Tissue Proteomics Research Articles

Enabling Global Analysis of Protein Citrullination via Biotin Thiol Tag-Assisted Mass Spectrometry.

Citrullination is a key post-translational modification (PTM) that affects protein structures and functions. Although it has been linked to various biological processes and disease pathogenesis, the underlying mechanism remains poorly understood due to a lack of effective tools to enrich, detect, and localize this PTM. Herein, we report the design and development of a biotin thiol tag that enables derivatization, enrichment, and confident identification of citrullination via mass spectrometry. We perform global mapping of the citrullination proteome of mouse tissues. In total, we identify 691 citrullination sites from 432 proteins which represents the largest data set to date. We discover novel distribution and functions of this PTM. This study depicts a landscape of protein citrullination and lays the foundation for further deciphering their physiological and pathological roles.

Effects of Malate Ringer's solution on myocardial injury in sepsis and enforcement effects of TPP@PAMAM-MR

BackgroundMyocardial dysfunction played a vital role in organ damage after sepsis. Fluid resuscitation was the essential treatment in which Lactate Ringer's solution (LR) was commonly used. Since LR easily led to hyperlactatemia, its resuscitation effect was limited. Malate Ringer's solution (MR) was a new resuscitation crystal liquid. Whether MR had a protective effect on myocardial injury in sepsis and the relevant mechanism need to be studied.MethodsThe cecal ligation and puncture (CLP) inducing septic model and lipopolysaccharide (LPS) stimulating cardiomyocytes were used, and the cardiac function, the morphology and function of mitochondria were observed. The protective mechanism of MR on myocardial injury was explored by proteomics. Then the effects of TPP@PAMAM-MR, which consisted of the mitochondria- targeting polymer embodied malic acid, was further observed.ResultsCompared with LR, MR resuscitation significantly prolonged survival time, improved the cardiac function, alleviated the damages of liver, kidney and lung following sepsis in rats. The proteomics of myocardial tissue showed that differently expressed proteins between MR and LR infusion involved oxidative phosphorylation, apoptosis. Further study found that MR decreased ROS, improved the mitochondrial morphology and function, and ultimately enhanced mitochondrial respiration and promoted ATP production. Moreover, MR infusion decreased the expression of apoptosis-related proteins and increased the expression of anti-apoptotic proteins. TPP@PAMAM@MA was a polymer formed by wrapping l-malic acid with poly amido amine (PAMAM) modified triphenylphosphine material. TPP@PAMAM-MR (TPP-MR), which was synthesized by replacing the l-malic acid of MR with TPP@PAMAM@MA, was more efficient in targeting myocardial mitochondria and was superior to MR in protecting the sepsis-inducing myocardial injury.ConclusionMR was suitable for protecting myocardial injury after sepsis. The mechanism was related to MR improving the function and morphology of cardiomyocyte mitochondria and inhibiting cardiomyocyte apoptosis. The protective effect of TPP-MR was superior to MR.

Proteomic Portrait of Human Lymphoma Reveals Protein Molecular Fingerprint of Disease Specific Subtypes and Progression.

The online version contains supplementary material available at 10.1007/s43657-022-00075-w.

Protein regulation mechanism of cold tolerance in Haemaphysalis longicornis.

Ticks are external parasitic arthropods that can transmit a variety of pathogens by sucking blood. Low-temperature tolerance is essential for ticks to survive during the cold winter. Exploring the protein regulation mechanism of low-temperature tolerance of Haemaphysalis longicornis could help to explain how ticks survive in winter. In this study, the quantitative proteomics of several tissues of H. longicornis exposed to low temperature were studied by data independent acquisition technology. Totals of 3 699, 3 422, and 1 958 proteins were identified in the salivary gland, midgut, and ovary, respectively. The proteins involved in energy metabolism, cell signal transduction, protein synthesis and repair, and cytoskeleton synthesis changed under low-temperature stress. The comprehensive analysis of the protein regulation of multiple tissues of female ticks exposed to low temperature showed that maintaining cell homeostasis, maintaining cell viability, and enhancing cell tolerance were the most important means for ticks to maintain vital signs under low temperature. The expression of proteins involved in and regulating the above cell activities was the key to the survival of ticks under low temperatures. Through the analysis of a large amount of data, we found that the expression levels of arylamine N-acetyltransferase, inositol polyphosphate multikinase, and dual-specificity phosphatase were up-regulated under low temperature. We speculated that they might have important significance in low-temperature tolerance. Then, we performed RNA interference on the mRNA of these 3 proteins, and the results showed that the ability of female ticks to tolerate low temperatures decreased significantly.

