Label-free Proteomic Analysis Research Articles

Identifying putative allergens from Cenostigma pluviosum pollen using proteomic bioinformatics.

Routinely, signs and symptoms of pollinosis worsen during the flowering period of the Cenostigma pluviosum var. peltophoroides (Sibipiruna) trees. This study aimed to determine whether Sibipiruna pollen contains allergenic proteins. The pollen from mature Sibipiruna anthers was morphologically characterized using optical, scanning electron and emission microscopy. Additionally, biochemical characterization was conducted through Shotgun Label-Free Proteomic Analysis. Three hundred and forty-nine proteins were identified using the UNIPROT database and thirty-six were confirmed as homologous allergenic proteins in the Allergome database. At the first time, Sibipiruna pollen allergenic proteins have been described and this study provides a deeper understanding of the allergenic proteins present in this pollen. These preliminary findings can be useful to assist in the development of targeted extracts for the study of sensitization and potential immunotherapy in the future.

Investigating the effect of chronic stress, depressive-like pathology and cognitive impairments on acute myocardial infarction: sex-differentiated effects

Abstract Background/Introduction Depression is an independent risk factor for cardiovascular disease (CVD) with the prevalence rates being higher in women than men in the general population and among patients with CVD. Furthermore, an association between myocardial infarction and cognitive deficits has been proposed, but the pathophysiological mechanisms that are responsible for the brain-heart axis interaction have not been elucidated. Purpose The present study aims to: 1) evaluate sex differences in the effect of chronic unpredictable stress (CUS) on myocardial infarct size (IS) and 2) determine the molecular pathways affected by CUS in the heart. Methods Adult male and female C57BL/6J mice, were randomly divided into 4 groups (n=7/group): CON (Control, sham surgery), iCON (Control, myocardial ischemia/reperfusion (IR)), STR (Stress, sham surgery) and iSTR (Stress, IR). Mice were intermittently exposed to the CUS protocol consisted of 4 different stressors for 6 consecutive weeks. Locomotor activity (open field-OF), anxiety-like alterations (OF, elevated plus-maze-EPM test), depressive-like pathology (tail suspension test- TST) and cognition (Y-maze and Novel Object Recognition-NOR tests) were evaluated. After behavioral evaluation, the animals were subjected to 30 min I followed by 24 h of R or sham surgery and infarct size (IS) was determined via double Evan’s Blue and triphenyltetrazolium chloride staining. In a second series of experiments (n=5/group), the ischemic part of the myocardium was collected at 24h R and subjected to label free proteomic analysis, in order to identify alterations associated with the effect of CUS and IR. Results CUS induced anxiety, depressive-like pathology and cognitive deficits as indicated by the increased time spent in the closed arms of the EPM (p<0.005), the increased immobility time (TST, p<0.05), the reduced preference for the novel object (NOR, p<0.05), and the significant body weight reduction (p<0.001), in both male and female mice. CUS significantly increased IS (p<0.001) in both male and female mice. Proteomic analysis revealed that CUS affected the heart proteome, related to endoplasmic reticulum stress, mitochondrial damage and apoptosis, of both sexes in the absence of IR. Female mice were more susceptible to IR damage in absence of CUS with 248 significant genes (FDR<0.05) being deregulated mainly belonging to Keap-Nrf2-ARE signaling pathway, in contrast to 168 significant genes in male mice. In male mice, CUS exacerbated the IR injury proteome changes mainly related to induction of apoptosis and mitochondrial dysregulation (292 significant genes, FDR<0.05 for males vs 102 for females). Conclusions Chronic exposure to stress increases depressive-like pathology and cognitive deficits, leading to heart proteome alterations and increased IS in both sexes. Sex differences were observed indicating that the coexistence of CUS and IR render the male heart more susceptible to myocardial damage.

Multiomics Reveals a Mechanism: Glycogen Synthesis, Galactose Metabolism, and Ethanol Degradation Pathways, the Durable Role of Neutralizing Antibodies in Preventing COVID-19.

