nanoarray was first investigated on sEVs from a cell culture medium, where sEV subpopulations could be clearly distinguished, and three traditional sEV-specific proteins (CD81, CD9, and FLOT1) could be identified by proteomic analysis. A total of 3946, 3951, and 3940 proteins were identified from 50, 90, and 150 nm sEV subpopulations, respectively, which is almost twice the number compared to those obtained from the conventional approach. The concept was further applied to complex real-case sample analysis from prostate cancer patients. Machine learning and gene ontology (GO) information analysis of the identified proteins indicate that different-sized sEV subpopulations contain unique protein cargos and have distinct cellular components and molecular functions. Further receiver operating characteristic curve (ROC) analysis of the top five differential proteins from the three sEV subpopulations demonstrated the high accuracy of the proposed approach toward prostate cancer diagnosis (AUC > 0.99). More importantly, several proteins involved in focal adhesion and antigen processing and presentation pathways were found to be upregulated in prostate cancer patients, which may serve as potential biomarkers of prostate cancer. These results suggest that the sEV subpopulation-based AAO nanoarray is of great value in facilitating the early diagnosis and prognosis of cancer and opens a new avenue for sEVs in liquid biopsy.

Epicardial placement of human placental membrane protects from heart injury in a swine model of myocardial infarction.

Cardiac ischemic reperfusion injury (IRI) is paradoxically instigated by reestablishing blood-flow to ischemic myocardium typically from a myocardial infarction (MI). Although revascularization following MI remains the standard of care, effective strategies remain limited to prevent or attenuate IRI. We hypothesized that epicardial placement of human placental amnion/chorion (HPAC) grafts will protect against IRI. Using a clinically relevant model of IRI, swine were subjected to 45 min percutaneous ischemia followed with (MI + HPAC, n = 3) or without (MI only, n = 3) HPAC. Cardiac function was assessed by echocardiography, and regional punch biopsies were collected 14 days post-operatively. A deep phenotyping approach was implemented by using histological interrogation and incorporating global proteomics and transcriptomics in nonischemic, ischemic, and border zone biopsies. Our results established HPAC limited the extent of cardiac injury by 50% (11.0 ± 2.0% vs. 22.0 ± 3.0%, p = 0.039) and preserved ejection fraction in HPAC-treated swine (46.8 ± 2.7% vs. 35.8 ± 4.5%, p = 0.014). We present comprehensive transcriptome and proteome profiles of infarct (IZ), border (BZ), and remote (RZ) zone punch biopsies from swine myocardium during the proliferative cardiac repair phase 14 days post-MI. Both HPAC-treated and untreated tissues showed regional dynamic responses, whereas only HPAC-treated IZ revealed active immune and extracellular matrix remodeling. Decreased endoplasmic reticulum (ER)-dependent protein secretion and increased antiapoptotic and anti-inflammatory responses were measured in HPAC-treated biopsies. We provide quantitative evidence HPAC reduced cardiac injury from MI in a preclinical swine model, establishing a potential new therapeutic strategy for IRI. Minimizing the impact of MI remains a central clinical challenge. We present a new strategy to attenuate post-MI cardiac injury using HPAC in a swine model of IRI. Placement of HPAC membrane on the heart following MI minimizes ischemic damage, preserves cardiac function, and promotes anti-inflammatory signaling pathways.

Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals

This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ∼20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. SignificanceWe present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general.

Metabolic changes and propensity for inflammation, fibrosis, and cancer in livers of mice lacking lysosomal acid lipase

Lysosomal acid lipase (LAL) is the sole lysosomal enzyme responsible for the degradation of cholesteryl esters and triacylglycerols at acidic pH. Impaired LAL activity leads to LAL deficiency (LAL-D), a severe and fatal disease characterized by ectopic lysosomal lipid accumulation. Reduced LAL activity also contributes to the development and progression of non-alcoholic fatty liver disease (NAFLD). To advance our understanding of LAL-related liver pathologies, we performed comprehensive proteomic profiling of livers from mice with systemic genetic loss of LAL (Lal−/−) and from mice with hepatocyte-specific LAL-D (hepLal−/−). Lal−/− mice exhibited drastic proteome alterations, including dysregulation of multiple proteins related to metabolism, inflammation, liver fibrosis, and cancer. Global loss of LAL activity impaired both acidic and neutral lipase activities and resulted in hepatic lipid accumulation, indicating a complete metabolic shift in Lal−/− livers. Hepatic inflammation and immune cell infiltration were evident, with numerous upregulated inflammation-related gene ontology biological process terms. In contrast, both young and mature hepLal−/− mice displayed only minor changes in the liver proteome, suggesting that loss of LAL solely in hepatocytes does not phenocopy metabolic alterations observed in mice globally lacking LAL. These findings provide valuable insights into the mechanisms underlying liver dysfunction in LAL-D and may help in understanding why decreased LAL activity contributes to NAFLD. Our study highlights the importance of LAL in maintaining liver homeostasis and demonstrates the drastic consequences of its global deficiency on the liver proteome and liver function.