Hippo-released WWC1 facilitates AMPA receptor regulatory complexes for hippocampal learning.

Learning and memory rely on changes in postsynaptic glutamergic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type receptor (AMPAR) number, spatial organization, and function. The Hippo pathway component WW and C2 domain-containing protein 1 (WWC1) regulates AMPAR surface expression and impacts on memory performance. However, synaptic binding partners of WWC1 and its hierarchical position in AMPAR complexes are largely unclear. Using cell-surface proteomics in hippocampal tissue of Wwc1-deficient mice and by generating a hippocampus-specific interactome, we show that WWC1 is a major regulatory platform in AMPAR signaling networks. Under basal conditions, the Hippo pathway members WWC1 and large tumor-suppressor kinase (LATS) are associated, which might prevent WWC1 effects on synaptic proteins. Reduction of WWC1/LATS binding through a point mutation at WWC1 elevates the abundanceof WWC1 in AMPAR complexes and improves hippocampal-dependent learning and memory. Thus, uncoupling of WWC1 from the Hippo pathway to AMPAR-regulatory complexes provides an innovative strategy to enhance synaptic transmission.

Prediction of Pathogenesis and Potential Therapeutic Targets for Asthma Based on Proteomics of Mouse Lung Tissue

Objective To predict the mechanism and potential therapeutic targets of asthma based on proteomic analysis and network pharmacology.Methods The mouse model of asthma was established via intraperitoneal injection of 200 μl suspension containing 100 μg ovalbumin(OVA)and 2 mg aluminum hydroxide and intranasal administration with 5% OVA.Maxquant system was used to retrieve the protein and gene data.The analysis of variance and t test were performed to obtain differential proteins,and then clustering map and target set of differential proteins were established.The protein-protein interaction network of differential proteins was constructed.The pathogenesis of asthma was investigated via gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis.Results A total of 5063 genes were identified,from which 904 differentially expressed genes were selected with the thresholds of fold change(model/control)≥2 and P≤0.05 as well as thresholds of fold change(model/control)≤1/2 and P≤0.05.The 904 genes were classified into 3 clusters.The 904 differentially expressed genes included 595 up-regulated genes and 309 down-regulated genes in the model group compared with the control group.The pathogenesis of asthma was associated with regulatory metabolism,Fc gamma-R mediated phagocytosis,leukocyte transendothelial migration,tumor necrosis factor signaling pathway,Toll-like receptor signaling pathway,B cell receptor signaling pathway,phosphoinositol 3-kinase/protein kinase B signaling pathway,vascular smooth muscle contraction and cell adhesion signaling pathway.ITGB3,CYBB,SYK,VWF,ITGB2,MYD88,COMP,VEGFA,and FCGR2B were identified as the therapeutic targets for asthma.Meanwhile,the biological processes such as signal transduction,redox process,immune response,inflammatory response,cell adhesion,positive regulation of GTPase activity,apoptosis,and extracellular matrix formation were the main participants in asthma.Conclusion This study systematically revealed the pathogenesis,biological processes,and 9 potential therapeutic targets of asthma.

Toward structural-omics of the bovine retinal pigment epithelium

The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.

A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes.

We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.

Simultaneous solving high-resolution structures of various enzymes from human kidney microsomes.