Since the emergence and rapid dissemination of Coronavirus disease 2019 (COVID-19), over 774 million individuals globally have achieved recovery to today. There is some case flashing into here and there all over the world. Neutralizing Antibody (NAb) against Severe Acute Respiratory Syndrome Coronavirus-Type 2 (SARS-CoV-2) play a paramount role in conferring effective and lasting protection for several months. This protective effect decreases with time thus increasing the chance of reinfection. Therefore, we can provide the body with a lasting protective effect by maintaining NAb level. However, how to maintain Nab level remains elusive. To address this question, we recruited 80 patients with confirmed COVID-19 and collected 480 consecutive blood samples and performed NAb testing six months after their recovery. The NAb level were categorized into two groups: a low-titer NAb group (≤20) and a high-titer NAb group (>20). To achieve a comprehensive understanding of the changes in NAb level, 16 serum samples were randomly selected for an untargeted metabolomic analysis, whereas 9 samples were designated for a label-free proteomic analysis. We successfully identified differentially expressed 751 metabolites and 845 proteins. In both the low and high NAb titer groups, we identified three key differential proteins, phosphoglucose translocase 2(PGM2), UDP-Glc 4-epimerase (GALE), and alcohol dehydrogenase 1B (ADH1B), that play important roles in fluctuating NAb level through the glycogen synthesis, galactose metabolism and ethanol degradation pathways. These three key differential proteins may serve as potential biomarkers for maintaining NAb level and enhancing immune protection in patients recovering from COVID-19.

Protective properties of milk-derived peptide QEPV in attenuating oxidative stress through AMPK/PPARα signaling pathways

Peptides derived from fermented milk have demonstrated diverse bioactivities. In this study, we investigated the protective effects of Gln-Glu-Pro-Val (QEPV) against hydrogen peroxide (H2O2) induced oxidative stress in RAW 264.7 cells and further evaluated its potential in Drosophila melanogaster (D. melanogaster). Pre-incubation with QEPV in vitro dose-dependently promoted cell viability, suppressed oxidative damage, and increased antioxidant enzyme activities in a low-level oxidative stress model. QEPV remarkably extended lifespan under the low-level oxidative stress, validating its practical applicability. These effects were attributed to the upregulation of 5′ adenosine monophosphate-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor alpha (PPARα) signaling pathways, as revealed by label-free proteomic analysis. To confirm the roles of these two signaling pathways, antagonists of AMPK (Dorsomorphin) and PPARα (GW6471) were applied in vitro and in vivo. The protective effects of QEPV were reversed by both antagonists. Overall, QEPV exhibits protective properties by selectively upregulating the AMPK and PPARα signaling pathways, indicating its potential application as an antioxidant food ingredient.

Effects of ferulic acid grafted-chitosan hydrocolloid on the quality preservation of golden pompano (Trachinotus blochii) fillets during refrigerated storage with emphasis on lable-free proteomics

The effect of ferulic acid grafted-chitosan hydrocolloid (CS-g-FA) on the quality preservation of golden pompano fillets during refrigerated storage was investigated with emphasis on label-free proteomics analysis. It was indicated that CS-g-FA significantly inhibited spoilage bacteria growth, decreased total volatile basic nitrogen (TVB-N) content, retarded lipid and protein oxidation, and delayed water migration in fillets, thus maintaining the texture properties of fillets. In detail, CS-g-FA treatment caused the least total viable counts of 6.55 logCFU/g, TVB-N content of 21.56 mg N/100g, thiobarbituric acid reactive substances value of 1.50 mg MDA/kg, and carbonyl value of 1.26 μmol/g protein, respectively, after 15 day. Furthermore, 27 shared differentially expressed proteins (DEPs) closely related with freshness were identified compared to the fresh sample. CS-g-FA inhibited structural proteins degradation, while reduced the expression of metabolic enzymes to maintain fillets quality and extend the shelf-life. Several DEPs could be identified as potential proteomics markers for golden pompano freshness assessment. Thus, CS-g-FA serve as promising coating for quality preservation of aquatic products.

Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus

Transmissible gastroenteritis virus (TGEV) causes high mortality in young piglets (< 3 days of age). With aging, the susceptibility/morbidity/mortality rates drop. We previously hypothesized that the age-related changes in the intestinal mucus could be responsible for this resistance. Hence, this study investigated the effect of porcine intestinal mucus from 3-day and 3-week-old pigs on the free mobility of the virulent TGEV Miller strain, and on the infection in swine testicle (ST) cells. Single particle tracking (SPT) revealed that TGEV had significantly higher diffusion coefficients in 3-day mucus compared to 3-week mucus. TGEV and charged and uncharged control nanoparticles diffused freely in 3-day mucus but were hindered by 3-week mucus in the diffusion model; TGEV mimicked the diffusion behavior of negatively charged carboxylated particles. Inoculation of ST cells with TGEV in the presence of 3-week mucus resulted in a significantly lower average number of infected cells (30.9 ± 11.9/5 fields) compared with 3-day mucus (84.6 ± 16.4/5 fields). These results show that 3-week mucus has a significant TGEV-blocking activity compared to 3-day mucus in free diffusion and infection of the underlying susceptible cells. Additionally, a label-free proteomics analysis revealed an increased expression of mucin 13, known for negatively regulating the tight junctions in intestinal epithelium, in 3-day-old pigs. In 3-week-old pigs, a higher expression of mucin 2, a type of secreted mucin which is known for inhibiting coronavirus infection, was observed. Concludingly, this study demonstrated a protective effect of 3-week mucus against viral infections.

4D label-free proteome analysis of the liver damage mechanism in mice with chronic benzene exposure

4D label-free proteome analysis of the liver damage mechanism in mice with chronic benzene exposure

Parallel sample processing for mass spectrometry-based single cell proteomics

BackgroundSingle cell mass spectrometry (scMS) has shown great promise for label free proteomics analysis recently. To present single cell samples for proteomics analysis by MS is not a trivial task. Existing methods rely on robotic liquid handlers to scale up sample preparation throughput. The cost associated with specialized equipment hinders the broad adoption of these workflows, and the sequential sample processing nature limits the ultimate throughput. ResultsIn this work, we report a parallel sample processing workflow that can simultaneously process 10 single cells without the need of robotic liquid handlers for scMS. This method utilized 3D printed microfluidic devices to form reagent arrays on a glass slide, and a magnetic beads-based streamlined sample processing workflow to present peptides for LC-MS detection. We optimized key operational parameters of the method and demonstrated the quantification consistency among 10 parallel processed samples. Finally, the utility of the method in differentiating cell lines and studying the proteome change induced by drug treatment were demonstrated. SignificanceThe present method allows parallel sample processing for single cells without the need of expensive liquid handlers, which has great potential to further improve throughput and decrease the barrier for single cell proteomics.

Circulating Exosomes Studied by Label-free Proteomics Analysis Reveal Transition Signatures from Diabetes Mellitus to Diabetic Kidney Disease

Background: Diabetic kidney disease (DKD) is a common microvascular complication of diabetic mellitus (DM). At present, the early diagnosis of DKD mainly depends on microalbuminuria, which is prone to be affected by confounding factors such as urinary tract infections. Methods: To identify the more stable early diagnosis markers, the whole proteome in the circulating exosomes from controls, DM patients, and DKD patients was quantified by label-free proteomics analysis and then validated with parallel reaction monitoring. Results: Three hundred ninety-one quantitative proteins were detected, and the expression trends of 7 proteins in the validation phase were consistent with that in the discovery phase. The expression level assessment results revealed that the expression of EFEMP1 and ApoA4 in the DKD group was significantly higher than those in DM and controls. Correlation analysis showed that EFEMP1 and APOA4 were positively correlated with urinary microalbumin and urinary albumin creatinine ratio and had excellent diagnostic values for distinguishing DKD from DM and controls. Conclusions: ApoA4 and EFEMP1 could serve as the early diagnosis markers of DKD. These findings provide a possibility for the development of a clinical diagnostic index that can efficiently distinguish DKD from DM in the near future.