Astrocytic endothelin-1 overexpression impairs learning and memory ability in ischemic stroke via altered hippocampal neurogenesis and lipid metabolism.

Vascular etiology is the second most prevalent cause of cognitive impairment globally. Endothelin-1, which is produced and secreted by endothelial cells and astrocytes, is implicated in the pathogenesis of stroke. However, the way in which changes in astrocytic endothelin-1 lead to poststroke cognitive deficits following transient middle cerebral artery occlusion is not well understood. Here, using mice in which astrocytic endothelin-1 was overexpressed, we found that the selective overexpression of endothelin-1 by astrocytic cells led to ischemic stroke-related dementia (1 hour of ischemia; 7 days, 28 days, or 3 months of reperfusion). We also revealed that astrocytic endothelin-1 overexpression contributed to the role of neural stem cell proliferation but impaired neurogenesis in the dentate gyrus of the hippocampus after middle cerebral artery occlusion. Comprehensive proteome profiles and western blot analysis confirmed that levels of glial fibrillary acidic protein and peroxiredoxin 6, which were differentially expressed in the brain, were significantly increased in mice with astrocytic endothelin-1 overexpression in comparison with wild-type mice 28 days after ischemic stroke. Moreover, the levels of the enriched differentially expressed proteins were closely related to lipid metabolism, as indicated by Kyoto Encyclopedia of Genes and Genomes pathway analysis. Liquid chromatography-mass spectrometry nontargeted metabolite profiling of brain tissues showed that astrocytic endothelin-1 overexpression altered lipid metabolism products such as glycerol phosphatidylcholine, sphingomyelin, and phosphatidic acid. Overall, this study demonstrates that astrocytic endothelin-1 overexpression can impair hippocampal neurogenesis and that it is correlated with lipid metabolism in poststroke cognitive dysfunction.

Prediction of worsening heart failure in hypertrophic cardiomyopathy using plasma proteomics

ObjectiveHeart failure (HF) is one of the most common and lifestyle-limiting complications of hypertrophic cardiomyopathy (HCM). Prediction of worsening HF using clinical measures alone remains limited. Moreover, the mechanisms by...

The proteomic landscape of soft tissue sarcomas

Soft tissue sarcomas (STS) are rare and diverse mesenchymal cancers with limited treatment options. Here we undertake comprehensive proteomic profiling of tumour specimens from 321 STS patients representing 11 histological subtypes. Within leiomyosarcomas, we identify three proteomic subtypes with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. Characterisation of undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas with low infiltrating CD3 + T-lymphocyte levels nominates the complement cascade as a candidate immunotherapeutic target. Comparative analysis of proteomic and transcriptomic profiles highlights the proteomic-specific features for optimal risk stratification in angiosarcomas. Finally, we define functional signatures termed Sarcoma Proteomic Modules which transcend histological subtype classification and show that a vesicle transport protein signature is an independent prognostic factor for distant metastasis. Our study highlights the utility of proteomics for identifying molecular subgroups with implications for risk stratification and therapy selection and provides a rich resource for future sarcoma research.

DIPG-14. PROTEOGENOMICS PROFILING REVEALS ENRICHED NON-HISTONE PROTEIN METHYLTRANSFERASES AS NEW THERAPEUTIC TARGETS IN DIPG

Abstract Diffuse intrinsic pontine glioma (DIPG) is a devastating brain tumour arising in the brainstems of children. Despite advances in genomics and treatments, the survival rate remains zero, with a median of less than a year, making it the leading cause of death among children with brain tumours. A mutation in histone H3 protein (H3K27M) has been identified as a genetic initiation event and affects global K27 trimethylation on histone H3 proteins and DNA methylation in DIPG. The epigenetic changes caused by the H3K27M mutation suggest the existence of an H3K27M-specific transcriptome and proteome. To deepen our knowledge of DIPG, we conducted a proteogenomic analysis of DIPG tissues by using high-resolution mass spectrometry for comprehensive proteome profiling, including total proteome, phosphoproteome, and methylproteome. Integrating proteomics data with DNA methylation and transcriptomics (bulk RNAseq and single-cell RNAseq) provided new insights into DIPG tumorigenesis. Our multi-omics analyses reveal enriched translation machinery, negative regulation of apoptosis process, and non-histone protein methyltransferase proteins, suggesting their previously unknown roles in DIPG cell growth and survival. Furthermore, our findings indicate that DIPG tissues have lower global mean protein phosphorylation and higher global mean protein methylation compared to normal brains, implying that DIPG may use methyl-signaling rather than phospho-signaling for tumour growth. The translation elongation proteins EEF1A1 and EEF1A2 are the most highly methylated proteins in DIPG. Methylation modifications such as K55me2, K79me3, and K165me2 of EEF1A1 are significantly higher in DIPG tissues compared to normal brains. These enriched methylpeptides are substrates of the non-histone methyltransferases METTL13 and METTL21B, which are enriched in the multi-omics analysis. Knocking down these methyltransferases in DIPG cells significantly decreases their target protein methylation, reduces global protein synthesis, and inhibits cell growth in vitro. Thus, proteogenomic analysis of DIPG reveals tumour-enriched non-histone methyltransferases, METTL13 and METTL21B as new therapeutic targets.