The ability to investigate tissues and organs through an integrated systems biology approach has been thought to be unobtainable in the field of structural biology, where the techniques mainly focus on a particular biomacromolecule of interest. Here we report the use of cryo-electron microscopy (cryo-EM) to define the composition of a raw human kidney microsomal lysate. We simultaneously identify and solve cryo-EM structures of four distinct kidney enzymes whose functions have been linked to protein biosynthesis and quality control, biosynthesis of retinoic acid, gluconeogenesis and glycolysis, and the regulation and metabolism of amino acids. Interestingly, all four of these enzymes are directly linked to cellular processes that, when disrupted, can contribute to the onset and progression of diabetes. This work underscores the potential of cryo-EM to facilitate tissue and organ proteomics at the atomic level.

Susceptibility of Rice Crop to Salt Threat: Proteomic, Metabolomic, and Physiological Inspections.

Rice is a staple food crop worldwide; however, salinity stress is estimated to reduce its global production by 50%. Knowledge about initial molecular signaling and proteins associated with sensing salinity among crop plants is limited. We characterized early salt effects on the proteome and metabolome of rice tissues. Omics results were validated by western blotting and multiple reaction monitoring assays and integrated with physiological changes. We identified 8160 proteins and 2045 metabolites in rice tissues. Numerous signaling pathways were induced rapidly or partially by salinity. Combined data showed the most susceptible proteins or metabolites in each pathway that likely affected the sensitivity of rice to salinity, such as PLA1, BON3 (involved in sensing stress), SnRK2, pro-resilin, GDT1, G-proteins, calmodulin activators (Ca2+ and abscisic acid signaling), MAPK3/5, MAPKK1/3 (MAPK pathway), SOS1, ABC F/D, PIP2-7, and K+ transporter-23 (transporters), OPR1, JAR1, COL1, ABA2, and MAPKK3 (phytohormones). Additionally, our results expanded the stress-sensing function of receptor-like kinases, phosphatidylinositols, and Na+ sensing proteins (IPUT1). Combined analyses revealed the most sensitive components of signaling pathways causing salt-susceptibility in rice and suggested potential targets for crop improvement.

Brain Tissue-Derived Extracellular Vesicles in Alzheimer's Disease Display Altered Key Protein Levels Including Cell Type-Specific Markers.

Brain tissue-derived extracellular vesicles (bdEVs) play neurodegenerative and protective roles, including in Alzheimer's disease (AD). Extracellular vesicles (EVs) may also leave the brain to betray the state of the CNS in the periphery. Only a few studies have profiled the proteome of bdEVs and source brain tissue. Additionally, studies focusing on bdEV cell type-specific surface markers are rare. We aimed to reveal the pathological mechanisms inside the brain by profiling the tissue and bdEV proteomes in AD patients. In addition, to indicate targets for capturing and molecular profiling of bdEVs in the periphery, CNS cell-specific markers were profiled on the intact bdEV surface. bdEVs were separated and followed by EV counting and sizing. Brain tissue and bdEVs from age-matched AD patients and controls were then proteomically profiled. Total tau (t-tau), phosphorylated tau (p-tau), and antioxidant peroxiredoxins (PRDX) 1 and 6 were measured by immunoassay in an independent bdEV separation. Neuron, microglia, astrocyte, and endothelia markers were detected on intact EVs by multiplexed ELISA. Overall, concentration of recovered bdEVs was not affected by AD. Proteome differences between AD and control were more pronounced for bdEVs than for brain tissue. Levels of t-tau, p-tau, PRDX1, and PRDX6 were significantly elevated in AD bdEVs compared with controls. Release of certain cell-specific bdEV markers was increased in AD. Several bdEV proteins are involved in AD mechanisms and may be used for disease monitoring. The identified CNS cell markers may be useful tools for peripheral bdEV capture.

Two-Dye Versus Three-Dye DIGE for Comparative Testis Tissue Proteomic Analysis.

