Proteomic Studies Research Articles

A split-GAL4 driver line resource for Drosophila neuron types.

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system (CNS) have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types in Drosophila melanogaster and other species. We describe here a collection of 3060 lines targeting a range of cell types in the adult Drosophila CNS and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. Previously published and new lines are included, all validated for driver expression and curated for optimal cell-type specificity across diverse cell types. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.

A split-GAL4 driver line resource for Drosophila neuron types

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system (CNS) have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types in Drosophila melanogaster and other species. We describe here a collection of 3060 lines targeting a range of cell types in the adult Drosophila CNS and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. Previously published and new lines are included, all validated for driver expression and curated for optimal cell-type specificity across diverse cell types. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.

New potential susceptibility factors contributing to tomato bacterial spot disease.

The label-free shotgun proteomics analysis carried out in this study aimed to understand the molecular mechanisms that contribute towards tomato susceptibility to Xanthomonas euvesicatoria pv. perforans (Xep). To achieve this, comparative proteomics was performed on susceptible inoculated plants with the bacterium and the control group (saline solution) at 24 and 48 h after inoculation (hai). The results revealed that most of the identified proteins showed increased abundance in the infected group and were classified into different gene ontology groups. Eight of these proteins were related to susceptibility in other pathosystems, suggesting their potential involvement in the development of bacterial spot in tomato. Some of these proteins are involved in the negative regulation of salicylic acid, PR proteins and reactive oxygen species (ROS), as well as contributing to the acquisition of sugars by the pathogen. The results obtained in this study provided us with valuable information for understanding the molecular mechanisms that lead to tomato susceptibility to Xep and will help in developing tomato cultivars resistant to bacterial spot. SIGNIFICANCE: Our proteomic study of tomato plants during infection by Xep allowed for the identification of potential proteins that contribute to bacterial spot tomato disease development. These proteins can act in different ways to favor the pathogen, such as the negative modulation of phytohormones involved in plant defense, the inhibition of PR proteins and reactive oxygen species, as well as to collaborate in the acquisition of sugar for pathogen nutrition.

Molecular mechanism of protein-lipid interactions in steamed egg gelation and deterioration: A quantitative proteomic study.

Steamed egg (SE), a traditional egg dish, exhibits steaming time-dependent textural properties. This study investigated the molecular mechanisms underlying SE gel formation and deterioration through quantitative proteomics combined with physicochemical characterization. Results showed optimal gel formation at 11 min steaming, while prolonged steaming (23 min) led to gel cracking and sensory deterioration. Textural analysis showed the hardness of SE continued to increase with the increase of steaming time, but the water-holding capacity decreased significantly. Quantitative proteomic analyses revealed that lysozyme and ovalbumin may play a key role in SE formation by influencing protein aggregation through their chargeability and high glycosylation. In addition, the extension of the steaming time disrupted the structure of apolipoproteins, especially low-density lipoprotein (LDL), under the influence of NaCl. The protein parts of LDL were partially involved in the gel structure while the lipid parts were partially free, and these changes might be the main reasons for the creation of voids in the egg custard gels and the decrease of the water-holding capacity. Our findings provide molecular insights into SE gel formation and deterioration, offering theoretical guidance for improving the texture of commercial SE products.

New methods at the transition from research to routine diagnostics

Pathology, traditionally focused on classification and diagnosis, is continuously evolving through new technologies. Advances in proteomics, epigenetics, tissue staining, and 3D imaging expand the possibilities of classical morphology. The aim of this study was to investigate how modern technologies can improve diagnostic accuracy and therapy selection and how they can be integrated into pathologic routine diagnostics. Recent studies in proteomics, epigenetics, multiplex tissue staining, and 3D tissue imaging were analyzed to assess their application and the challenges of clinical implementation. The analysis shows significant potential for pathologic diagnostics. Proteomics provides adeeper understanding of the molecular architecture of tumors, while epigenetics and 3D genome architecture offer new insights into genetic regulation and tumor heterogeneity. Multiplex tissue staining and 3D tissue imaging improve spatial tissue analysis. Despite the potential to improve diagnostics, high costs, technical complexity, and lack of standardization hinder integration into clinical practice. Nevertheless, these technologies offer promising approaches for optimizing diagnostics and therapy selection. Research and interdisciplinary collaboration are crucial to successfully integrating these innovations into routine clinical practice.