Comparative proteomic profiling of plasma exosomes in patients with lung cancer with brain metastasis and liver metastasis.

e21123 Background: Brain or liver metastases are the main causes of lung cancer-related death. Predicting liver or brain metastases before having evidence from imaging of the tumors is challenging, but important for early patient intervention. Accumulating evidence has suggested that circulating exosomes in the blood could mediate cancer metastasis by transferring specific proteins to the target cells. Methods: Using liquid chromatography-MS/MS, we analyzed the proteomic profiles of plasma exosomes derived from 42 metastatic lung cancer patients (including 26 solitary brain metastasis (BM) and 16 solitary liver metastasis (LM)), 25 local advanced (LA) lung cancer patients without metastasis, and 5 healthy controls (HC), and explored organ-specific proteomic biomarkers. Results: 120 and 143 differentially expressed exosomal proteins were found to be the dysregulated candidates in BM and LM of lung cancer (BM-DEEPs, LM-DEEPs), as compared to the LA lung cancer samples, respectively. The bioinformatics analyses indicated the homogeneity and heterogeneity in BM-DEEPs and LM-DEEPs. In terms of homogeneity, they were mainly involved in the protein activation cascade, collagen-containing extracellular matrix, and ECM-receptor interaction. In terms of heterogeneity, the BM-DEEPs were significantly enriched in S100 protein and calcium-dependent protein, while the LM-DEEPs were mainly enriched in integrin, lipoprotein, heat shock protein and proteoglycans. Moreover, our study also revealed the heterogeneity in plasma-derived exosome proteomics in patients with non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC), which partly explained the different metastatic characteristics of NSCLC and SCLC. Additionally, we found that MUC5B and SELL could be used as a reliable diagnostic marker of BM, while APOH, CD81 and CCT5 could help to diagnose LM in lung cancer patients. Conclusions: For the first time, we revealed the comprehensive and comparative proteomic profiles of plasma-derived exosomes from lung cancer patients with solitary brain and liver metastasis. We further proposed some potential biomarkers and pathological mechanisms, which could serve as excellent resource for further studies investigating lung cancer metastasis.

Multidimensional separation methods can improveseparation performance forextremely complicated proteomics samples and provide a powerful tool for comprehensive proteome profiling of low-microgram samples.

Tweetable abstract Multidimensional separation methods with improved sensitivity andpeak capacity and throughput allow in-depth proteome profiling of low-microgram samples.

Comprehensive and deep profiling of the plasma proteome with protein corona on zeolite NaY

Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers. However, the vast dynamic range renders the profiling of proteomes extremely challenging. Here, we synthesized zeolite NaY and developed a simple and rapid method to achieve comprehensive and deep profiling of the plasma proteome using the plasma protein corona formed on zeolite NaY. Specifically, zeolite NaY and plasma were co-incubated to form plasma protein corona on zeolite NaY (NaY-PPC), followed by conventional protein identification using liquid chromatography-tandem mass spectrometry. NaY was able to significantly enhance the detection of low-abundance plasma proteins, minimizing the “masking” effect caused by high-abundance proteins. The relative abundance of middle- and low-abundance proteins increased substantially from 2.54% to 54.41%, and the top 20 high-abundance proteins decreased from 83.63% to 25.77%. Notably, our method can quantify approximately 4000 plasma proteins with sensitivity up to pg/mL, compared to only about 600 proteins identified from untreated plasma samples. A pilot study based on plasma samples from 30 lung adenocarcinoma patients and 15 healthy subjects demonstrated that our method could successfully distinguish between healthy and disease states. In summary, this work provides an advantageous tool for the exploration of plasma proteomics and its translational applications.

Data Independent Acquisition Reveals In-Depth Serum Proteome Changes in Canine Leishmaniosis.

