Label-free Protein Quantification Research Articles

Transcriptomics coupled with proteomics reveals osimertinib-induced myocardial mitochondrial dysfunction

Osimertinib, an irreversible epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) used for cancer treatment, can cause significant cardiac toxicity. However, the specific mechanism of osimertinib-induced cardiotoxicity is not fully understood. In this study, we administered osimertinib to mice and neonatal rat ventricular myocytes (NRVMs). We observed significant structural and functional damage to the hearts of these mice, along with a marked increase in cardiac injury biomarkers and accompanying ultrastructural damage to mitochondria. We integrated 4D label-free protein quantification and RNA-Seq methods to analyze the sequencing data of NRVMs under osimertinib treatment (0 and 2.5 μM). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis evidenced that differentially expressed genes (DEGs)and differentially expressed proteins (DEPs) were distinctly enriched for oxidative phosphorylation (OXPHOs). Simultaneously, osimertinib primarily affected the contents of adenosine triphosphate (ATP). Further investigations revealed that osimertinib disrupts the functions of the ATP synthase (complex V), leading to a reduction in ATP production. Taken together, our data demonstrated that osimertinib causes mitochondrial dysfunction, which in turn leads to the onset of cardiac toxicity.

TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes.

Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribosome activity. Dual luciferase reporter assays were used to assess ribosomal modus. Ribosomal RNA expression and processing were determined by RT-qPCR, while RiboMethSeq and HydraPsiSeq were used to determine rRNA modification profiles. Label-free protein quantification of total cell lysates, isolated ribosomes and secreted proteins was done by LC-MS/MS. A three-day TGF-β2 stimulation induced total protein synthesis in SW1353 chondrocytic cells and human articular chondrocytes. Specifically, TGF-β2 induced cap-mediated protein synthesis, while IRES-mediated translation was not (P53 IRES) or little affected (CrPv IGR and HCV IRES). Three rRNA post-transcriptional modifications (PTMs) were affected by TGF-β2 stimulation (18S-Gm1447 downregulated, 18S-ψ1177 and 28S-ψ4598 upregulated). Proteomic analysis of isolated ribosomes revealed increased interaction with eIF2 and tRNA ligases and decreased association of eIF4A3 and heterogeneous nuclear ribonucleoprotein (HNRNP)s. In addition, thirteen core ribosomal proteins were more present in ribosomes from TGF-β2 stimulated cells, albeit with a modest fold change. A prolonged stimulation of chondrocytic cells with TGF-β2 induced ribosome activity and changed the mode of translation. These functional changes could be coupled to alterations in accessory proteins in the ribosomal proteome.

VPBrowse: Genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins.

SWATH is a data acquisition strategy acclaimed for generating quantitatively accurate and consistent measurements of proteins across multiple samples. Its utility for proteomics studies in nonlaboratory animals, however, is currently compromised by the lack of sufficiently comprehensive and reliable public libraries, either experimental or predicted, and relevant platforms that support their sharing and utilization in an intuitive manner. Here we describe the development of the Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), an on-line platform for genome-based representation of the Bos taurus proteome, which is equipped with an interactive database and tools for searching, visualization, and building quantitative mass spectrometry assays. In its current version (VPBrowse 1.0), it contains high-quality fragmentation spectra acquired on QToF instrument for over 36,000 proteotypic peptides, the experimental evidence for over 10,000 proteins. Data can be downloaded in different formats to enable analysis using popular software packages for SWATH data processing whilst normalization to iRT scale ensures compatibility with diverse chromatography systems. When applied to published blood plasma dataset from the biomarker discovery study, the resource supported label-free quantification of additional proteins not reported by the authors previously including PSMA4, a tissue leakage protein and a promising candidate biomarker of animal's response to dehorning-related injury.

Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation.

To improve the coverage in bottom-up proteomics, S-aminoethylation of cysteine residues (AE-Cys) was carried out with 2-bromoethylamine, followed by cleavage with lysyl endopeptidase (Lys-C) or Lys-C/trypsin. A model study with bovine serum albumin showed that the C-terminal side of AE-Cys was successfully cleaved by Lys-C. The frequency of side reactions at amino acids other than Cys was less than that in the case of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts in the data-dependent acquisition mode after AE-Cys modification afforded a greater number of identified protein groups, especially membrane proteins. In addition, label-free quantification of proteins in mouse nonsmall cell lung cancer (NSCLC) tissue in the data-independent acquisition mode after AE-Cys modification showed improved NSCLC pathway coverage and greater reproducibility. Furthermore, the AE-Cys method could identify an epidermal growth factor receptor peptide containing the T790 M mutation site, a well-established lung-cancer-related mutation site that has evaded conventional bottom-up methods. Finally, AE-Cys was found to fully mimic Lys in terms of collision-induced dissociation fragmentation, ion mobility separation, and cleavage by Lys-C/trypsin, except for sulfoxide formation during sample preparation.