Circulating proteomic profiles are associated with type 2 diabetes in Asian populations - a longitudinal study.

Type 2 diabetes (T2D) is a major global concern, with Asia at its epicenter in recent years. Proteins, products of gene transcription, serve as dynamic biomarkers for pinpointing perturbed pathways in disease development. Previous T2D proteomic association studies primarily focused on European populations. The aim of this study was to investigate the relationship between plasma proteins and the incidence of T2D in Asian participants. We examined the association of 4,775 plasma proteins with incident T2D in a Singapore multi-ethnic cohort of 1,659 Asian participants (539 cases and 1,120 controls) using logistic regression. We used two-sample Mendelian randomization and colocalization analysis to evaluate the causal relationship between proteins and T2D. Our analysis revealed 522 proteins that were associated with incident T2D after adjusting for age, sex, and ethnicity, and 17 proteins that remained significantly associated after adjusting for other T2D risk factors such as fasting glucose, waist circumference, and triglycerides. Among the 522 proteins associated with incident T2D, the change in 205 plasma proteins, observed in parallel with the development of T2D at baseline and six-years follow-up, were further associated with incident T2D. The associated proteins showed enrichment in neuron generation, glycosaminoglycan binding, and insulin-like growth factor binding. Two-sample Mendelian randomization analysis suggested three plasma proteins, GSTA1, INHBC, and FGL1, play causal roles in the development of T2D, with colocalization evidence supporting GSTA1 and INHBC. Our findings reveal plasma protein profiles linked to the onset of T2D in Asian populations, offering insights into the biological mechanisms of T2D development.

P0046 Proteomic Profiles Associated with Residual Ultrastructural Anomalies in the Epithelium of IBD patients in Endoscopic Remission

Abstract Background Increased permeability, mucosal barrier and epithelial anomalies (crypt distortion, wider crypt lumen, epithelial gaps) as well as altered tight junctions have been described in active ulcerative colitis (UC) and Crohn’s Disease (CD). Probe based Confocal laser endomicroscopy (pCLE) is able to monitor epithelial anomalies in vivo1. This study aimed at comparing the proteomic profiles of the colonic epithelium associated with pCLE anomalies in UC, CD and non-IBD subjects. Methods Biopsies were collected in IBDs in endoscopic remission (n=37) and non-IBD control (CT) (n=10) undergoing colonoscopy with pCLE as previously described1. Biopsy sampled in the right colon and the rectum were analysed by mass spectrometry label free proteomics, with enrichment of epithelial cells using laser capture microdissection2. Comparisons of epithelial protein profiles, in presence (1) or absence (0) of fluorescein leaks were obtained in the colon and rectum, in CD, UC and non-IBD-CT. Significant proteins obtained were confronted and the entire protein profiles were evaluated using Gene Ontology functional annotations. Results Colon and rectum samples analyses provided 3227 and 3303 protein identifications (≥50% occurrence in minimum 1 group). Unique proteins (≥50% occurrence in only 1 group) were identified in the colon (n=40) and rectum (n=18). Differential analyses (0vs1) in the colon highlighted 165 and 152 significant proteins in CD and UC respectively, from which 13 were in common. In non-IBD CT (0vs1) 88 proteins were discriminant, with 9 and 6 being shared with CD and UC respectively. In the rectum, 74 and 172 discriminant proteins were obtained in CD and UC, from which 16 were also found significant in colon CD and UC protein lists(0vs1). DAZAP, STK4, LAMC1 and PDCD10 showed similar distribution tendencies in both segments in CD0vs1. While HNRPH1 and 2, VASP, TMX1 and PREP distributions were akin in UC0vs1 in both segments (Fig.1.A). GO analyses highlighted more numerous proteins with a decrease when leaks were observed in IBDs than in non-IBD-CT (Fig.2. Right arm of volcano plots). These proteins are associated with junction proteins, matrix and cytoskeleton, proteasome, protease, peptidase functions, or are involved in apoptosis and innate immune controls and morphogenesis. STK4 product, a key regulator of the HIPPO and MAPK pathways, showed a drop (0>1) in IBDs and non-IBD CT with leaks (Fig.1.B). Conclusion This proteomic study reveals proteins with perturbed epithelial distributions associated with pCLE fluorescein leaks. Functional analyses are required to disclose and understand our findings and might confirm very early epithelial key players involved in IBD epithelial homeostasis loss. References 1Jean-Philippe Loly, Sophie Vieujean, Catherine Reenaers, Catherine Van Kemseke, Laurence Seidel ScD, Edouard Louis, Joan Somja In-Depth Assessment of Endoscopic Remission in Inflammatory Bowel Disease Treated by Anti-TNF or Vedolizumab Inflamm Bowel Dis. 2024 Feb 1;30(2):240-246. doi: 10.1093/ibd/izad066. DOI: 10.1093/ibd/izad066 2.Angela-Maria Merli, Sophie Vieujean, Charlotte Massot, Noella Blétard, Florence Quesada Calvo, Dominique Baiwir, Gabriel Mazzucchelli, Laurence Servais, Odile Wéra, Cécile Oury, Laurence de Leval, Christine Sempoux, Roberto Manzini, Sena Bluemel, Michael Scharl, Gerhard Rogler, Edwin De Pauw, C Coimbra Marques, Arnaud Colard, Anne Vijverman, Philippe Delvenne, Edouard Louis, Marie-Alice Meuwis Solute carrier family 12 member 2 as a proteomic and histological biomarker of dysplasia and neoplasia in ulcerative colitis J Crohns Colitis 2020 Sep 13:jjaa168. doi: 10.1093/ecco-jcc/jjaa168.

