Proteomic Responses Research Articles

Global Co-regulatory Cross Talk Between m6A and m5C RNA Methylation Systems Coordinate Cellular Responses and Brain Disease Pathways.

N6 adenosine and C5 cytosine modification of mRNAs, tRNAs and rRNAs are regulated by the behaviour of distinct sets of writer, reader and eraser effector proteins which are conventionally considered to function independently. Here, we provide evidence of global cross-regulatory and functional interaction between the m6A and m5C RNA methylation systems. We first show that m6A and m5C effector protein transcripts are subject to reciprocal base modification supporting the existence of co-regulatory post-transcriptional feedback loops. Using global mass spectrometry proteomic data generated after biological perturbation to identify proteins which change in abundance with effector proteins, we found novel co-regulatory cellular response relationships between m6A and m5C proteins such as between the m6A eraser, ALKBH5, and the m5C writer, NSUN4. Gene ontology analysis of co-regulated proteins indicated that m6A and m5C RNA cross-system control varies across cellular processes, e.g. proteasome and mitochondrial mechanisms, and post-translational modification processes such as SUMOylation and phosphorylation. We also uncovered novel relationships between effector protein networks including contributing to intellectual disability pathways. Finally, we provided in vitro confirmation of colocalisation between m6A-RNAs and the m5C reader protein, ALYREF, after synaptic NMDA activation. These findings have important implications for understanding control of RNA metabolism, cellular proteomic responses, and brain disease mechanisms.

Primary cortical cell tri-culture to study effects of amyloid-β on microglia function and neuroinflammatory response.

Microglia play a critical role in neurodegenerative disorders, such as Alzheimer's disease, where alterations in microglial function may result in pathogenic amyloid-β (Aβ) accumulation, chronic neuroinflammation, and deleterious effects on neuronal function. However, studying these complex factors in vivo, where numerous confounding processes exist, is challenging, and until recently, in vitro models have not allowed sustained culture of critical cell types in the same culture. We employed a rat primary tri-culture (neurons, astrocytes, and microglia) model and compared it to co-culture (neurons and astrocytes) and mono-culture (microglia) to study microglial function (i.e., motility and Aβ clearance) and proteomic response to exogenous Aβ. The cultures were exposed to fluorescently-labeled Aβ (FITC-Aβ) particles for varying durations. Epifluorescence microscopy images were analyzed to quantify the number of FITC-Aβ particles and assess cytomorphological features. Cytokine profiles from conditioned media were obtained. Live-cell imaging was employed to extract microglia motility parameters. FITC-Aβ particles were more effectively cleared in the tri-culture compared to the co-culture. This was attributed to microglia engulfing FITC-Aβ particles, as confirmed via epifluorescence and confocal microscopy. FITC-Aβ treatment significantly increased microglia size, but had no significant effect on neuronal surface coverage or astrocyte size. Upon FITC-Aβ treatment, there was a significant increase in proinflammatory cytokines in tri-culture, but not in co-culture. Aβ treatment altered microglia motility evident as a swarming-like motion. The results suggest that neuron-astrocyte-microglia interactions influence microglia function and highlight the utility of the tri-culture model for studies of neuroinflammation, neurodegeneration, and cell-cell communication.

Biotechnological potential of silver nanoparticles synthesized by green method to control phytopathogenic bacteria: contributions from a proteomic analysis.