The global analysis of the proteome is an important tool in cell biology. Comparative proteomic evaluations can identify and compare the composition, dynamics, and modifications between different samples. Comparing tissue proteomes under different conditions is crucial for advancing the biomedical field. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a sensitive and robust biochemical method that can compare multiple protein samples over a broad dynamic range on the same analytical gel and can be used to establish differentially expressed protein profiles between different sample groups. 2D-DIGE involves fluorescently labeling protein samples with CyDye flours, via a two-dye or a three-dye system, pre-separation by isoelectric point, and molecular weight. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization, thus enabling accurate high-resolution analysis of differences in protein abundance between samples. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of two-dye and three-dye DIGE minimal labeling.

A modest change in housing temperature alters whole body energy expenditure and adipocyte thermogenic capacity in mice.

Typical vivarium temperatures (20-26°C) induce facultative thermogenesis in mice, a process attributable in part to uncoupling protein-1 (UCP1). The impact of modest changes in housing temperature on whole body and adipose tissue energetics in mice remains unclear. Here, we determined the effects of transitioning mice from 24°C to 30°C on total energy expenditure and adipose tissue protein signatures. C57BL/6J mice were housed at 24°C for 2 wk and then either remained at 24°C (n = 16/group, 8M/8F) or were transitioned to 30°C (n = 16/group, 8M/8F) for 4 wk. Total energy expenditure and its components were determined by indirect calorimetry. Interscapular brown adipose tissue (iBAT) and inguinal white adipose tissue (iWAT) proteins were quantified by Western blot and quantitative proteomics. Transitioning from 24°C to 30°C reduced total energy expenditure in both male (-25%) and female (-16%) mice, which was attributable to lower basal energy expenditure in males (-36%) and females (-40%). Total iBAT UCP1 protein content was 50% lower at 30°C compared with 24°C, whereas iWAT UCP1 protein content was similar between conditions. iBAT UCP1 protein content remained 20-fold greater than iWAT at 30°C. In iBAT and iWAT, 183 and 41 proteins were differentially expressed between 24°C and 30°C, respectively. iWAT proteins (257) differentially expressed between sexes at 30°C were not differentially expressed at 24°C. Thus, 30°C housing lowers total energy expenditure of mice when compared with an ambient temperature (24°C) that falls within the National Research Council's guidelines for housing laboratory mice. Lower iBAT UCP1 content accompanied chronic housing at 30°C. Furthermore, housing temperature influences sexual dimorphism in the iWAT proteome. These data have implications regarding the optimization of preclinical models of human disease.NEW & NOTEWORTHY Housing mice at 30°C reduced the basal and total energy expenditure compared with 24°C, which was accompanied by a reduction in brown adipose tissue UCP1 content. Proteomic profiling demonstrated the brown adipose tissue and white adipose tissue proteomes were largely influenced by housing temperature and sex, respectively. Therefore, 30°C housing revealed sexual dimorphism in the white adipose tissue proteome that was largely absent in animals housed at 24°C.

Meat Quality and Muscle Tissue Proteome of Crossbred Bulls Finished under Feedlot Using Wet Distiller Grains By-Product

Wet distiller grains (WDG) are a corn by-product rich in protein and fiber that can be used in feedlot diets. This study evaluated F1 Angus-Nellore bulls fed on a control diet vs. WDG (n = 25/treatment). After a period of 129 days on these feeds, the animals were slaughtered and Longissimus thoracis samples were collected for both a meat quality evaluation and gel-based proteomic analyses. A greater ribeye area (99.47 cm²) and higher carcass weight (333.6 kg) (p < 0.05) were observed in the WDG-finished cattle compared to the control (80.7 cm²; 306.3 kg). Furthermore, there were differences (p < 0.05) in the intramuscular fat between the WDG and control animals (IMF = 2.77 vs. 4.19%), which led to a significant decrease (p < 0.05) in saturated fatty acids (FA). However, no differences (p > 0.10) were observed in terms of tenderness, evaluated using Warner–Bratzler shear force (WBSF). The proteomic and bioinformatic analyses revealed substantial changes in the biological processes, molecular functions, and cellular components of the WDG-finished cattle compared to the control. Proteins related to a myriad of interconnected pathways, such as contractile and structural pathways, energy metabolism, oxidative stress and cell redox homeostasis, and transport and signaling. In this experiment, the use of WDG supplementation influenced the protein expression of several proteins, some of which are known biomarkers of beef quality (tenderness and color), as well as the protein–protein interactions that can act as the origins of increases in muscle growth and reductions in IMF deposition. However, despite the effects on the proteome, the tenderness, evaluated by WBSF, and fatty acid profile were not compromised by WDG supplementation.