Comprehensive profiling of serum proteome provides valuable clues of health status and pathophysiological processes, making it the main strategy in biomarker discovery. However, the high dynamic range significantly decreases the number of detectable proteins, obstructing the insights into the underlying biological processes. To circumvent various serum enrichment methods, obtain high-quality proteome wide information using the next-generation proteomic, and study host response in canine leishmaniosis, we applied data-independent acquisition mass spectrometry (DIA-MS) for deep proteomic profiling of clinical samples. The non-depleted serum samples of healthy and naturally Leishmania-infected dogs were analyzed using the label-free 60-min gradient sequential window acquisition of all theoretical mass spectra (SWATH-MS) method. As a result, we identified 554 proteins, 140 of which differed significantly in abundance. Those were included in lipid metabolism, hematological abnormalities, immune response, and oxidative stress, providing valuable information about the complex molecular basis of the clinical and pathological landscape in canine leishmaniosis. Our results show that DIA-MS is a method of choice for understanding complex pathophysiological processes in serum and serum biomarker development.

Deep Proteome Profiling of White Adipose Tissue Reveals Marked Conservation and Distinct Features Between Different Anatomical Depots

White adipose tissue is deposited mainly as subcutaneous adipose tissue (SAT), often associated with metabolic protection, and abdominal/visceral adipose tissue, which contributes to metabolic disease. To investigate the molecular underpinnings of these differences, we conducted comprehensive proteomics profiling of whole tissue and isolated adipocytes from these two depots across two diets from C57Bl/6J mice. The adipocyte proteomes from lean mice were highly conserved between depots, with the major depot-specific differences encoded by just 3% of the proteome. Adipocytes from SAT (SAdi) were enriched in pathways related to mitochondrial complex I and beiging, whereas visceral adipocytes (VAdi) were enriched instructural proteins and positive regulators of mTOR presumably to promote nutrient storage and cellular expansion. This indicates that SAdi are geared toward higher catabolic activity, while VAdi are more suited for lipid storage. By comparing adipocytes from mice fed chow or Western diet (WD), we define a core adaptive proteomics signature consisting of increased extracellular matrix proteins and decreased fatty acid metabolism and mitochondrial Coenzyme Qbiosynthesis. Relative to SAdi, VAdi displayed greater changes with WD including a pronounced decrease in mitochondrial proteins concomitant with upregulation of apoptotic signaling and decreased mitophagy, indicating pervasive mitochondrial stress. Furthermore, WD caused a reduction in lipid handling and glucose uptake pathwaysparticularly in VAdi, consistent with adipocyte de-differentiation. By overlaying the proteomics changes with diet in whole adipose tissue and isolated adipocytes, we uncovered concordance between adipocytes and tissue only in the visceral adipose tissue, indicating a unique tissue-specific adaptation to sustained WD in SAT. Finally, an in-depth comparison of isolated adipocytes and 3T3-L1 proteomes revealed a high degree of overlap, supporting the utility of the 3T3-L1 adipocyte model. These deep proteomes provide an invaluable resource highlighting differences between white adipose depots that may fine-tune their unique functions and adaptation to an obesogenic environment.

A proteogenomic view of Parkinson’s disease causality and heterogeneity

The pathogenesis and clinical heterogeneity of Parkinson’s disease (PD) have been evaluated from molecular, pathophysiological, and clinical perspectives. High-throughput proteomic analysis of cerebrospinal fluid (CSF) opened new opportunities for scrutinizing this heterogeneity. To date, this is the most comprehensive CSF-based proteomics profiling study in PD with 569 patients (350 idiopathic patients, 65 GBA + mutation carriers and 154 LRRK2 + mutation carriers), 534 controls, and 4135 proteins analyzed. Combining CSF aptamer-based proteomics with genetics we determined protein quantitative trait loci (pQTLs). Analyses of pQTLs together with summary statistics from the largest PD genome wide association study (GWAS) identified 68 potential causal proteins by Mendelian randomization. The top causal protein, GPNMB, was previously reported to be upregulated in the substantia nigra of PD patients. We also compared the CSF proteomes of patients and controls. Proteome differences between GBA + patients and unaffected GBA + controls suggest degeneration of dopaminergic neurons, altered dopamine metabolism and increased brain inflammation. In the LRRK2 + subcohort we found dysregulated lysosomal degradation, altered alpha-synuclein processing, and neurotransmission. Proteome differences between idiopathic patients and controls suggest increased neuroinflammation, mitochondrial dysfunction/oxidative stress, altered iron metabolism and potential neuroprotection mediated by vasoactive substances. Finally, we used proteomic data to stratify idiopathic patients into “endotypes”. The identified endotypes show differences in cognitive and motor disease progression based on previously reported protein-based risk scores.Our findings not only contribute to the identification of new therapeutic targets but also to shape personalized medicine in CNS neurodegeneration.