Silver nanoparticles (AgNPs) synthesized through green synthesis routes are widely used as antimicrobial agents due to their advantages such as biocompatibility, stability, sustainability, speed and cost-effectiveness. Although AgNPs appear to be more potent than silver ions, the mechanisms related to their antibacterial activity are not yet fully understood. The most common proposed mechanism of AgNPs' toxicity so far is the release of silver ions and/or specific functions of the particles. In this context, the present study aimed to investigate the mechanisms of action of AgNPs synthesized using noni fruit peels (Morinda citrifolia) against the phytopathogen Xanthomonas campestris pv. campestris (Xcc) through proteomics. Xcc was treated with AgNPs (32 µM), AgNO3 (32 µM), or received no treatment (Ctrl - control condition), and its proteomic response was comprehensively characterized to elucidate the antimicrobial mechanisms of AgNPs in the phytopathogenic microorganism. A total of 352 differentially abundant proteins were identified. Most proteins were regulated in the AgNPs × Ctrl and AgNPs × AgNO3 comparisons/conditions. When Xcc treated with 32 µM AgNPs were compared to controls, the results showed 134 differentially abundant proteins, including 107 increased and 27 decreased proteins. In contrast, when Xcc treated with 32 µM AgNO3 were compared to Ctrl, the results showed only 14 differentially abundant proteins, including 10 increased proteins and 4 decreased proteins. Finally, when Xcc treated with 32 µM AgNPs were compared to Xcc treated with 32 µM AgNO3, the results showed 204 differentially abundant proteins, including 75 increased proteins and 129 decreased proteins. Gene ontology enrichment analysis revealed that most of the increased proteins were involved in important biological processes such as metal ion homeostasis, detoxification, membrane organization, metabolic processes related to amino acids and carbohydrates, lipid metabolic processes, proteolysis, transmembrane transport, and others. The AgNPs used in this study demonstrated effective antimicrobial activity against the phytopathogenic bacteria Xcc. Furthermore, the obtained results contribute to a better understanding of the mechanisms of action of AgNPs in Xcc and may aid in the development of strategies to control Xcc in brassica.

Sex and organ specific proteomic responses to vitamin C deficiency in the brain, heart, liver, and spleen of Gulo-/- mice.

Recent advances in mass spectrometry have indicated that the water-soluble antioxidant vitamin C differentially modulates the abundance of various proteins in the hepatic tissue of female and male mice. In this study, we performed LC-MS/MS to identify and quantify proteins that correlate with serum vitamin C concentrations in the whole brain, heart, liver, and spleen tissues in mice deficient for the enzyme L-Gulonolactone oxidase required for vitamin C synthesis in mammals. This work shows for the first time that various biological processes affected by a vitamin C deficiency are not only sex specific dependent but also tissue specific dependent even though many proteins have been identified and quantified in more than three organs. For example, the abundance of several complex III subunits of the mitochondrial electron transport chain correlated positively with the levels of serum vitamin C only in the liver and not in the other tissues examined in this study even though such proteins were identified in all the organs analyzed. Western blot analyses on the Uqcrc1 and Uqcrfs1 complex III subunits validated the mass spectrometry results. Interestingly, the ferritin subunits represented the few quantified protein complexes that correlated positively with serum vitamin C in all the organs examined. Concomitantly, serum ferritin light chain 1 was inversely correlated with vitamin C levels in the serum. Thus, our study provides an initial comprehensive atlas of proteins significantly correlating with vitamin C in four organs in mice that will be a useful resource to the scientific community.

Dual Fractions Proteomic Analysis of Silica Nanoparticle Interactions with Protein Extracts

Dual-fraction proteomics reveals a novel class of proteins impacted by nanoparticle exposure. Background: Nanoparticles (NPs) interact with cellular proteomes, altering biological processes. Understanding these interactions requires comprehensive analyses beyond solely characterizing the NP corona. Methods: We utilized a dual-fraction mass spectrometry (MS) approach to analyze both NP-bound and unbound proteins in Saccharomyces cerevisiae sp. protein extracts exposed to silica nanoparticles (SiNPs). We identified unique protein signatures for each fraction and quantified protein abundance changes using spectral counts. Results: Strong correlations were observed between protein profiles in each fraction and non-exposed controls, while minimal correlation existed between the fractions themselves. Linear models demonstrated equal contributions from both fractions in predicting control sample abundance. Combining both fractions revealed a larger proteomic response to SiNP exposure compared to single-fraction analysis. We identified 302/56 proteins bound/unbound to SiNPs and an additional 196 “impacted” proteins demonstrably affected by SiNPs. Conclusion: This dual-fraction MS approach provides a more comprehensive understanding of nanoparticle interactions with cellular proteomes. It reveals a novel class of “impacted” proteins, potentially undergoing conformational changes or aggregation due to NP exposure. Further research is needed to elucidate their biological functions and the mechanisms underlying their impact.