Key hepatic signatures of human and mouse nonalcoholic steatohepatitis: A transcriptome-proteome data meta-analysis.

BackgroundDespite the global prevalence of nonalcoholic fatty liver disease (NAFLD), its pathophysiology remains unclear. In this study, we established highly confident nonalcoholic steatohepatitis (NASH) gene signatures and evaluated the pathological mechanisms underlying NASH through a systematic meta-analysis of transcriptome and proteome datasets obtained from NASH patients and mouse models.MethodsWe analyzed NASH transcriptome datasets from 539 patients and 99 mice. A whole-liver tissue proteome dataset was used to confirm the protein level dysregulation of NASH signatures significant in both humans and mice.ResultsIn total, 254 human and 1,917 mouse NASH gene signatures were established. Up-regulated genes of 254 human signatures were associated with inflammation, steatosis, apoptosis, and extracellular matrix organization, whereas down-regulated genes were associated with response to metal ions and lipid and amino acid metabolism. When different mouse models were compared against humans, models with high fat and high fructose diet most closely resembled the genetic features of human NAFLD. Cross-species analysis revealed 66 genes that were concordantly dysregulated between human and mouse NASH. Among these, 14 genes were further validated to be dysregulated at the protein level. The resulting 14 genes included some of the well-established NASH associated genes and a promising NASH drug target. Functional enrichment analysis revealed that dysregulation of amino acid metabolism was the most significant hepatic perturbation in both human and mouse NASH.ConclusionsWe established the most comprehensive hepatic gene signatures for NASH in humans and mice to date. To the best of our knowledge, this is the first study to collectively analyze the common signatures between human and mouse NASH on a transcriptome–proteome scale.

Tissue proteome analysis revealed an association between cancer, immune system response, and the idiopathic granulomatous mastitis.

Idiopathic Granulomatous Mastitis (IGM) is a disease that clinically mimics breast cancers with symptoms of pain, edema, erythema, nipple discharge, nipple retraction, and fistula. Although IGM is considered to be formed by autoimmune responses or infections, the molecular mechanism behind formation and progress is unknown. Therefore, in this study, we aimed to investigate molecular mechanisms underlying IGM formation, progress, and recurrence by monitoring the changes at the proteome level. Protein extracts prepared from IGM (n = 15) and within-control tissues (n = 15) were subjected to nHPLC followed by LC-MS/MS proteomic analysis. Label-free quantitation analysis revealed that sixty differentially regulated between the two groups. Those proteins were classified based on their role in metabolic pathways using bioinformatics tools. Based on DAVID analysis, 16 of the differently regulated proteins were associated with the immune system, while 17 proteins were involved in cancer metabolism. STRING analysis showed that five of the differentially regulated proteins were associated with combined immune deficiency which were PNP, TAP1, ITGAL, PRKDC, and PTPRC while the other proteins were involved in insulin response and neutrophil degranulation. This study is one of the very few studies that investigated the changes in protein expressions of IGM tissues compared to controls. For the first time, we have shown the relationship of IGM with the immune system at the protein level and also underlined the cancer-like behavior of the disease. Furthermore, the proteins that were pointed out as combined immune deficiency-related proteins may have value as diagnostic markers for idiopathic granulomatous mastitis although further studies are needed to shed more light on the pathogenesis of the disease.