Comparison of lignocellulosic enzymes and CAZymes between ascomycetes (Trichoderma) and basidiomycetes (Ganoderma) species: a proteomic approach

Abstract Wood decomposing ascomycetes and basidiomycetes group of fungi are the most valuable microbes on the earth’s ecosystem that recycles the source of carbon; therefore, they are essential for the biorefinery industries. To understand the robustness of the enzymes and their metabolic pathways in the fungal system, label-free quantification of the total proteins was performed. The fungi showed a comparable quantity of protein abundance [Trichoderma citrinoviride (285), Thermoascus aurantiacus (206), Ganoderma lucidum MDU-7 (102), G. lucidum (242)]. Differentially regulated proteins of ascomycetes and basidiomycetes were analyzed, and their heatmap shows upregulated and downregulated proteins [25 differentially expressed proteins in T. citrinoviride (8.62 % up-regulated and 91.37 % down-regulated) and G. lucidum (5.74 % up-regulated and 94.25 % down-regulated)] by using the normalized peptide-spectrum match (PSMs) and log2fold change. These proteins were similarly matched to the carbohydrate active enzymes family (CAZymes) like glycoside hydrolase (GH family), carbohydrate-binding module (CBM family) with auxiliary activities, and also involved in the hydrolysis of carbohydrate, lignin, xylan, polysaccharides, peptides, and oxido-reductase activity that helps in antioxidant defense mechanism. The lignocellulolytic enzymes from two different divisions of fungi and proteomics studies gave a better understanding of carbon recycling and multi-product lignocellulosic biorefinery processes.

Collision Induced Unfolding Enables the Quantitation of Isomass Biotherapeutics in Complex Biological Matrices.

Quantitative mass spectrometry has been widely used to evaluate the concentrations of molecules within a variety of biological matrices. Typically, such quantitative mass spectrometry analyses are predicated upon the production of mass-resolved precursor or fragment ions, leading to challenges surrounding the quantification of isomeric or conformationally distinct analytes. As such, new approaches are required for the label-free quantification of isomass proteins. Native ion-mobility MS (nIM-MS) in combination with collision induced unfolding (CIU) is a potentially enabling approach for such quantitative mass spectrometry methods as the technique can rapidly separate and detect many biomacromolecule isoforms. CIU uses collisional activation to capture the unfolding trajectory of ions in the gas phase, producing different intermediate structures that can be leveraged to distinguish protein structures that exhibit identical sizes at lower energies. Here we describe the deployment of quantitative CIU methodology to measure the concentrations of isomass pairs of biotherapeutics and sequence homologues in both standard and biological matrices. Our results cover three antibody pairs and include examples of mixed therapies where multiple biologics are commonly provided to patients. In all cases, CIU enables the production of resolved features for each antibody mixture probed, producing calibration curves with correlation coefficients ranging from 0.92 to 0.99, limits of detection ranging from 300 to 5000 nM and sensitivities ranging from 8.7 × 10-5 nM-1 to 6 × 10-3 μM-1. We conclude our report by projecting the future utility of CIU-enabled quantitative MS methods.

Acetyl-Proteomic Profiling of Sorghum bicolor Seedlings after Chitin Treatment Reveals the Involvement of Acetylated Chlorophyll a/b Binding Proteins in the Innate Immune Response.

Plant pathogen-associated molecular pattern-triggered immunity (PTI) is affected by post-translational modifications, but the role of acetylation in the PTI responses of Sorghum bicolor remains unclear. In this study, a comprehensive acetyl-proteomic analysis was performed on sorghum seedlings treated with chitin based on label-free protein quantification. Chitin rapidly induced 15 PTI-related genes and 5 defense enzymes. Acetylation was upregulated in sorghum after the chitin treatment, and 579, 895, and 929 acetylated proteins, peptides, and sites, respectively, were identified using high-performance liquid chromatography-tandem mass spectrometry. Acetylation and expression of chlorophyll a/b binding proteins (Lhcs) were significantly upregulated, and they were localized in chloroplasts. Additionally, we found that the expression of Lhcs in vivo enhanced chitin-mediated acetylation. The findings of this study provide a comprehensive assessment of the lysine acetylome in sorghum and a foundation for future study into the regulatory mechanisms of acetylation during chlorophyll synthesis.

Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation

Hemolymph is the circulatory fluid that fills the body cavity of crustaceans, analogous to blood in vertebrates. Hemolymph coagulation, similar to blood clotting in vertebrates, plays a crucial role in wound healing and innate immune responses. Despite extensive studies on the clotting process in crustaceans, no comparative quantitative analysis of the protein composition of non-clotted and clotted hemolymph in any decapod has been reported. In this study, we used label-free protein quantification with high-resolution mass spectrometry to identify the proteomic profile of hemolymph in crayfish and quantify significant changes in protein abundances between non-clotted and clotted hemolymph. Our analysis identified a total of two-hundred and nineteen proteins in both hemolymph groups. Furthermore, we discussed the potential functions of the top most high and low-abundant proteins in hemolymph proteomic profile. The quantity of most of the proteins was not significantly changed during coagulation between non-clotted and clotted hemolymph, which may indicate that clotting proteins are likely pre-synthesized, allowing for a swift coagulation response to injury. Four proteins still showed abundance differences (p < 0.05, fold change>2), including C-type lectin domain-containing proteins, Laminin A chain, Tropomyosin, and Reverse transcriptase domain-containing proteins. While the first three proteins were down-regulated, the last one was up-regulated. The down-regulation of structural and cytoskeletal proteins may affect the process of hemocyte degranulation needed for coagulation, while the up-regulation of an immune-related protein might be attributed to the phagocytosis ability of viable hemocytes during coagulation.

Unraveling the Bombus terrestris Hemolymph, an Indicator of the Immune Response to Microbial Infections, through Complementary Mass Spectrometry Approaches

Pollinators, including Bombus terrestris, are crucial for maintaining biodiversity in ecosystems and for agriculture. Deciphering their immune response under stress conditions is a key issue for protecting these populations. To assess this metric, we analyzed the B. terrestris hemolymph as an indicator of their immune status. Hemolymph analysis was carried out using mass spectrometry, MALDI molecular mass fingerprinting was used for its effectiveness in assessing the immune status, and high-resolution mass spectrometry was used to measure the impact of experimental bacterial infections on the "hemoproteome". By infecting with three different types of bacteria, we observed that B. terrestris reacts in a specific way to bacterial attacks. Indeed, bacteria impact survival and stimulate an immune response in infected individuals, visible through changes in the molecular composition of their hemolymph. The characterization and label-free quantification of proteins involved in specific signaling pathways in bumble bees by bottom-up proteomics revealed differences in protein expression between the non-experimentally infected and the infected bees. Our results highlight the alteration of pathways involved in immune and defense reactions, stress, and energetic metabolism. Lastly, we developed molecular signatures reflecting the health status of B. terrestris to pave the way for diagnosis/prognosis tools in response to environmental stress.

New panel of biomarkers to discriminate between amelanotic and melanotic metastatic melanoma.

Melanoma is a form of skin cancer that can rapidly invade distant organs. A distinctive feature of melanomas is their pigmentation status, as melanin is present in most skin melanomas, whilst many metastatic tumors could become amelanotic. Besides the obvious malfunction of the key genes of the melanin pathway, the amelanotic tumors could bear a characteristic molecular signature accounting for their aggressivity. Using mass spectrometry-based proteomics we report here a distinctive panel of biomarkers for amelanotic aggressive melanoma that differ from the less invasive pigmented cells. The developed method allows the label-free quantification of proteins identified by LC-MS/MS analysis. We found a set of proteins comprising AHNAK, MYOF, ANXA1, CAPN2, ASPH, EPHA2, THBS1, TGM2, ACTN4 along with proteins involved in cell adhesion/migration (integrins, PLEC, FSCN1, FN1) that are highly expressed in amelanotic melanoma. Accompanying the down regulation of pigmentation specific proteins such as tyrosinase and TYRP1, these biomarkers are highly specific for a type of highly invasive melanoma. Interestingly, the LC-MS/MS proteomics analysis in hypoxia revealed that the abundance of this specific set of proteins found in normoxia was rather unaltered in these conditions. These biomarkers could therefore predict a metastatic behaviour for the amelanotic cells in the early stages of the tumor development and thus serve in melanoma prognostic. Applying this algorithm to related databases including melanoma samples published by independent laboratories/public databases we confirm the specificity of the newly found signatures. Overall, we begin to unravel the molecular alterations in the amelanotic melanoma and how basic proteomics offers insights into how to assess the clinical, pathological and misdiagnosis differences between the main subtypes of melanoma.