Comparative Physiological, Biochemical, and Leaf Proteome Responses of Contrasting Wheat Varieties to Drought Stress.

Drought stress severely affects crop productivity and threatens food security. As current trends of global warming are predicted to exacerbate droughts, developing drought-resilient crops becomes urgent. Here, we used the drought-tolerant (BW35695) and drought-sensitive (BW4074) wheat varieties to investigate the physiological, biochemical, and leaf proteome responses underpinning drought tolerance. In response to drought, the tolerant variety had higher osmolyte accumulation and maintained higher leaf water content than the sensitive variety. BW35695 also had an enhanced antioxidant enzyme capacity and reduced reactive oxygen species (ROS), resulting in diminished membrane lipid damage, as reflected by malondialdehyde content. Proteomic analysis revealed that drought-induced differential expression of proteins involved in diverse biological processes in both wheat varieties, including primary and secondary metabolism, protein synthesis/folding/degradation, defense/ROS detoxification, energy, transcription, and cell structure. Notably, photosynthesis emerged as the most enriched biochemical process targeted for suppression in the drought-tolerant BW35695 wheat, but not in drought-sensitive BW4074, possibly as a survival strategy for averting cell damage inflicted by photosynthesis-derived ROS. Additionally, protein synthesis-related proteins were highly upregulated in BW35695, presumably to drive cell-wide stress-adaptive responses. The protein network identified here will be useful in further studies to understand the molecular basis for divergent drought response phenotypes in crops.

349P Comparison of short- and long-term proteomic response to the fast skeletal myosin inhibitor, sevasemten (EDG-5506), in Becker muscular dystrophy (BMD)

349P Comparison of short- and long-term proteomic response to the fast skeletal myosin inhibitor, sevasemten (EDG-5506), in Becker muscular dystrophy (BMD)

A Moderate Water Deficit Induces Profound Changes in the Proteome of Developing Maize Ovaries.

Water deficit is a major cause of yield loss for maize (Zea mays), leading to ovary abortion when applied at flowering time. To help understand the mechanisms involved in this phenomenon, the proteome response to water deficit has been analysed in developing ovaries at the silk emergence stage and five days later. Differential analysis, abundance pattern clustering and co-expression networks were performed in order to draw a general picture of the proteome changes all along ovary development and under the effect of water deficit. The results show that even mild water deficit has a major impact on ovary proteome, but this impact is very different from a response to stress. A part of the changes can be related to a slowdown of ovary development, while another part cannot. In particular, ovaries submitted to water deficit show an increase in proteins involved in protein biosynthesis and in vesicle transport together with a decrease in proteins involved in amino acid metabolism and proteolysis. According to the functions of increased proteins, the changes may be linked to auxin, brassinosteroids and jasmonate signalling but not abscisic acid.

Sleeve-gastrectomy results in improved metabolism and a massive stress response of the liver proteome in a mouse model of metabolic dysfunction-associated steatohepatitis