AP2A1 modulates cell states between senescence and rejuvenation.

Aging proceeds with the accumulation of senescent cells in multiple organs. These cells exhibit increased size compared to young cells, which promotes further senescence and age-related diseases. Currently, the molecular mechanism behind the maintenance of such huge cell architecture undergoing senescence remains poorly understood. Here we focus on the reorganization of actin stress fibers induced upon replicative senescence in human fibroblasts, widely used as a senescent cell model. We identified, together with our previous proteomic study, that AP2A1 (alpha 1 adaptin subunit of the adaptor protein 2) is upregulated in senescent cells along the length of enlarged stress fibers. Knockdown of AP2A1 reversed senescence-associated phenotypes, exhibiting features of cellular rejuvenation, while its overexpression in young cells advanced senescence phenotypes. Similar functions of AP2A1 were identified in UV- or drug-induced senescence and were observed in epithelial cells as well. Furthermore, we found that AP2A1 is colocalized with integrin β1, and both proteins move linearly along stress fibers. With the observations that focal adhesions are enlarged in senescent cells and that this coincides with strengthened cell adhesion to the substrate, these results suggest that senescent cells maintain their large size by reinforcing their effective anchorage through integrin β1 translocation along stress fibers. This mechanism may work efficiently in senescent cells, compared with a case relying on random diffusion of integrin β1, given the enlarged cell size and resulting increase in travel time and distance for endocytosed vesicle transportation.

The relevance of endoplasmic reticulum lumen and Anoctamin-8 for major depression: Results from a systems biology study.

Major depressive disorder (MDD) is a highly prevalent and debilitating disorder, yet its pathophysiology has not been fully elucidated. The aim of this study is to identify novel potential proteins and biological processes associated with MDD through a systems biology approach. Original articles involving the measurement of proteins in the blood of patients diagnosed with MDD were selected. Data on the differentially expressed proteins (DEPs) in each article were extracted and imported into R, and the pathfindR package was used to identify the main gene ontology terms involved. Data from the STRING database were combined with the DEPs identified in the original studies to create expanded networks of protein-protein interactions (PPIs). An R script was developed to obtain the five most reliable connections from each DEP and to create the networks, which were visualized through Cytoscape software. Out of 510 articles found, eight that contained all the values necessary for the analysis were selected, including 1112 adult patients with MDD and 864 controls. A total of 240 DEPs were identified, with the most significant gene ontology term being "endoplasmic reticulum lumen" (46 DEPs, p-value=5.5x10-13). An extended PPI network was obtained, where Anoctamin-8 was the most central protein. Using systems biology contributed to the interpretation of data obtained in proteomic studies on MDD and expanded the findings of these studies. The combined use of these methodologies can provide new insights into the pathophysiology of psychiatric disorders, identifying novel biomarkers to improve diagnostic, prognostic, and treatment strategies in MDD.

Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes

The deployment of liquid chromatography-mass spectrometry-based plasma proteomics experiments in a large cohort is sparse, leading to a lack of data available for benchmarking, method development or validation. Comprised of 6,426 plasma analyses, The Environmental Determinants of Diabetes in the Young (TEDDY) proteomics validation study constitutes one of the largest targeted proteomics experiments in the literature to date. The proteomics data from this study were generated over the course of 2.5 years from over 900 study subjects, each providing up to 29 longitudinal samples. The data also includes 916 quality control samples. The targeted mass spectrometry assay was comprised of 694 peptides mapping to 167 proteins and the panel was measured in each subject and QC sample. The targeted proteomic dataset presented here can be used as a resource for new computational methods development, such as for batch correction, as well as for benchmarking and comparing the performance of different methods/tools.

Integrating Forensic Autopsies with Proteomic Profiling for Suicide Risk Assessment: A Comprehensive Review of Literature.

Suicide is a major global public health concern that affects people of all ages, with over 700000 individuals intentionally ending their lives every year. Suicide is a multifactorial event related to multiple risk factors interlocking with each other, among which neurobiological factors are considered to be an objective measure of the incidence of this phenomenon and can be used as a measurable tool for evaluating suicidal tendencies. The aim of this study is to thoroughly examine available data and assess candidate proteins as prospective biomarkers for predicting suicides and ascertaining the manner of death in forensic cases. An electronic search was conducted on PubMed, Science Direct Scopus, and the Excerpta Medica Database. The systematic review adhered to PRISMA guidelines and encompassed case series, prospective and retrospective studies, and short communications published in English. The focus was on proteomics and suicide, specifically, those studies where researchers conducted human proteomic analyses on specimens obtained from individuals who completed or attempted suicide. A total of 14 studies met the inclusion criteria, resulting in a dataset of numerous candidate protein biomarkers. These include tenascin-C, potassium voltage-gated channel subfamily Q member 3, vimentin-immunoreactive astrocytes, glutathione S-transferase theta 1, iron transport proteins, Acrystallin chain B, manganese superoxide dismutase, glial fibrillary acidic protein, various glycolytic pathway proteins, 14-3-3 eta and 14-3-3 theta proteins, specific cytoskeleton proteins, C-reactive protein, serum amyloid A protein 1, extrinsic coagulation pathway proteins, the vacuolar-type proton pump ATPase subunit, plasma apolipoprotein A-IV, and ER stress proteins. These proteins are proposed as a panel of biomarkers to be evaluated in conjunction with other clinical predictors of suicide. This review aims to provide a comprehensive summary of all proteomic studies conducted on cases of attempted or completed suicide. By doing so, it seeks to bridge existing gaps in knowledge and pave the way for future investigations. The ultimate goal is to potentially identify a suicide biomarker.

Danggui niantong decoction attenuates synovial fibrosis through regulating PI3k/AKT signaling pathway.