Effects of slurry ice treatment on the physicochemical changes and proteome of large yellow croaker (Larimichthys crocea)

Large yellow croaker (Larimichthys crocea) is susceptible to oxidative denaturation during storage. This work is to investigate the quality alterations by analyzing its physicochemical changes and proteomics throughout preservation under refrigeration, frozen, and slurry ice (SI) conditions. Results revealed that the freshness of large yellow croaker, as evaluated by indicators such as total volatile basic nitrogen, total viable count, and thiobarbituric acid reactive substances, was well maintained while stored in the SI group. Meanwhile, the water distribution in the muscle tissue of group SI exhibited slower fluctuations, thereby preserving the integrity of fish muscle cells. Based on label-free proteomic analysis, a considerable downregulation was observed in the mitogen-activated protein kinase (MAPK) signaling pathway, indicating that SI decelerated this metabolic pathway and effectively delayed the deterioration of muscle. Therefore, the application of SI provides potential for maintaining the quality stability of large yellow croaker.

Identification of energy metabolism anomalies and serum biomarkers in the progression of premature ovarian failure via extracellular vesicles’ proteomic and metabolomic profiles

BackgroundPremature ovarian failure (POF) is a clinical condition characterized by the cessation of ovarian function, leading to infertility. The underlying molecular mechanisms remain unclear, and no predictable biomarkers have been identified. This study aimed to investigate the protein and metabolite contents of serum extracellular vesicles to investigate underlying molecular mechanisms and explore potential biomarkers.MethodsThis study was conducted on a cohort consisting of 14 POF patients and 16 healthy controls. The extracellular vesicles extracted from the serum of each group were subjected to label-free proteomic and unbiased metabolomic analysis. Differentially expressed proteins and metabolites were annotated. Pathway network clustering was conducted with further correlation analysis. The biomarkers were confirmed by ROC analysis and random forest machine learning.ResultsThe proteomic and metabolomic profiles of POF patients and healthy controls were compared. Two subgroups of POF patients, Pre-POF and Pro-POF, were identified based on the proteomic profile, while all patients displayed a distinguishable metabolomic profile. Proteomic analysis suggested that inflammation serves as an early factor contributing to the infertility of POF patients. For the metabolomic analysis, despite the dysfunction of metabolism, oxidative stress and hormone imbalance were other key factors appearing in POF patients. Signaling pathway clustering of proteomic and metabolomic profiles revealed the progression of dysfunctional energy metabolism during the development of POF. Moreover, correlation analysis identified that differentially expressed proteins and metabolites were highly associated, with six of them being selected as potential biomarkers. ROC curve analysis, together with random forest machine learning, suggested that AFM combined with 2-oxoarginine was the best diagnostic biomarker for POF.ConclusionsOmics analysis revealed that inflammation, oxidative stress, and hormone imbalance are factors that damage ovarian tissue, but the progressive dysfunction of energy metabolism might be the critical pathogenic pathway contributing to the development of POF. AFM combined with 2-oxoarginine serves as a precise biomarker for clinical POF diagnosis.

Cytoskeleton-associated gelsolin responds to the midgut distention process in saline meal-fed Aedes aegypti and affects arbovirus dissemination from the midgut.

The mosquito, Aedes aegypti, is the principal vector for several arboviruses. The mosquito midgut is the initial tissue that gets infected with an arbovirus acquired along with a blood meal from a vertebrate host. Blood meal ingestion leads to midgut tissue distention thereby increasing the pore size of the surrounding basal lamina. This allows newly synthesized virions to exit the midgut by traversing the distended basal lamina to infect secondary tissues of the mosquito. We conducted a quantitative label-free proteomic time course analysis with saline meal-fed Ae. aegypti females to identify host factors involved in midgut tissue distention. Around 2000 proteins were detected during each of the seven sampling time points and 164 of those were uniquely expressed. Forty-five of 97 differentially expressed proteins were upregulated during the 96-h time course and most of those were involved in cytoskeleton modulation, metabolic activity, and vesicle/vacuole formation. The F-actin-modulating Ae. aegypti (Aa)-gelsolin was selected for further functional studies. Stable knockout of Aa-gelsolin resulted in a mosquito line, which showed distorted actin filaments in midgut-associated tissues likely due to diminished F-actin processing by gelsolin. Zika virus dissemination from the midgut of these mosquitoes was diminished and delayed. The loss of Aa-gelsolin function was associated with an increased induction of apoptosis in midgut tissue indicating an involvement of Aa-gelsolin in apoptotic signaling in mosquitoes. Here, we used proteomics to discover a novel host factor, Aa-gelsolin, which affects the midgut escape barrier for arboviruses in mosquitoes and apoptotic signaling in the midgut.