BackgroundBariatric surgery has been shown to improve the histopathological findings in patients with obesity and metabolic dysfunction-associated steatohepatitis, but there are also reports about non-responders or progressive disease after bariatric interventions. Therefore, it is of utmost importance to understand the pathophysiological processes in the liver after bariatric surgery. Materials and methodsIn the present study, 4 weeks old male C57/Bl6 mice were fed a Western Diet to induce metabolic dysfunction-associated steatohepatitis and sleeve-gastrectomy (SG), or sham operation in the pair-fed and ad libitum control group were performed. Mice were observed for two or eight weeks after surgery and metabolic assessment was performed throughout the experiment. Histopathology, flow cytometry and proteomic analyses were conducted to evaluate hepatic inflammation, liver metabolism and affected signaling pathways. ResultsWeight loss was higher, and metabolism significantly improved after SG. Two weeks after SG major inflammatory and regulatory disturbances in the liver were observed. The proportion of hepatic CD3+NK1.1+ cells were decreased, and proteins involved in apoptosis like Fas, Casp1 and Casp9 or in the acute phase response were upregulated in SG mice. These disturbances decreased in the long-term and we observed an increase of many proteins involved in lipid metabolism eight weeks following SG. ConclusionsThe rapid weight loss and decrease of hepatic fat after SG lead to a proinflammatory response in the liver in the early phase after surgery, which changes to a more moderate immune response in the long-term. We suggest a preoperative risk stratification and postoperative surveillance depending on the histopathological findings.

Physiological and proteomic responses of Posidonia oceanica to phytotoxins of invasive Caulerpa species

The invasive green algae Caulerpa taxifolia (M. Vahl) C. Agardh, 1817 and Caulerpa cylindracea Sonder, 1845 are widely diffused in the Mediterranean Sea, where they compete for space with the endemic seagrass Posidonia oceanica (Linnaeus) Delile, 1813, a keystone species in Mediterranean marine biodiversity. The present study aims to explore the possible effects of bioactive metabolites from the invasive algae on the seagrass, which may imply an allelopathic action. In particular, the study focuses on the effects of the algal alkaloid caulerpin and the sesquiterpene caulerpenyne. Changes in leaf growth, chlorophyll content, and leaf protein expression of P. oceanica genets under treatments were evaluated after 28 days of cultivation in mesocosms. Caulerpenyne strongly inhibited the growth of adult leaves and the formation of new ones, while inducing the elongation of the intermediate leaves and increased total chlorophyll content; on the contrary, caulerpin did not significantly influence leaf growth and the formation of new ones. A total of 107 differentially accumulated proteins common to the two treatments were also identified using the proteomic approach. Both molecules induced cells to maintain homeostasis, enhancing the amino acid metabolism or fatty acid biosynthesis. Despite these disruptions, P. oceanica demonstrated a more efficient response to stress induced by caulerpin, stimulating the biosynthesis of essential amino acids to maintain cellular homeostasis and mitigate damage caused by reactive oxygen species (ROS). Overall, obtained results supports the possible role of caulerpenyne, and not caulerpin, as an effector in allelopathic interactions among invasive Caulerpa species and P. oceanica in the Mediterranean.

Enhanced feature matching in single-cell proteomics characterizes IFN-γ response and co-existence of cell states

Proteome analysis by data-independent acquisition (DIA) has become a powerful approach to obtain deep proteome coverage, and has gained recent traction for label-free analysis of single cells. However, optimal experimental design for DIA-based single-cell proteomics has not been fully explored, and performance metrics of subsequent data analysis tools remain to be evaluated. Therefore, we here formalize and comprehensively evaluate a DIA data analysis strategy that exploits the co-analysis of low-input samples with a so-called matching enhancer (ME) of higher input, to increase sensitivity, proteome coverage, and data completeness. We assess the matching specificity of DIA-ME by a two-proteome model, and demonstrate that false discovery and false transfer are maintained at low levels when using DIA-NN software, while preserving quantification accuracy. We apply DIA-ME to investigate the proteome response of U-2 OS cells to interferon gamma (IFN-γ) in single cells, and recapitulate the time-resolved induction of IFN-γ response proteins as observed in bulk material. Moreover, we uncover co- and anti-correlating patterns of protein expression within the same cell, indicating mutually exclusive protein modules and the co-existence of different cell states. Collectively our data show that DIA-ME is a powerful, scalable, and easy-to-implement strategy for single-cell proteomics.