121 (PB111) - Systematic evaluation of label-free protein quantification pipelines in 12 mouse syngeneic models

Background: The widespread application of omics technologies in the past two decades has significantly expanded our knowledge of cancer biology. Proteins act as the link between genetic code and phenotype and can better reflect the dynamic state of a cell. With rapid advances in the field of proteomics, especially the label-free proteomics quantification technology powered by LC-MS/MS, it is now a routine to characterize and quantify thousands of proteins in tumor samples in a timely manner. Data-dependent acquisition (DDA) has been the workhorse for bottom-up proteomics within the past few years, however, it suffers from a high percentage of missing data originating from its stochastic nature.

Label-Free Quantification (LFQ) of Fecal Proteins for Potential Pregnancy Detection in Polar Bears.

Reliable pregnancy diagnostics would be beneficial for monitoring polar bear (Ursus maritimus) populations both in situ and ex situ, but currently there is no method of non-invasive pregnancy detection in this species. Recent reports in several carnivore species described the identification of fecal proteins that may serve as pregnancy biomarkers; however, repeatability has been limited. The objective of the current analysis was to utilize an unbiased, antibody-free, label-free method for the identification and quantification of fecal proteins to determine if differences associated with pregnancy are detectable in polar bears. Protein was extracted from fecal samples (n = 48) obtained from parturient (n = 6) and non-parturient (n = 6) profiles each at four timepoints: pre-breeding season, embryonic diapause, early placental pregnancy, and mid-placental pregnancy. Protein was prepared and analyzed on the Thermo Orbitrap Eclipse nanoLC-MS/MS system. A total of 312 proteins was identified and quantified; however, coefficients of variation (CV) were high for both abundance ratio variability (384.8 ± 61.0% SEM) and within group variability (86.8 ± 1.5%). Results of this study suggest that the inconsistencies in specific protein concentrations revealed previously by antibody-based assays may not be due to that methodology’s limitations, but rather, are reflective of true variation that exists among samples.

Label-Free Quantitative Proteomics Unravel the Impacts of Salt Stress on Dendrobium huoshanense.

Salt stress is a constraint on crop growth and productivity. When exposed to high salt stress, metabolic abnormalities that disrupt reactive oxygen species (ROS) homeostasis result in massive oxygen radical deposition. Dendrobium huoshanense is a perennial orchid herb that thrives in semi-shade conditions. Although lots of studies have been undertaken on abiotic stresses (high temperature, chilling, drought, etc.) of model plants, few studies were reported on the mechanism of salt stress in D. huoshanense. Using a label-free protein quantification method, a total of 2,002 differential expressed proteins were identified in D. huoshanense. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that proteins involved in vitamin B6 metabolism, photosynthesis, spliceosome, arginine biosynthesis, oxidative phosphorylation, and MAPK signaling were considerably enriched. Remarkably, six malate dehydrogenases (MDHs) were identified from deferentially expressed proteins. (NAD+)-dependent MDH may directly participate in the biosynthesis of malate in the nocturnal crassulacean acid metabolism (CAM) pathway. Additionally, peroxidases such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as antioxidant enzymes involved in glutathione biosynthesis and some vitamins biosynthesis were also identified. Taken together, these results provide a solid foundation for the investigation of the mechanism of salt stress in Dendrobium spp.