SWATH-proteomics reveals Mathurameha, a traditional anti-diabetic herbal formula, attenuates high glucose-induced endothelial dysfunction through the EGF/NO/IL-1β regulatory axis

Mathurameha is a traditional Thai herbal formula with a clinically proven effect of blood sugar reduction in patients with diabetes mellitus, but its anti-diabetic complication potential is largely unknown. This study aimed to elucidate the effects of Mathurameha and its underlying mechanisms against high glucose-induced endothelial dysfunction in human endothelial EA.hy926 cells. After confirming no cytotoxic effects, the cells were treated with normal glucose (NG), high glucose (HG), or high glucose plus Mathurameha (HG + M) for 24 h. A quantitative label-free proteomic analysis using the sequential window acquisition of all theoretical mass spectra (SWATH-MS) approach identified 24 differentially altered proteins among the three groups: 7 between HG and NG, 9 between HG + M and NG, and 13 between HG + M and HG. Bioinformatic analyses suggested a potential anti-diabetic action through the epidermal growth factor (EGF) pathway. Subsequent functional validations demonstrated that Mathurameha reduced the EGF secretion and the intracellular reactive oxygen species (ROS) level in high glucose-treated cells. Mathurameha also exhibited a stimulatory effect on nitric oxide (NO) production while significantly reducing the secretion of endothelin-1 (ET-1) and interleukin-1β (IL-1β) in high glucose-treated cells. In conclusion, our findings demonstrated that Mathurameha attenuated high glucose-induced endothelial dysfunction through the EGF/NO/IL-1β regulatory axis. SignificanceThis study reveals the potential of Mathurameha, a traditional Thai herbal formula, in mitigating high glucose-induced endothelial dysfunction, a common complication in diabetes mellitus. Using proteomics and bioinformatic analyses followed by functional validations, the present study highlights the protective effects of Mathurameha through the EGF/NO/IL-1β regulatory axis. These findings support its potential use as a therapeutic intervention for diabetic vascular complications and provide valuable information for developing more effective anti-diabetic drugs.

Quantitative label-free proteomic analysis of mouse ovarian antral follicles following oral exposure to a human-relevant mixture of three phthalates.

Dibutyl phthalate (DBP), di-2-ethylhexyl phthalate (DEHP), and benzyl butyl phthalate (BBP) are used in personal and medical care products. In the ovary, antral follicles are essential for steroidogenesis and ovulation. DBP, BBP, and DEHP are known to inhibit mouse antral follicle growth and ovulation in vitro, and associate with decreased antral follicle counts in women. Given that the in vivo effects of a three-phthalate mixture on antral follicles are unknown, we evaluated the effects of a human-relevant mixture of DBP, BBP, and DEHP on ovarian follicles through proteome profiling analysis. Adult CD-1 female mice were fed corn oil (vehicle), or two dose levels of a phthalate mixture based on estimated exposures in general (32 µg/kg/d; PHT 32) and occupationally exposed (500 µg/kg/d; PHT 500) populations for 10 d. Antral follicles (>250 µm) were isolated and subjected to proteome profiling via label-free tandem mass spectrometry. A total of 5,417 antral follicle proteins were detected, of which 194 were differentially abundant between vehicle and PHT 32, and 136 between vehicle and PHT 500. Bioinformatic analysis revealed significantly different responses between the two phthalate doses. Protein abundance differences in the PHT 32 exposure mapped to cytoplasm, mitochondria, and lipid metabolism; whereas those in the PHT 500 exposure mapped to cytoplasm, nucleus, and phosphorylation. When both doses altered proteins mapped to common processes, the associated predicted transcription factors were different. These findings provide novel mechanistic insight into phthalate-associated, ovary-driven reproductive outcomes in women.

Synaptic Vesicle-Related Proteins and Ubiquilin 2 in Cortical Synaptosomes Mediate Cognitive Impairment in Vascular Dementia Rats.