Danggui Niantong Decoction (DGNTD) is a traditional Chinese medicine compound formula that has been demonstrated to possess efficacy in the treatment of rheumatoid arthritis (RA) and osteoarthritis (OA), as well as for dispelling moisture and relieving pain. As mentioned before, DGNTD is essential for synovial inflammation in RA. The primary features of the OA synovial membrane are low-grade inflammation, hyperplasia with enhanced fibroblast-like synoviocytes (FLS) proliferation, and fibrosis, which can cause pain and stiffness. However, it is still unknown how DGNTD functions in the OA synovium. Clarify the influence of DGNTD on OA synovium and investigate potential mechanisms of action. The principal constituents of DGNTD were detected using liquid chromatography-mass spectrometry (LC-MS) analysis. To evaluate the effect of DGNTD on synovial inflammation and fibrosis, a transforming growth factor beta (TGF-β)-stimulated rat FLS cell model and a rat OA animal model based on anterior cruciate ligament transection (ACLT) and partial medial meniscectomy (MMx) were employed. Our results showed that 322 components were detected using LC-MS. In vivo, DGNTD therapy reduced pain, synovial inflammation, and fibrosis. The therapy significantly reduced levels of pain-related molecules, specifically calcitonin gene-related peptide (CGRP) and inducible nitric oxide synthase (iNOS), as well as fibrotic markers, including alpha smooth muscle actin (α-SMA) and type III collagen alpha-1 (Col3a1), in the synovium. A proteomics study demonstrated that DGNTD decreased the fibrotic protein Col3a1. DGNTD reduced the mRNA expression of pro-inflammatory and fibrotic markers (tumor necrosis factor alpha (TNF-α), interleukin-1 beta(IL-1β), interleukin-6(IL-6), α-SMA, Col3a1and TGF-β) in TGF-β-induced FLS. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and validation results revealed that DGNTD inhibits synovial fibrosis via the phosphatidylinositol 3-kinase (PI3K)/protein Kinase B (AKT) signaling pathway. DGNTD partially relieves pain, synovitis, and synovial fibrosis by regulating the PI3K/AKT pathway. These findings provide fresh information about the underlying mechanisms and successful therapy of OA, as well as a theoretical and experimental foundation for the clinical management of OA using DGNTD.

A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research

Recent developments in mass spectrometry-based proteomics have established it as a robust tool for system-wide analyses essential for pathophysiological research. While post-mortem samples are a critical source for these studies, our understanding of how body decomposition influences the proteome remains limited. Here, we have revisited published data and conducted a clinically relevant time-course experiment in mice, revealing organ-specific proteome regulation after death, with only a fraction of these changes linked to protein autolysis. The liver and spleen exhibit significant proteomic alterations within hours post-mortem, whereas the heart displays only modest changes. Additionally, subcellular compartmentalization leads to an unexpected surge in proteome alterations at the earliest post-mortem interval (PMI). Additionally, we have conducted a comprehensive analysis of semi-tryptic peptides, revealing distinct consensus motifs for different organs, indicating organ-specific post-mortem protease activity. In conclusion, our findings emphasize the critical importance of considering PMI effects when designing proteomics studies, as these effects may significantly overshadow the impacts of diseases. Preferably, the samples should be taken in the operation room, especially for studies including subcellular compartmentalization or trans-organ comparison. In single-organ studies, the planning should involve careful control of PMI.

Proteomic Profiling Reveals Alterations in Metabolic and Cellular Pathways in Severe Obesity and Following Metabolic Bariatric Surgery.

In this study, we investigated the impact of bariatric surgery on the adipose proteome to better understand the metabolic and cellular mechanisms underlying weight loss following the procedure. A total of 46 patients with severe obesity were included, with samples collected both before and after bariatric surgery. Additionally, 15 healthy, non-obese individuals who did not undergo surgery served as controls and were studied once. We utilized quantitative liquid chromatography tandem mass spectrometry analysis to conduct a large-scale proteomic study on abdominal subcutaneous biopsies obtained from the study participants. Our proteomic profiling revealed that among the 2254 compared proteins, 46 were upregulated, and 34 were downregulated 6 months post-surgery compared to baseline (FDR < 0.01). We observed a downregulation of proteins associated with mitochondrial integrity, amino acid catabolism, and lipid metabolism in the patients with severe obesity compared to the controls. Bariatric surgery was associated with an upregulation in pathways related to mitochondrial function, protein synthesis, folding and trafficking, actin cytoskeleton regulation, and DNA binding and repair. These findings emphasize the significant changes in metabolic and cellular pathways following bariatric surgery, highlighting the potential mechanisms underlying the observed health improvements post-bariatric surgery. The data provided alongside this paper will serve as a valuable resource for the development of targeted therapeutic strategies for obesity and related metabolic complications.