Decreased Contraction Rate, Altered Calcium Transients, and Increased Proliferation seen in Patient‐specific iPSC‐CMs Modeling Ebstein’s Anomaly and Left Ventricular Noncompaction

IntroductionPatients presenting with Ebstein’s anomaly (EA) have right heart dysfunction, mainly tricuspid valve insufficiency, and often manifest with left ventricular noncompaction (LVNC). Apart from a few sarcomeric variant associations, the genetic etiology and pathogenesis of combined EA/LVNC remain largely unknown. In a familial case where 10 of 17 members, including four fetal deaths, inherited EA/LVNC in an autosomal dominant pattern, we discovered a novel and damaging missense variant in the gene KLHL26 that segregates with disease. The KLHL26 (p.R237C) variant comprises an altered electrostatic surface profile, likely decoupling the CUL3‐interactome and altering protein turnover.ObjectiveOur in vitro patient‐specific studies enable the discovery of EA/LVNC developmental pathways and possibly related forms of heart failure and cardiomyopathy that may inform early clinical interventions and improve long‐term patient outcomes.HypothesisWe hypothesize that the KLHL26 variant is etiologic for this familial EA/LVNC case.MethodsWe differentiated a family trio (a heart‐healthy daughter and EA/LVNC‐affected mother and daughter) of induced pluripotent stem cells into cardiomyocytes (iPSC‐CMs) in a blinded manner on three iPSC clones per subject. Using flow cytometry, immunofluorescence, and biomechanical, electrophysiological, and automated contraction methods, we investigated iPSC‐CM differentiation efficiency between D10‐20, contractile properties and cell cycle regulation at D20, and sarcomere organization at D60. We further conducted differential analyses following label‐free protein and RNA‐Seq quantification at D20. Via CRISPR‐Cas9 gene editing, we plan to characterize KLHL26 variant‐specific iPSC‐CM alterations and connect findings to discoveries from patient‐specific studies.ResultsAll iPSC lines differentiated into CMs with an increased percentage of cTnT+ cells in the affected daughter line. In comparison to the unaffected, affected iPSC‐CMs had fewer contractions per minute and altered calcium transients, mainly a higher amount of total calcium release, faster rate of rise and faster rate of fall. The affected daughter line further had shorter shortening and relaxation times, higher proliferation, lower apoptosis, and a smaller cell surface area per nucleus. The affected mother line trended in a similar direction to the affected daughter line. There were no gross differences in sarcomere organization between the lines. We also discovered differential expression of candidate proteins such as kinase VRK1 and collagen COL5A1 from proteomic profiling.DiscussionThese discoveries suggest that EA/LVNC characteristics or pathogenesis may result from decreased contractile ability, altered calcium transients, and cell cycle dysregulation. Through CRISPR‐Cas9 correction and introduction of the KLHL26 variant in the daughter lines, we will build upon this understanding to inform exploration of critical clinical targets for EA/LVNC and related forms of cardiomyopathy and heart failure.

Plasma Proteome of Brain-Dead Organ Donors as a Predictor of Graft-Related Outcomes After Heart Transplantation

<h3>Purpose</h3> Most solid organ transplantations are performed using organs from brain-dead donors. The inflammatory, cardiovascular, hormonal, and metabolic changes related to brain death may affect the quality of the transplanted organs and expose the recipients to pathological changes. We aimed to systemically characterize the plasma proteome of brain-dead heart transplant donors and to search for donor plasma proteins that would be related to graft-related outcome. <h3>Methods</h3> Plasma samples from 53 human brain-dead donors were analyzed by label-free protein quantification using high-definition mass spectrometry. Uni-and multivariate analyses were applied to determine potential proteome differences between brain-dead donors and healthy controls (n=24), and the enriched biological pathways were analyzed. Individual donor protein levels were correlated with clinical transplant outcomes, and predictive donor scores using the significant proteins were constructed. <h3>Results</h3> Uni-and multivariate analyses revealed that brain-dead donors have a distinct plasma proteome, with the levels of 237 of 463 proteins being changed compared to healthy controls. Significant pathways included upregulated coagulation, gluconeogenesis and glycolysis, and downregulated complement, LXR/RXR and production of nitric oxide and reactive oxygen species in macrophages. Lysine-specific demethylase 3A was moderately correlated with any grade and severe PGD in point-biserial correlation. Myosin Va and proteasome activator complex subunit 2 were significantly associated with acute rejections with hemodynamic compromise within 30 days in univariate and multivariate Cox regression analyses. Furthermore, lysine-specific demethylase 3A and moesin were associated with worse graft-related 1-year survival in univariate analysis. <h3>Conclusion</h3> Our detailed analysis revealed that brain death significantly altered plasma proteome. We further discovered altered donor protein signatures that are related to pathological changes such as cardiomyocyte and endothelial dysfunction, inflammation, and vascular growth and arteriogenesis, and correlate with clinical post-transplant outcomes. The current study can be leveraged to discover predictive donor protein signatures in future cohorts, which may lead to biomarker discovery for better donor organ evaluation.