Synaptic dysfunction is considered the best neuropathological correlate of cognitive decline in vascular dementia (VaD). However, the alterations of synaptic proteins at the synaptosomal level in VaD remain unclear. In this study, a VaD model was established in male rats using bilateral common carotid artery occlusion (2VO). We performed a novel object recognition task to evaluate cognitive impairment. Immunohistochemistry was used to assess the expression of neuron-specific nuclear binding protein (NeuN). Brain synaptosomes were isolated and subjected to label-free proteomic analysis to quantify and identify the synaptic features of differentially expressed proteins (DEPs). Synaptic and hub protein expression was detected in synaptosomes using western blotting. We found that male rats with VaD presented impaired memory and decreased NeuN protein expression in the cortex. Synaptosome proteomic analysis revealed 604 DEPs, with 493 and 111 markedly downregulated and upregulated proteins, respectively. KEGG analysis and SynGO annotation revealed that the synaptic vesicle (SV) cycle may be a key signaling pathway in VaD. Hub protein analysis of the main nodes in the protein network identified UBQLN2 and SV-related proteins, including CLTC, SNAP91, AP2S1, CLTA, VAMP2, EPN1, UBQLN2, AP2B1, AP2A2, and AP2M1. Western blotting showed that the levels of SV2A, CLTC, AP2S1, and VAMP2 decreased in the synaptosomes of 2VO rats, while UBQLN2 expression significantly increased. Our results suggest that the disruption in the presynaptic SV cycle is a key event in male rats with VaD, which could be characterized by the aberrant SV2A expression. SV-related proteins and UBQLN2 may be essential in synaptopathy. Thus, targeting the specific molecular markers in synaptosomes may be critical for the development of mechanism-directed therapies against VaD.

Insights into the evolution and mechanisms of response to heat stress by whole genome sequencing and comparative proteomics analysis of the domesticated edible mushroom Lepista sordida

ABSTRACT Lepista sordida is a valuable edible mushroom rich in natural bioactive compounds. In the present study, a high-quality whole-genome of a domesticated strain of L. sordida was sequenced, revealing a 40.67 Mb genome in 13 contigs. Phylogenetic analysis revealed that L. sordida is evolutionarily closely related to edible mushroom Lyophyllum decastes and Hypsizygus marmoreus. Heat stress has a significant effect on the yield and quality of mushrooms, but the molecular basis for this is poorly understood in L. sordida. A label-free comparative proteomic analysis was performed under different heat stress conditions. The growth of L. sordida mycelia was inhibited, and nuclear apoptosis occurred under heat stress. Ca2+ and MAPK signaling pathways were found to be involved in heat stress signal transduction. It is hypothesized that the expression of various heat shock proteins plays a crucial role in the response to heat stress. In addition, the components of the ubiquitin-proteasome system and the thioredoxin system were upregulated, preventing the accumulation of misfolded proteins and possibly supporting the response to heat stress. In summary, these results provide a fundamental insight into the evolution and heat stress-responsive mechanisms in L. sordida and may facilitate the breeding of heat-tolerant strains for artificial cultivation.

Design, synthesis, antimicrobial activity, and mechanism of novel 3-(2,4-dichlorophenyl)-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives.

Plant pathogens cause substantial crop losses annually, posing a grave threat to global food security. Fungicides have usually been used for their control, but the rapid development of pesticide resistance renders many ineffective, therefore the search for novel and efficient green pesticides to prevent and control plant diseases has become the top priority in crop planting. The results of bioassay studies indicated that most of the target compounds showed certain antimicrobial activity in vitro. In particular, compound X7 showed high inhibitory activity against Xanthomonas oryzae pv. oryzae (Xoo), with an EC50 value of 27.47 μg mL-1, surpassing conventional control agents such as thiazole zinc (41.55 μg mL-1) and thiodiazole copper (53.39 μg mL-1). Further studies on molecular docking showed that X7 had a strong binding affinity with 2FBW. The morphological change observed by scanning electron microscopy indicated that the surface of Xoo appears wrinkled and cracked under X7 treatment and a total of 2662 proteins were identified by label-free proteomic analysis. Three experiments have elucidated the mechanism whereby X7 induced considerable changes in the physiological and biochemical properties of Xoo, which in turn affected the reproduction and growth of bacteria. This work represents a pivotal advancement, offering important reference for the research and development therapeutics in combating plant pathogens. © 2024 Society of Chemical Industry.