Lost in translation? Evidence for a muted proteomic response to thermal stress in a stenothermal Antarctic fish and possible evolutionary mechanisms.

Stenothermal Antarctic notothenioid fishes are noteworthy for their history of isolation in extreme cold and their corresponding lack of the canonical heat shock response. Despite extensive transcriptomic studies, the mechanistic basis for stenothermy has not been fully elucidated. Given that the proteome better represents an organism's physiology, the possibility exists that some aspects of stenothermy arise posttranscriptionally. Here, Antarctic emerald rockcod (Trematomus bernacchii) were sampled after exposure to chronic and/or acute high temperatures, followed by a thorough assessment of proteomic responses in the brain, gill, and kidney. Few cellular stress response proteins were induced, and overall responses were modest in terms of the numbers of differentially expressed proteins and their fold changes. Inconsistencies in protein induction across treatments and tissues are suggestive of dysregulation, rather than an adaptive response. Changes in regulation of the translational machinery in Antarctic notothenioids could explain these patterns. Some components of translational regulatory pathways are highly conserved [e.g., Ser-52, eukaryotic translation initiation factor 2α (eIF2α)], but other proteins comprising the cellular "integrated stress response," specifically, the eIF2α kinases general control nonderepressible 2 (GCN2) and PKR-like endoplasmic reticulum kinase (PERK), may have evolved along different trajectories in Antarctic fishes. Taken together, these observations suggest a novel hypothesis for stenothermy and the absence of a coordinated cellular stress response in Antarctic fishes.NEW & NOTEWORTHY Antarctic fishes have some of the lowest known heat tolerances among vertebrates, but the molecular mechanisms underlying this pattern are not fully understood. By combining detailed analyses of protein expression patterns in several tissues under various heat treatments with a broader evolutionary perspective, this study offers a novel hypothesis to explain the narrow range of temperature tolerance in this extraordinary group of fishes.

Cell-based therapies reverse the heart failure-altered right ventricular proteome.

Background Congenital heart defects can lead to right ventricular (RV) pressure-overload and heart failure. Cell-based therapies, including mesenchymal stromal cells (MSCs) and c-kit positive cells (CPCs) have been studied clinically as options to restore heart function in disease states. Many studies have indicated these cells act through paracrine mechanisms to prevent apoptosis, promote cellular function, and regulate gene/protein expression. We aimed to determine the proteomic response of diseased hearts to cell therapy Methods We utilized an animal model of RV pressure overload created by banding the pulmonary artery (PAB). Two weeks post-banding, bone marrow-derived mesenchymal stromal cells (MSCs) and 3 populations of CPCs (nCPCs, cCPCs, ES-CPCs) were delivered to the RV free wall. RV function and cellular retention were measured for four weeks post-injection, at which point hearts were extracted and the RV was excised for liquid chromatography and tandem mass spectrometry. Resulting RV proteomes were compared and analyzed using systems biology and bioinformatics. Results Proteomic profiling identified 1156 total proteins from the RV, of which 5.97% were significantly changed after PAB. This disease-altered proteome was responsive to cellular therapy, with 72% of the PAB-altered proteome being fully or partially reversed by MSC therapy. This was followed by nCPCs (54%), ES-CPCs (52%), and cCPCs (39%). Systems biology and bioinformatics analysis showed MSC, nCPC, or ES-CPC cell therapy is associated with a decrease in predicted adverse cardiac effects. We also observed an effect of cell therapy on the non-altered RV proteome, however, this was associated with minor predicted pathological endpoints. Conclusions Our data indicate MSCs, ES-CPCs, and nCPCs significantly reverse the PAB-altered proteome towards a pre-disease state. These results indicate cell-based therapies show promise in improving RV function after pressure overload through partial restoration of the disease-altered cardiac proteome.

Environmental conditions elicit a slow but enduring response of histone post-translational modifications in Mozambique tilapia.