Quantitative analysis of the polar cod (Boreogadus saida) hepatic proteome highlights interconnected responses in cellular adaptation and defence mechanisms after dietary benzo[a]pyrene exposure.

Increased industrial offshore activities in northern waters raise the question of impact of polycyclic aromatic hydrocarbons (PAHs) on key Arctic marine species. One of these is the ecologically important polar cod (Boreogadus saida), which is the primary food source for Arctic marine mammals and seabirds. In the present work, we have conducted the first comprehensive proteomics study with this species by exploring the effects of dietary PAH exposure on the hepatic proteome, using benzo[a]pyrene (BaP) as a PAH model-compound. Functional annotation and pathway analyses of the proteins affected by BaP revealed a concerted cellular response for handling and adopting to its exposure, involving numerous interconnected signalling pathways and metabolic processes. In accordance with BaP being a strong aryl hydrocarbon receptor (Ahr) agonist, a prominent activation of the canonical Ahr signalling pathway was observed, including upregulation of Ahr target proteins like cytochrome P450 enzymes and microsomal glutathione transferase. Furthermore, cellular pathways for handling oxidative stress, protein misfolding and degradation, as well as endoplasmic reticulum stress and calcium homeostasis, were also activated by BaP, possibly as a result of the formation of harmful and redox reactive BaP metabolites via phase I metabolism. Activation of proteins that participate in the acute-phase response was also observed, suggesting prevalent tissue- and cellular damage that triggers the immune system and inflammatory responses. Our results at the protein level aligns well with previous analyses on the effects of BaP on the polar cod liver transcriptome and support that exposure to BaP and structural similar PAHs can cause adverse effects on polar cod physiology. Although more data is required for demonstrating how these molecular responses propagate to higher levels of biological organisation, increased knowledge about the initial cellular and molecular mechanisms that induce toxicity is a key-step towards a mechanistically informed impact assessment of PAH pollutants in the Arctic.

Insights into the molecular underpinning of type 2 diabetes complications.

Type 2 diabetes (T2D) complications pose a significant global health challenge. Omics technologies have been employed to investigate these complications and identify the biological pathways involved. In this review, we focus on four major T2D complications: diabetic kidney disease, diabetic retinopathy, diabetic neuropathy, and cardiovascular complications. We discuss advancements in omics research, summarizing findings from genetic, epigenomic, transcriptomic, proteomic, and metabolomic studies across different ancestries and disease-relevant tissues. We stress the importance of integrating multi-omics techniques to elucidate the biological mechanisms underlying T2D complications and advocate for ancestrally diverse studies. Ultimately, these insights will improve risk prediction for T2D complications and inform translation strategies.

Antibody Responses and the Vaccine Efficacy of Recombinant Glycosyltransferase and Nicastrin Against Schistosoma japonicum.

Schistosomiasis is a neglected tropical disease and the second most common parasitic disease after malaria. While praziquantel remains the primary treatment, concerns about drug resistance highlight the urgent need for new drugs and effective vaccines to achieve sustainable control. Previous proteomic studies from our group revealed that the expression of Schistosoma japonicum glycosyltransferase and nicastrin as proteins was higher in single-sex males than mated males, suggesting their critical roles in parasite reproduction and their potential as vaccine candidates. In this study, bioinformatic tools were employed to analyze the structural and functional properties of these proteins, including their signal peptide regions, transmembrane domains, tertiary structures, and protein interaction networks. Recombinant forms of glycosyltransferase and nicastrin were expressed and purified, followed by immunization experiments in BALB/c mice. Immunized mice exhibited significantly elevated specific IgG antibody levels after three immunizations compared to adjuvant and PBS controls. Furthermore, immunization with recombinant glycosyltransferase and nicastrin significantly reduced the reproductive capacity of female worms and liver egg burden, though egg hatchability and adult worm survival were unaffected. These findings demonstrate that recombinant glycosyltransferase and nicastrin are immunogenic and reduce female worm fecundity, supporting their potential as vaccine candidates against schistosomiasis.