Heart proteomic profiling discovers MYH6 and COX5B as biomarkers for sudden unexplained death

Sudden unexplained death (SUD) is not uncommon in forensic pathology. Yet, diagnosis of SUD remains challenging due to lack of specific biomarkers. This study aimed to screen differentially expressed proteins (DEPs) and validate their usefulness as diagnostic biomarkers for SUD cases. We designed a three-phase investigation, where in the discovery phase, formalin-fixed paraffin-embedded (FFPE) heart specimens were screened through label-free proteomic analysis of cases dying from SUD, mechanical injury and carbon monoxide (CO) intoxication. A total of 26 proteins were identified to be DEPs for the SUD cases after rigorous criterion. Bioinformatics and Adaboost-recursive feature elimination (RFE) analysis further revealed that three of the 26 proteins (MYH6, COX5B and TNNT2) were potential discriminative biomarkers. In the training phase, MYH6 and COX5B were verified to be true DEPs in cardiac tissues from 29 independent SUD cases as compared with a serial of control cases (n = 42). Receiver operating characteristic (ROC) analysis illustrated that combination of MYH6 and COX5B achieved optimal diagnostic sensitivity (89.7 %) and specificity (84.4 %), with area under the curve (AUC) being 0.91. A diagnostic software based on the logistic regression formula derived from the training phase was then constructed. In the validation phase, the diagnostic software was applied to eight authentic SUD cases, seven (87.5 %) of which were accurately recognized. Our study provides a valid strategy towards practical diagnosis of SUD by integrating cardiac MYH6 and COX5B as dual diagnostic biomarkers.

Multi-omics analysis of five species of milk and specific composition links within each species

The gold standard of milk is human milk, not cow milk. The present study expects to explored the comprehensive nutritional value of different kinds of milk and the differences between them through multi-omics analysis and found functional components that are more similar to human milk. This study employed untargeted LC-MS/MS metabolomics, untargeted LC-MS/MS lipidomics, and 4D label-free proteomics analysis techniques. The findings revealed substantial disparities in metabolites, lipids, and proteins among the five types of milk. Notably, pig milk exhibited a remarkable abundance of N-acetylneuraminic acid (Neu5Ac) and specific polar lipids. Yak milk stood out with significantly elevated levels of creatine and lipoprotein lipase (LPL) compared to other species. Buffalo milk boasted the highest concentrations of L-isoleucine, echinocystic acid, and alkaline phosphatase, tissue-nonspecific isozyme (ALPL). The concentrations of iminostilbene and osteopontin (OPN) were higher in cow milk.

Differential Responses to Aging Among the Transcriptome and Proteome of Mesenchymal Progenitor Populations.

The biological aging of stem cells (exhaustion) is proposed to contribute to the development of a variety of age-related conditions. Despite this, little is understood about the specific mechanisms which drive this process. In this study, we assess the transcriptomic and proteomic changes in 3 different populations of mesenchymal progenitor cells from older (50-70 years) and younger (20-40 years) individuals to uncover potential mechanisms driving stem cell exhaustion in mesenchymal tissues. To do this, we harvested primary bone marrow mesenchymal stem and progenitor cells (MPCs), circulating osteoprogenitors (COP), and adipose-derived stem cells (ADSCs) from younger and older donors, with an equal number of samples from men and women. These samples underwent RNA sequencing and label-free proteomic analysis, comparing the younger samples to the older ones. There was a distinct transcriptomic phenotype in the analysis of pooled older stem cells, suggestive of suppressed proliferation and differentiation; however, these changes were not reflected in the proteome of the cells. Analyzed independently, older MPCs had a distinct phenotype in both the transcriptome and proteome consistent with altered differentiation and proliferation with a proinflammatory immune shift in older adults. COP cells showed a transcriptomic shift to proinflammatory signaling but no consistent proteomic phenotype. Similarly, ADSCs displayed transcriptomic shifts in physiologies associated with cell migration, adherence, and immune activation but no proteomic change with age. These results show that there are underlying transcriptomic changes with stem cell aging that may contribute to a decline in tissue regeneration. However, the proteome of the cells was inconsistently regulated.