This study sheds new light on the timescale through which histone post-translational modifications (PTMs) respond to environmental stimuli, demonstrating that the histone PTM response does not necessarily precede the proteomic response or acclimation. After a variety of salinity treatments were administered to Mozambique tilapia (Oreochromis mossambicus) throughout their lifetimes, we quantified 343 histone PTMs in the gills of each fish. We show here that histone PTMs differ dramatically between fish exposed to distinct environmental conditions for 18 months, and that the majority of these histone PTM alterations persist for at least 4 weeks, irrespective of further salinity changes. However, histone PTMs respond minimally to 4-week-long periods of salinity acclimation during adulthood. The results of this study altogether signify that patterns of histone PTMs in individuals reflect their prolonged exposure to environmental conditions.

Physiological and Proteomic Analysis of Various Priming on Rice Seed under Chilling Stress.

Rice (Oryza sativa L.) cultivation using direct seeding is susceptible to chilling stress, particularly during seed germination and early seedling growth in the early season of a double cropping system. Alternatively, seed priming with various plant growth-promoting hormones is an effective technique to promote rapid and uniform emergence under chilling stress. Therefore, we evaluated the impact of gibberellin A3 (GA3) and brassinolide (BR) priming on rice seed emergence, examining their proteomic responses under low-temperature conditions. Results indicated that GA3 and BR increased the seed germination rate by 22.67% and 7.33% at 72 h and 35% and 15% at 96 h compared to the control (CK), respectively. Furthermore, proteomic analysis identified 2551, 2614, and 2592 differentially expressed proteins (DEPs) in GA, BR, and CK, respectively. Among them, GA exhibited 84 upregulated and 260 downregulated DEPs, while BR showed 112 upregulated and 102 downregulated DEPs, and CK had 123 upregulated and 81 downregulated DEPs. Notably, under chilling stress, both GA3 and BR are involved in peroxide metabolism, phenylpropanoid biosynthesis, and inositol phosphate metabolism, enhancing antioxidant capacity and providing energy substances for germination. In addition, GA3 triggers the specific regulation of stress responsive protein activation, GTP activation, and ascorbic acid biosynthesis and promotes the stability and integrity of cell membranes, as well as the synthesis of cell walls, providing physical defense for seeds to resist low temperatures. At the same time, BR triggers specific involvement in ribosome synthesis and amino acid synthesis, promoting biosynthetic ability and metabolic regulation to maintain plant life activities under low-temperature stress. Furthermore, the various genes' expression (OsJ_16716, OsPAL1, RINO1) confirmed GA3 and BR involved in peroxide metabolism, phenylpropanoid biosynthesis, and inositol phosphate metabolism, enhancing antioxidant capacity and providing energy substances for germination. This study provides valuable insights into how rice seed embryo responds to and tolerates chilling stress with GA3 seed priming.

Integrated sperm movement, proteomics, and phosphoproteomics elucidate the roles of osmolality, ions, and key proteins in sperm activation of Nile tilapia (Oreochromis niloticus)

Nile tilapia (Oreochromis niloticus) is an important aquaculture fish around the world and has a wide range of tolerance to salinity, providing great economic value in aquaculture industry and showing an excellent ecological adaptation. However, the best sperm activation condition and sperm activation mechanism of this euryhaline fish remains unclear. In this study, we applied the sperm movement analysis, proteomics, and phosphoproteomics to explore the effects of osmolality and ions and to reveal sperm activation mechanism of Nile tilapia. Our results showed that low osmolality contributed to sperm activation compared with high osmolality. Adding Na+ and Ca2+ enhanced sperm motility after sperm activation. Under 100 mOsm·kg−1, adding 44 mM Na+ and 4 mM Ca2+ was a successful protocol for sperm activation. Proteomics and phosphoproteomics analyses identified 677 differentially expressed proteins and 245 differentially expressed phosphorylated proteins, respectively, among which 21 proteins and 11 phosphorylated proteins as key molecules were involved in Ca2+ mediated signal transduction, glucose metabolism, lipid metabolism, and apoptotic cell death. Key protein ORAI1 promoted extracellular Ca2+ influx to activate Ca2+ mediated signal transduction. Converting glycogenolysis and glycolysis to pyruvate metabolism and fatty acid β-oxidation was a critical energy metabolic adaptation mechanism. The Hsp90 was a critical sperm activation biomarker in loosing of sperm motility and apoptosis. A putative proteomic and phosphoproteomic response network was constructed to reveal the sperm activation mechanism of Nile tilapia. Our study provides a new insight into sperm activation mechanism of this euryhaline fish and facilitates future application of best activation protocol to the fertilization and breeding of Nile tilapia.