371 Decreased Contraction Rate, Altered Calcium Transients, and Increased Proliferation seen in Patient-specific iPSC-CMs Modeling Ebsteins Anomaly and Left Ventricular Noncompaction

OBJECTIVES/GOALS: In a familial case where 10 of 17 members inherited EA/LVNC in an autosomal dominant pattern, we discovered a novel, damaging missense variant in the gene KLHL26 that segregates with disease and comprises an altered electrostatic surface profile, likely decoupling the CUL3-interactome. We hypothesize that this KLHL26 variant is etiologic of EA/LVNC. METHODS/STUDY POPULATION: We differentiated a family trio (a heart-healthy daughter and EA/LVNC-affected mother and daughter) of induced pluripotent stem cells into cardiomyocytes (iPSC-CMs) in a blinded manner on three iPSC clones per subject. Using flow cytometry, immunofluorescence, and biomechanical, electrophysiological, and automated contraction methods, we investigated iPSC-CM differentiation efficiency between D10-20, contractility analysis and cell cycle regulation at D20, and sarcomere organization at D60. We further conducted differential analyses following label-free protein and RNA-Seq quantification at D20. Via CRISPR-Cas9 gene editing, we plan to characterize KLHL26 variant-specific iPSC-CM alterations and connect findings to discoveries from patient-specific studies. RESULTS/ANTICIPATED RESULTS: All iPSC lines differentiated into CMs with an increased percentage of cTnT+ cells in the affected daughter line. In comparison to the unaffected, affected iPSC-CMs had fewer contractions per minute and altered calcium transients, mainly a higher amount of total calcium release, faster rate of rise and faster rate of fall. The affected daughter line further had shorter shortening and relaxation times, higher proliferation, lower apoptosis, and a smaller cell surface area per cardiac nucleus. The affected mother line trended in a similar direction to the affected daughter line. There were no gross differences in sarcomere organization between the lines. We also discovered differential expression of candidate proteins such as kinase VRK1 and collagen COL5A1 from proteomic profiling. DISCUSSION/SIGNIFICANCE: These discoveries suggest that EA/LVNC characteristics or pathogenesis may result from decreased contractile ability, altered calcium transients, and cell cycle dysregulation. Through the KLHL26 variant correction and introduction in the daughter lines, we will build upon this understanding to inform exploration of critical clinical targets.

Spatiotemporal profiling of the bovine oviduct fluid proteome around the time of ovulation

Understanding the composition of the oviduct fluid (OF) is crucial to better comprehend the microenvironment in which sperm capacitation, fertilization and early embryo development take place. Therefore, our aim was to determine the spatiotemporal changes in the OF proteome according to the anatomical region of the oviduct (ampulla vs. isthmus), the proximity of the ovulating ovary (ipsilateral vs. contralateral side) and the peri-ovulatory stage (pre-ovulatory or Pre-ov vs. post-ovulatory or Post-ov). Oviducts from adult cyclic cows were collected at a local slaughterhouse and pools of OF were analyzed by nanoLC-MS/MS and label-free protein quantification (n = 32 OF pools for all region × stage × side conditions). A total of 3760 proteins were identified in the OF, of which 65% were predicted to be potentially secreted. The oviduct region was the major source of variation in protein abundance, followed by the proximity of the ovulating ovary and finally the peri-ovulatory stage. Differentially abundant proteins between regions, stages and sides were involved in a broad variety of biological functions, including protein binding, response to stress, cell-to-cell adhesion, calcium homeostasis and the immune system. This work highlights the dynamic regulation of oviduct secretions and provides new protein candidates for interactions between the maternal environment, the gametes and the early embryo.

Coupling suspension trapping-based sample preparation and data-independent acquisition mass spectrometry for sensitive exosomal proteomic analysis.