LC-MS/MS-based proteomics and metabolomics of HCT-116 colorectal cancer cells: A potential anticancer activity of atorvastatin

Colorectal cancer (CRC) is the third most prevalent tumor in men, the second most common in women, and the fourth leading cause of mortality worldwide. Statins reduce cholesterol levels by hampering the function of 3-hydroxy-3-methyl-glutaryl-CoA reductase enzymes in cholesterol synthesis. Strains have shown anticancer effects against CRC. However, statins’ anticancer mechanism is yet unknown. Liquid chromatography–mass spectrometry (LC–MS)-based untargeted metabolomics and proteomics were employed to study statins’ effects on CRC using the CRC cell line HCT-116. These approaches were utilized to identify potential underlying metabolic pathways and proteins altered in atorvastatin (a statin)-treated HCT-116 cells. Compared to the control, atorvastatin significantly altered numerous metabolites in HCT-116 cells, including a reduction in the levels of decanoylcarnitine and octanoyl-L-carnitine and in the biosynthesis and metabolism of amino acids like alanine and citrate cycle. Proteomic study showed that atorvastatin-treated HCT-116 cells expressed 127 proteins differently from controls. Novel findings were among them, such as centromere-associated protein E, cytochrome c oxidase subunit 6A1 mitochondrial, and hyaluronan synthase 1. The findings indicate that atorvastatin may have potential anticancer characteristics and highlight the essential role metabolomics and proteomics to understand complex metabolic pathways and proteins relevant to cancer and develop novel treatment targets.

The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies

The proximity extension assay (PEA) enables large-scale proteomic investigations across numerous proteins and samples. However, discrepancies between measurements, known as batch-effects, potentially skew downstream statistical analyses and increase the risks of false discoveries. While implementing bridging controls (BCs) on each plate has been proposed to mitigate these effects, a clear method for utilizing this strategy remains elusive. Here, we characterized batch effects in PEA proteomics and identified three types: protein-specific, sample-specific, and plate-wide. We developed a robust regression-based method called BAMBOO (Batch Adjustments using Bridging cOntrOls) to correct them. Simulations comparing BAMBOO with established correction techniques (median centering, median of the difference (MOD), and ComBat) revealed that median centering and ComBat were significantly impacted by outliers within the BCs, whereas BAMBOO and MOD were more robust when no plate-wide effects were introduced. Optimal batch correction was achieved with 10–12 BCs. We validated the simulation results using experimental data and found that BAMBOO and MOD had a reduced incidence of false discoveries compared to alternative methods. Our findings emphasize the prevalence of batch effects in PEA proteomic studies and advocate for BAMBOO as a robust and effective tool to enhance the reliability of large-scale analyses in the proteomic field.

Proteomics Response of Photosynthetic Machinery to Abiotic Stresses: A Review

Abiotic stress, including drought, salinity, extreme temperatures, and light intensity, profoundly affects plant growth and development. Plants being sessile cannot escape the stress conditions, , thus have developed either evading or tolerance mechanisms during evolution. In plants several processes are affected by drought e.g. there is inhibition of growth, reduction in photosynthesis, and yield, and increased membrane damage. Plants respond to drought or tolerate stress by downregulation of growth, photosynthetic machinery and membrane fluidity, increased cuticle thickness, osmolyte accumulation, increased defense chemicals, and secondary metabolites, and stress responding proteins e.g. Late Embryogenic Abundance and Heat Shock proteins etc. The root architecture is elaborated, and leaf rolling occurs. Futher, there is an increase in the cell's antioxidant potential and antioxidant enzyme activity. Most of these mechanisms are investigated using proteomics and protein techniques. With the advent of sensitive proteomics techniques and the availability of databases for several plants, proteomics experiments have become routine in stress based studies. Current review highlights the modulation in the photosynthetic and chloroplastic proteins in higher plants that proteomics and other protein determination studies have revealed, in response to stress treatment. It specifically discusses the latest developments in terms of protein changes in leaves or other tissues from the studies using stress treatment, since several reviews have already covered the earlier findings. Moreover, it further discusses the future role of proteomics studies in elucidating stress mechanisms in plants.