Gill ionocyte remodeling mediates blood pH regulation in rockfish (Sebastes diploproa) exposed to environmentally relevant hypercapnia.

Marine fishes excrete excess H+ using basolateral Na+-K+-ATPase (NKA) and apical Na+/H+ exchanger 3 (NHE3) in gill ionocytes. However, the mechanisms that regulate H+ excretion during exposure to environmentally relevant hypercapnia (ERH) remain poorly understood. Here, we explored transcriptomic, proteomic, and cellular responses in gills of juvenile splitnose rockfish (Sebastes diploproa) exposed to 3 days of ERH conditions (pH ∼7.5, ∼1,600 μatm Pco2). Blood pH was fully regulated at ∼7.75 despite a lack of significant changes in gill 1) mRNAs coding for proteins involved in blood acid-base regulation, 2) total NKA and NHE3 protein abundance, and 3) ionocyte density. However, ERH-exposed rockfish demonstrated increased NKA and NHE3 abundance on the ionocyte plasma membrane coupled with wider apical membranes and greater extension of apical microvilli. The observed gill ionocyte remodeling is consistent with enhanced H+ excretion that maintains blood pH homeostasis during exposure to ERH and does not necessitate changes at the expression or translation levels. These mechanisms of phenotypic plasticity may allow fishes to regulate blood pH during environmentally relevant acid-base challenges and thus have important implications for both understanding how organisms respond to climate change and for selecting appropriate metrics to evaluate its impact on marine ecosystems.NEW & NOTEWORTHY Splitnose rockfish exposed to environmentally relevant hypercapnia utilize existing proteins (rather than generate additional machinery) to maintain homeostasis.

The differential proteomic response to ischemic stroke in appalachian subjects treated with mechanical thrombectomy

IntroductionThe Appalachia region of North America is known to have significant health disparities, specifically, worse risk factors and outcomes for stroke. Appalachians are more likely to have comorbidities related to stroke, such as diabetes, obesity, and tobacco use, and are often less likely to have stroke interventions, such as mechanical thrombectomy (MT), for emergent large vessel occlusion (ELVO). As our Comprehensive Stroke Center directly serves stroke subjects from both Appalachian and non-Appalachian areas, inflammatory proteomic biomarkers were identified associated with stroke outcomes specific to subjects residing in Appalachia.MethodsThere were 81 subjects that met inclusion criteria for this study. These subjects underwent MT for ELVO, and carotid arterial blood samples acquired at time of intervention were sent for proteomic analysis. Samples were processed in accordance with the Blood And Clot Thrombectomy Registry And Collaboration (BACTRAC; clinicaltrials.gov; NCT 03153683). Statistical analyses were utilized to examine whether relationships between protein expression and outcomes differed by Appalachian status for functional (NIH Stroke Scale; NIHSS and Modified Rankin Score; mRS), and cognitive outcomes (Montreal Cognitive Assessment; MoCA).ResultsNo significant differences were found in demographic data or co-morbidities when comparing Appalachian to non-Appalachian subjects. However, time from stroke onset to treatment (last known normal) was significantly longer and edema volume significantly higher in patients from Appalachia. Further, when comparing Appalachian to non-Appalachian subjects, there were significant unadjusted differences in the NIHSS functional outcome. A comprehensive analysis of 184 proteins from Olink proteomic (92 Cardiometabolic and 92 Inflammation panels) showed that the association between protein expression outcomes significantly differed by Appalachian status for seven proteins for the NIHSS, two proteins for the MoCA, and three for the mRS.ConclusionOur study utilizes an ELVO tissue bank and registry to investigate the intracranial/intravascular proteomic environment occurring at the time of thrombectomy. We found that patients presenting from Appalachian areas have different levels of proteomic expression at the time of MT when compared to patients presenting from non-Appalachian areas. These proteins differentially relate to stroke outcome and could be used as prognostic biomarkers, or as targets for novel therapies. The identification of a disparate proteomic response in Appalachian patients provides initial insight to the biological basis for health disparity. Nevertheless, further investigations through community-based studies are imperative to elucidate the underlying causes of this differential response.