Acetylation and phosphorylation changes to cardiac proteins in experimental HFpEF due to metabolic risk reveal targets for treatment

AimsDespite the high prevalence of heart failure with preserved ejection fraction (HFpEF), the pathomechanisms remain elusive and specific therapy is lacking. Disease-causing factors include metabolic risk, notably obesity. However, proteomic changes in HFpEF are poorly understood, hampering therapeutic strategies. We sought to elucidate how metabolic syndrome affects cardiac protein expression, phosphorylation and acetylation in the Zucker diabetic fatty/Spontaneously hypertensive heart failure F1 (ZSF1) rat HFpEF model, and to evaluate changes regarding their potential for treatment. Main methodsZSF1 obese and lean rats were fed a Purina diet up to the onset of HFpEF in the obese animals. We quantified the proteome, phosphoproteome and acetylome of ZSF1 obese versus lean heart tissues by mass spectrometry and singled out targets for site-specific evaluation. Key findingsThe acetylome of ZSF1 obese versus lean hearts was more severely altered (21 % of proteins changed) than the phosphoproteome (9 %) or proteome (3 %). Proteomic alterations, confirmed by immunoblotting, indicated low-grade systemic inflammation and endothelial remodeling in obese hearts, but low nitric oxide-dependent oxidative/nitrosative stress. Altered acetylation in ZSF1 obese hearts mainly affected pathways important for metabolism, energy production and mechanical function, including hypo-acetylation of mechanical proteins but hyper-acetylation of proteins regulating fatty acid metabolism. Hypo-acetylation and hypo-phosphorylation of elastic titin in ZSF1 obese hearts could explain myocardial stiffening. SignificanceCardiometabolic syndrome alters posttranslational modifications, notably acetylation, in experimental HFpEF. Pathway changes implicate a HFpEF signature of low-grade inflammation, endothelial dysfunction, metabolic and mechanical impairment, and suggest titin stiffness and mitochondrial metabolism as promising therapeutic targets.

Roles of Exosomes in Chronic Rhinosinusitis: A Systematic Review.

The pathophysiology of chronic rhinosinusitis (CRS) is multifactorial and not entirely clear. The objective of the review was to examine the current state of knowledge concerning the role of exosomes in CRS. For this systematic review, we searched PubMed/MEDLINE, Scopus, CENTRAL, and Web of Science databases for studies published until 7 August 2022. Only original research articles describing studies published in English were included. Reviews, book chapters, case studies, conference papers, and opinions were excluded. The quality of the evidence was assessed with the modified Office and Health Assessment and Translation (OHAT) Risk of Bias Rating Tool for Human and Animal Studies. Of 250 records identified, 17 were eligible, all of which had a low to moderate risk of overall bias. Presented findings indicate that exosomal biomarkers, including proteins and microRNA, act as promising biomarkers in the diagnostics and prognosis of CRS patients and, in addition, may contribute to finding novel therapeutic targets. Exosomes reflecting tissue proteomes are excellent, highly available material for studying proteomic alterations noninvasively. The first steps have already been taken, but more advanced research on nasal exosomes is needed, which might open a wider door for individualized medicine in CRS.

A multi‑omics study of diagnostic markers and the unique inflammatory tumor micro‑environment involved in tuberous sclerosis complex‑related renal angiomyolipoma.