It has been a challenge to analyze minute amounts of proteomic samples in a facile and robust manner. Herein, we developed a quantitative proteomics workflow by integrating suspension trapping (S-Trap)-based sample preparation and label-free data-independent acquisition (DIA) mass spectrometry and then applied it for the analysis of microgram and even nanogram amounts of exosome samples. S-Trap-based sample preparation outperformed the traditional in-solution digestion-based approach and the commonly used filter-aided sample preparation (FASP)-based approach with regard to the number of proteins and peptides identified. Moreover, S-Trap-based sample preparation coupled with DIA mass spectrometry also showed the highest reproducibility for protein quantification. In addition, this approach allowed for identification and quantification of exosome proteins with low starting amounts (down to 50 ~ 200ng). Finally, the proposed method was successfully applied to label-free quantification of exosomal proteins extracted from MDA-MB-231 breast cancer cells and MCF-10A non-tumorigenic epithelial breast cells. Prospectively, we envision the integrated S-Trap sample preparation coupled with DIA quantification strategy as a promising alternative for highly efficient and sensitive analysis of trace amounts of proteomic samples (e.g., exosomal samples).

Integrative Transcriptomics and Proteomics Analyses to Reveal the Developmental Regulation of Metorchis orientalis: A Neglected Trematode With Potential Carcinogenic Implications.

Metorchis orientalis is a neglected zoonotic parasite of the gallbladder and bile duct of poultry, mammals, and humans. It has been widely reported in Asian, including China, Japanese, and Korea, where it is a potential threat to public health. Despite its significance as an animal and human pathogen, there are few published transcriptomic and proteomics data available. Transcriptome Illumina RNA sequencing and label-free protein quantification were performed to compare the gene and protein expression of adult and metacercariae-stage M. orientalis, resulting in 100,234 unigenes and 3,530 proteins. Of these, 13,823 differentially expressed genes and 1,445 differentially expressed proteins were identified in adult versus metacercariae. In total, 570 genes were differentially expressed consistent with the mRNA and protein level in the adult versus metacercariae stage. Differential gene transcription analyses revealed 34,228 genes to be expressed in both stages, whereas 66,006 genes showed stage-specific expression. Compared with adults, the metacercariae stage was highly transcriptional. GO and KEGG analyses based on transcriptome and proteome revealed numerous up-regulated genes in adult M. orientalis related to microtubule-based processes, microtubule motor activity, and nucleocytoplasmic transport. The up-regulated genes in metacercariae M. orientalis were mainly related to transmembrane receptor protein serine/threonine kinase activity, transmembrane receptor protein serine/threonine kinase signaling pathway. Transcriptome and proteome comparative analyses showed numerous up-regulated genes in adult stage were mainly enriched in actin filament capping, spectrin, and glucose metabolic process, while up-regulated genes in metacercariae stage were mainly related to cilium assembly, cilium movement, and motile cilium. These results highlight changes in protein and gene functions during the development of metacercariae into adults, and provided evidence for the mechanisms involved in morphological and metabolic changes at both the protein and gene levels. Interestingly, many genes had been proved associated with liver fibrosis and carcinogenic factors were identified highly expressed in adult M. orientalis, which suggests that M. orientalis is a neglected trematode with potential carcinogenic implications. These data provide attractive targets for the development of therapeutic or diagnostic interventions for controlling M. orientalis.

Plasma proteome of brain-dead organ donors predicts heart transplant outcome

The pathophysiological changes related to brain death may affect the quality of the transplanted organs and expose the recipients to risks. We probed systemic changes reflected in donor plasma proteome and investigated their relationship to heart transplant outcomes. Plasma samples from brain-dead multi-organ donors were analyzed by label-free protein quantification using high-definition mass spectrometry. Unsupervised and supervised statistical models were used to determine proteome differences between brain-dead donors and healthy controls. Proteome variation and the corresponding biological pathways were analyzed and correlated with transplant outcomes. Statistical models revealed that donors had a unique but heterogeneous plasma proteome with 237 of 463 proteins being changed compared to controls. Pathway analysis showed that coagulation, gluconeogenesis, and glycolysis pathways were upregulated in donors, while complement, LXR/RXR activation, and production of nitric oxide and reactive oxygen species in macrophages pathways were downregulated. In point-biserial correlation analysis, lysine-specific demethylase 3A was moderately correlated with any grade and severe PGD. In univariate and multivariate Cox regression analyses myosin Va and proteasome activator complex subunit 2 were significantly associated with the development of acute rejections with hemodynamic compromise within 30 days. Finally, we found that elevated levels of lysine-specific demethylase 3A and moesin were identified as predictors for graft-related 1-year mortality in univariate analysis. We show that brain death significantly changed plasma proteome signature Donor plasma protein changes related to endothelial cell and cardiomyocyte function, inflammation, and vascular growth and arteriogenesis could predict transplant outcome suggesting a role in donor evaluation.