Regulation of TIR-1/SARM-1 by miR-71 Protects Dopaminergic Neurons in a C. elegans Model of LRRK2-Induced Parkinson's Disease.

Parkinson's disease (PD) is a common neurodegenerative disorder characterized by symptoms such as bradykinesia, resting tremor, and rigidity, primarily driven by the degradation of dopaminergic (DA) neurons in the substantia nigra. A significant contributor to familial autosomal dominant PD cases is mutations in the LRRK2 gene, making it a primary therapeutic target. This study explores the role of microRNAs (miRNAs) in regulating the proteomic stress responses associated with neurodegeneration in PD using C. elegans models. Our focus is on miR-71, a miRNA known to affect stress resistance and act as a pro-longevity factor in C. elegans. We investigated miR-71's function in C. elegans models of PD, where mutant LRRK2 expression correlates with dopaminergic neuronal death. Our findings reveal that miR-71 overexpression rescues motility defects and slows dopaminergic neurodegeneration in these models, suggesting its critical role in mitigating the proteotoxic effects of mutant LRRK2. Conversely, miR-71 knockout exacerbates neuronal death caused by mutant LRRK2. Additionally, our data indicate that miR-71's neuroprotective effect involves downregulating the toll receptor domain protein tir-1, implicating miR-71 repression of tir-1 as vital in the response to LRRK2-induced proteotoxicity. These insights into miR-71's role in C. elegans models of PD not only enhance our understanding of molecular mechanisms in neurodegeneration but also pave the way for potential research into human neurodegenerative diseases, leveraging the conservation of miRNAs and their targets across species.

Integrated cellular response of the zebrafish (Danio rerio) heart to temperature change.

A decrease in environmental temperature represents a challenge to the cardiovascular system of ectotherms. To gain insight into the cellular changes that occur during cold exposure and cold acclimation we characterized the cardiac phosphoproteome and proteome of zebrafish following 24 h or one week exposure to 20 oC from 27 oC; or at multiple points during six weeks of acclimation to 20 oC from 27 oC. Our results indicate that cold exposure causes an increase in mitogen-activated protein kinase signaling, the activation of stretch sensitive pathways, cellular remodeling via ubiquitin-dependent pathways, and changes to the phosphorylation state of proteins that regulate myofilament structure and function including desmin and troponin T. Cold acclimation (2-6 weeks) led to a decrease in multiple components of the electron transport chain through time, but an increase in proteins for lipid transport, lipid metabolism, the incorporation of polyunsaturated fatty acids into membranes and protein turnover. For example, there was an increase in the levels of apolipoprotein C, prostaglandin reductase-3, and surfeit locus protein 4, involved in lipid transport, lipid metabolism, and lipid membrane remodeling. Gill opercular movements suggests that oxygen utilization during cold acclimation is reduced. Neither the amount of food consumed relative to body mass nor body condition were affected by acclimation. These results suggest that while oxygen uptake was reduced, energy homeostasis was maintained. This study highlights that the response of zebrafish to a decrease in temperature is dynamic through time and that investment in the proteomic response increases with the duration of exposure.