Tuberous sclerosis complex (TSC) is a rare disease that threatens multiple organs in the human body. TSC-associated renal angiomyolipoma (TSC-RAML) has potentially life-threatening complications and a generally poor prognosis. The present study aimed to find plasma proteomic diagnostics and disease-associated markers, and explore the tumor microenvironment using multi-omics. To achieve this goal, the plasma proteomics as well as tissue proteomics, bulk and single-cell RNA transcriptome from patients with TSC-RAML were examined and analyzed. The results suggested that plasma proteins such as MMP9 and C-C motif chemokine ligand 5 were able to differentiate TSC-RAML from sporadic angiomyolipoma and renal cyst. A correlation analysis revealed that plasma proteomics were associated with lymphangioleiomyomatosis, TSC-RAML grading and whole-body disease burden. Tissue proteomics of participants with TSC-RAML revealed disturbed small molecule catabolic process, mitochondrial matrix component and actin binding function. Bulk and single-cell RNA sequencing suggested a greater number of tumor-like cells, fibroblasts and mono-nuclear macrophages within the tumor microenvironment. The above results indicated that TSC-RAML exhibited a characteristic and disease-associated plasma proteomic profile. The unique microenvironment, made up of fibroblasts and mono-macrophages, may promote tumorigenesis and TSC-RAML progression.

Abstract A009: Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development

Abstract Background: Rhabdomyosarcoma (RMS) has a high unmet need in terms of precision therapy development as there are currently no approved immunotherapies or targeted therapies, and few in the developmental pipeline. Here we sought to identify cell surface oncoproteins as a target for novel RMS-directed immunotherapies. Methods: We first performed plasma membrane enrichment followed by mass spectrometry to define the cell surface landscape of 7 fusion(+) and 14 fusion(-) RMS patient-derived xenograft (PDX) models. The surfaceome data was filtered to only “high confidence” surface proteins by querying protein localization databases, Compartments (https://compartments.jensenlab.org/) and CIRFESS (https://gundrylab.shinyapps.io/cirfess/). We then developed a prioritization algorithm that uses a rank-product approach to score surface proteins. The input to the algorithm is a matrix that integrates multiple datasets to score the surface proteins based on their suitability to be an optimal immunotherapeutic target. In addition to the surfaceome data generated here, we also integrated matched RNA-sequencing data from eleven of the RMS PDX models, RNA-sequencing data from GTEx (n=15,253) and a recently developed normal tissue proteomics dataset (n=201) [Jiang. Cell. 2020], a list from Gene Ontology that included genes involved in muscle development pathways, and the gene dependency list for RMS in DepMap (https://depmap.org/portal/). Results: A total of 913 and 937 high confidence surface proteins were annotated from the mass spectrometry data for fusion(+) and fusion(−) samples, respectively. A dendrogram separated the surface protein profiles into two clusters based on fusion(+) and fusion(−) RMS subtypes, thus the algorithm was run separately on each subtype. Within the top 50% of prioritized targets, 88% and 86% of the targets overlapped and 12% and 14% were identified exclusively in fusion(+) and fusion(−) subtypes, respectively. ALK, a previously putative protein marker in fusion(+) RMS, scored in the top 10% of the fusion(+) targets based on the algorithm, and surprisingly we saw abundant ALK expression in 6/14 fusion(−) PDX samples. MEGF10, a novel target, was ranked as the top target for both fusion(+) and fusion(−) RMS. MEGF10 plays a role in cell adhesion, motility, and proliferation. It scored as a significant dependency in DepMap for RMS (p-value=0.0002). Based on RNA-sequencing and proteomics, MEGF10 shows no expression in most healthy tissues surveyed, with several orders of magnitude lower expression detected in RNASeq in muscle and brain tissue, but not in the proteomic datasets. Conclusion: Here, we defined the surfaceome of RMS, and found substantial overlap in surface proteins between fusion(+) and fusion(−) RMS subtypes. We validated previous observations that ALK is expressed in RMS, here verifying that the protein is expressed on the plasma membrane. MEGF10 appears to be a strong novel candidate target for RMS immunotherapies, and ongoing work to validate our proteogenomic findings will be reported. Citation Format: Rawan Shraim, Amber K. Weiner, Karina L. Conkrite, Alexander B. Radaoui, John M. Maris, Yael P. Mosse, Sharon J. Diskin, Ahmet Sacan, Benjamin A. Garcia, Peter J. Houghton, Raushan T. Kurmasheva, Poul Sorensen, Gregg B. Morin, Brian Mooney. Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A009.